OPUS/IR

Reference Manual

Version 7
© 2017 BRUKER OPTIK GmbH, Rudolf-Plank-Straße 27, D-76275 Ettlingen,
www.bruker.com

All rights reserved. No part of this manual may be reproduced or transmitted in any
form or by any means including printing, photocopying, microfilm, electronic sys-
tems etc. without our prior written permission. Brand names, registered trademarks
etc. used in this manual, even if not explicitly marked as such, are not to be consid-
ered unprotected by trademarks law. They are the property of their respective own-
er.

This manual is the original documentation for the OPUS spectroscopic software.
Table of Contents

1 Starting OPUS . . . . . . . . . . . . . . . . . . . . . 1
1.1 Us e r I n t e rf a c e . . . . . . . . . . . . . . . . . . . . . . . . 4

2 OPUS Basics . . . . . . . . . . . . . . . . . . . . . . 7
2.1 Ba si c S oftw are F ea tu r es . . . . . . . . . . . . . . . . 7
2.2 Workspace . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.3 Ac c e s s C o n t rol . . . . . . . . . . . . . . . . . . . . . . 11
2.4 Paths and Directories . . . . . . . . . . . . . . . . . 12
2.5 Us e r R i g h t s . . . . . . . . . . . . . . . . . . . . . . . . . 13
2 .6 Bro wser . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
2 . 6 . 1 Ma k e i n v i s i b l e . . . . . . . . . . . . . . . . . 16
2 . 6 . 2 Po p - u p men u s . . . . . . . . . . . . . . . . . 17
2 .7 Wi zard . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
2 . 7 . 1 Ma k e i n v i s i b l e . . . . . . . . . . . . . . . . . 20
2.7.2 Levels . . . . . . . . . . . . . . . . . . . . . . . 21
2.8 Spectrum Window . . . . . . . . . . . . . . . . . . . . 26
2.8.1 Enlarging or reducing the spectrum
w i nd o w . . . . . . . . . . . . . . . . . . . . . . 27
2.8.2 Fixing the size of the spectrum window 27
2.8.3 More than one s p e ct r u m i n t h e
spectrum window . . . . . . . . . . . . . . . 27
2.8.4 Pop-up menu in t he spectrum window . 28
2.8.5 Zooming in a spectral range . . . . . . . . 29
2 . 8.6 Zo o mi n g ou t a spectr al range . . . . . . . 30
2 . 8 . 7 Sc a l i n g a l l s p e c t r a . . . . . . . . . . . . . . 31
2.8.8 Maximizing each spectru m . . . . . . . . . 31
2 . 8.9 Sca l i n g o rdi na te . . . . . . . . . . . . . . . . 31
2.8.10 Shifting curve . . . . . . . . . . . . . . . . . . 32
2.8.11 Activating crosshair . . . . . . . . . . . . . 32
2.8.12 Deactivating crosshair . . . . . . . . . . . . 33
2.8.13 Changing color of th e spe ctrum . . . . . 33
2.8.14 Removing spectrum from spectrum
window . . . . . . . . . . . . . . . . . . . . . . 33
2.8.15 Adding annotations to spectrum . . . . . 34
2.8.16 Copying one spectrum . . . . . . . . . . . . 35

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2.8.17 Copying all spectra . . . . . . . . . . . . . . 35

2.8.18 Performing single peak p i c k . . . . . . . . 35
2.8.19 Settings of spectrum v i e w . . . . . . . . . 36
2.9 Defining F requency Range . . . . . . . . . . . . . . 40
2.10 Information View . . . . . . . . . . . . . . . . . . . . . 44
2.10.1 Make invisibl e . . . . . . . . . . . . . . . . . 44
2.10.2 Open a separate repo rt window . . . . . 45
2 .11 Toolb ar . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
2.12 Data Block . . . . . . . . . . . . . . . . . . . . . . . . . 48
2 .13 Decimals . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.14 Connecting to Spectrometer . . . . . . . . . . . . . 51
2 .15 Instru ment S ta tus . . . . . . . . . . . . . . . . . . . . 52
2.16 F i l e N a me E x t e n s i o n s . . . . . . . . . . . . . . . . . 53
2.17 Command Line Parameters . . . . . . . . . . . . . . 55
2.18 Changing OPUS Language . . . . . . . . . . . . . . 60
2 .19 Abort OP US . . . . . . . . . . . . . . . . . . . . . . . . 62
2 .20 Run OP US from C D . . . . . . . . . . . . . . . . . . . 62

3 File . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
3.1 Load File . . . . . . . . . . . . . . . . . . . . . . . . . . 64
3.2 Unload F ile . . . . . . . . . . . . . . . . . . . . . . . . 65
3 .3 Unlo ad A ll Fi les . . . . . . . . . . . . . . . . . . . . . 66
3.4 Save File /Save File As . . . . . . . . . . . . . . . . 66
3.5 Un d o C h a n g e s . . . . . . . . . . . . . . . . . . . . . . 71
3.6 Send File . . . . . . . . . . . . . . . . . . . . . . . . . . 72
3.7 Send File to GRAMS . . . . . . . . . . . . . . . . . . 73
3.8 Send File to InStep . . . . . . . . . . . . . . . . . . . 74
3.9 Delete Data Blocks . . . . . . . . . . . . . . . . . . . 74
3 .10 Exte rnal P rog ram . . . . . . . . . . . . . . . . . . . . 76
3.11 VisualBasic Script . . . . . . . . . . . . . . . . . . . 82
3.12 Load Data Point Table . . . . . . . . . . . . . . . . 84
3 .13 Scan OP US Fil es . . . . . . . . . . . . . . . . . . . . 85
3.14 Find OPUS Files . . . . . . . . . . . . . . . . . . . . . 87
3 .15 Clon e E ntry /Cl one Origi nal . . . . . . . . . . . . . 89
3.16 Add Comment . . . . . . . . . . . . . . . . . . . . . . 90
3.17 RS 232 Communication . . . . . . . . . . . . . . . . 91
3.18 Copy Data Block . . . . . . . . . . . . . . . . . . . . . 96
3.19 Change Data Block Type . . . . . . . . . . . . . . . 97
3.20 C o m p a re P a ram e t e rs . . . . . . . . . . . . . . . . . 98
3.21 LabJournal . . . . . . . . . . . . . . . . . . . . . . . 100
3.21.1 Lab journal view . . . . . . . . . . . . . . 1 02

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3 .22 New/Op en . . . . . . . . . . . . . . . . . . . . . . . . 106

3.23 Print . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
3.24 P ri n t P r e v i e w . . . . . . . . . . . . . . . . . . . . . . 106
3.25 P ri n t S etu p . . . . . . . . . . . . . . . . . . . . . . . . 107
3.26 Exit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107

4 Edit . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
4.1 Ed i t P a r a met e r . . . . . . . . . . . . . . . . . . . . . 110
4 .2 Repl ay . . . . . . . . . . . . . . . . . . . . . . . . . . 112
4.3 Attach Video Image . . . . . . . . . . . . . . . . . 113
4.3.1 Further setting options . . . . . . . . . . 114
4.3.2 Spectrum file in the browse r . . . . . . 1 16
4.3.3 Report view of graph d a t a b l o c k . . . . 116
4.4 Add Information . . . . . . . . . . . . . . . . . . . . 117
4.5 Setup Information Mask . . . . . . . . . . . . . . 1 21
4 .6 Import Structure . . . . . . . . . . . . . . . . . . . . 124
4.7 Edit/Create Structure . . . . . . . . . . . . . . . . 125
4.8 Attach Structure . . . . . . . . . . . . . . . . . . . . 129
4.9 Convert 3-D Jcamp . . . . . . . . . . . . . . . . . . 1 30
4.10 Create Spectrum from Struc t u re . . . . . . . . . 134
4.11 Setup Filelist . . . . . . . . . . . . . . . . . . . . . . 136
4.12 C ut . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.13 Copy /Paste . . . . . . . . . . . . . . . . . . . . . . 140
4 .14 Copy to Image Fi le . . . . . . . . . . . . . . . . . . 140

5 View . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
5 .1 Toolb ars . . . . . . . . . . . . . . . . . . . . . . . . . . 141
5 .2 Sta tus Bar . . . . . . . . . . . . . . . . . . . . . . . . 142
5 .3 Bro wser . . . . . . . . . . . . . . . . . . . . . . . . . . 142
5 .4 Wi z ard Ba r . . . . . . . . . . . . . . . . . . . . . . . . 142
5.5 Information View . . . . . . . . . . . . . . . . . . . . 143

6 Window . . . . . . . . . . . . . . . . . . . . . . . . 145
6.1 Ne w S p e c t r u m W i n d o w . . . . . . . . . . . . . . . 145
6.2 New 3D Window . . . . . . . . . . . . . . . . . . . . 146
6.3 New Report Window . . . . . . . . . . . . . . . . . 146
6 .4 Ne w Reg is te re d W ind ow . . . . . . . . . . . . . . . 148
6.4.1 TextView . . . . . . . . . . . . . . . . . . . . 1 49
6.5 Cascade . . . . . . . . . . . . . . . . . . . . . . . . . 150
6.6 Ti l e . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
6.7 Ar r a n g e I c o n s . . . . . . . . . . . . . . . . . . . . . . 152

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7 Measure . . . . . . . . . . . . . . . . . . . . . . . . 153
7.1 Ad va n ce d Me a su rement . . . . . . . . . . . . . . 1 57
7 . 1 . 1 Ba s i c . . . . . . . . . . . . . . . . . . . . . . . 1 61
7 . 1 . 2 Ad v a n c e d . . . . . . . . . . . . . . . . . . . . 1 64
7 . 1 . 3 Op t i c . . . . . . . . . . . . . . . . . . . . . . . 1 66
7.1.4 Acquisition . . . . . . . . . . . . . . . . . . . 1 66
7.1.5 FT . . . . . . . . . . . . . . . . . . . . . . . . . 166
7 . 1.6 D i sp l ay . . . . . . . . . . . . . . . . . . . . . 1 67
7.1.7 Background . . . . . . . . . . . . . . . . . . 168
7 . 1.8 Ch e ck S i gn a l . . . . . . . . . . . . . . . . . 169
7 . 1 . 9 Be a m P a t h . . . . . . . . . . . . . . . . . . . 1 73
7.1.10 Spectral Range Select i o n . . . . . . . . 174
7.1.11 Raman Measurements . . . . . . . . . . . 1 77
7.2 Setup Measurement Paramete rs . . . . . . . . . 178
7 . 2 . 1 Ba s i c . . . . . . . . . . . . . . . . . . . . . . . 1 80
7 . 2 . 2 Ad v a n c e d . . . . . . . . . . . . . . . . . . . . 1 81
7 . 2 . 3 Op t i c . . . . . . . . . . . . . . . . . . . . . . . 1 83
7.2.4 Acquisition . . . . . . . . . . . . . . . . . . . 1 85
7.2.5 FT . . . . . . . . . . . . . . . . . . . . . . . . . 193
7 . 2.6 D i sp l ay . . . . . . . . . . . . . . . . . . . . . 1 94
7.2.7 Background . . . . . . . . . . . . . . . . . . 194
7 . 2.8 Ch e ck S i gn a l . . . . . . . . . . . . . . . . . 194
7 . 3 Rou ti ne Mea su remen t . . . . . . . . . . . . . . . . 1 95
7.4 Repeated Measurements . . . . . . . . . . . . . . 196
7.5 Rapid Scan T ime Resolved M e a s u r e m e n t . . 198
7.6 Direct Command Entry . . . . . . . . . . . . . . . 199
7.7 Optic Setup and Service . . . . . . . . . . . . . . 201
7 . 7 . 1 Op t i c a l B e n c h . . . . . . . . . . . . . . . . . 2 01
7 . 7 . 2 De v i c e s / O p t i o n s . . . . . . . . . . . . . . . 2 03
7.7.3 Optic Communication . . . . . . . . . . . 2 06
7.7.4 Interferometer/AQP . . . . . . . . . . . . . 2 07
7 . 7.5 Exp o rt Op ti on s . . . . . . . . . . . . . . . . 2 08
7 . 7 . 6 Se r v i c e . . . . . . . . . . . . . . . . . . . . . 2 09
7.7.7 Control Panel . . . . . . . . . . . . . . . . . 211
7.8 Optics Diagnostics . . . . . . . . . . . . . . . . . . 212
7.8.1 Status display for non-Ethernet
based spectrometers . . . . . . . . . . . . 216
7 . 9 Te mp e rat u r e C o n t rol . . . . . . . . . . . . . . . . . 218
7.10 Interleaved Time Resolved Measurement . . 220
7.11 Sample Wheel Measurement . . . . . . . . . . . 222
7 .12 Twister Control/Ca libration . . . . . . . . . . . . 2 29
7.12.1 Calibrating Twister . . . . . . . . . . . . . 2 30

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7.12.2 Controlling Twister . . . . . . . . . . . . . 2 32

7.13 Pump Control . . . . . . . . . . . . . . . . . . . . . . 235
7.13.1 Control the pump . . . . . . . . . . . . . . 2 36
7.13.2 Control the pump by using a macro . . 237
7.14 Auto Sampler Configuration . . . . . . . . . . . . 2 39
7.15 Measure with Auto Sampler . . . . . . . . . . . . 2 41
7.16 Valve Control . . . . . . . . . . . . . . . . . . . . . . 241
7.17 Cleanness T est Setup . . . . . . . . . . . . . . . . 2 42
7.17.1 Reference m easurement of ATR
c ry s t a l . . . . . . . . . . . . . . . . . . . . . . 2 43
7.18 Cleanness Test . . . . . . . . . . . . . . . . . . . . 245
7.18.1 Performing cleanness tes t . . . . . . . . 245
7.18 .2 Test result . . . . . . . . . . . . . . . . . . . 2 46

8 Manipulate . . . . . . . . . . . . . . . . . . . . . . 247
8.1 Baseline Correction . . . . . . . . . . . . . . . . . 249
8.1.1 Standard Baseline Correction . . . . . . 249
8.1.2 Interactive Baseline Correction . . . . 251
8.1.3 Baseline Correction Methods . . . . . . 254
8.1.4 Examples of Baseline Correction . . . 257
8.2 Sp e c t ru m S u b t rac t i o n . . . . . . . . . . . . . . . . 259
8.3 AB <-> TR Conversion . . . . . . . . . . . . . . . 2 64
8.4 St rai gh t Li ne G en e ration . . . . . . . . . . . . . . 266
8.5 Spectrum Calculator . . . . . . . . . . . . . . . . . 267
8.6 Cu t . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
8.7 No r mal i z a t i o n . . . . . . . . . . . . . . . . . . . . . . 273
8.8 Make Compatible . . . . . . . . . . . . . . . . . . . 276
8 .9 Convert Spe ctra . . . . . . . . . . . . . . . . . . . . 279
8 .10 Smo oth . . . . . . . . . . . . . . . . . . . . . . . . . . 282
8.11 Derivative . . . . . . . . . . . . . . . . . . . . . . . . 286
8.12 F r equ e n cy C al i b rati on . . . . . . . . . . . . . . . . 2 88
8.12.1 Frequency Calibration Theory . . . . . 290
8.13 Raman Correction . . . . . . . . . . . . . . . . . . . 292
8.13.1 Raman Correction Theo ry . . . . . . . . 295
8.14 B l ack B o d y . . . . . . . . . . . . . . . . . . . . . . . 296
8.14.1 Black Body Theory . . . . . . . . . . . . . 2 97
8.15 Interferogram to Spectrum . . . . . . . . . . . . . 299
8 .16 Inverse FT . . . . . . . . . . . . . . . . . . . . . . . . 309
8.17 Post Zerofilling . . . . . . . . . . . . . . . . . . . . . 310
8.18 Fourier Self-Deconvolution . . . . . . . . . . . . 3 13
8.18.1 Fourier Self-Deconvolution Theory . . 316

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8.19 S y mm e t ri c F T . . . . . . . . . . . . . . . . . . . . . . 319
8.20 Kramers-Kronig-Transformat i o n . . . . . . . . . 320
8 .21 Spli t Interferog rams . . . . . . . . . . . . . . . . . 322
8.22 Spectrum from Interferogram s . . . . . . . . . . 324
8.23 E xtrap o l ati on . . . . . . . . . . . . . . . . . . . . . . 325
8.23.1 Extrapolation to 0cm-1 . . . . . . . . . . 3 26
8.23.2 Extrapolation to (infin i t y ) . . . . . . . . 328
8.24 Extended ATR Correction . . . . . . . . . . . . . 329
8 .25 1/cm <-> µm, nm . . . . . . . . . . . . . . . . . . . 335
8.25.1 Frequency Conversion Theory . . . . . 337
8.26 Averaging . . . . . . . . . . . . . . . . . . . . . . . . 341
8.26.1 Averaging Theory . . . . . . . . . . . . . . 3 43
8.27 Merge Spectral Ranges . . . . . . . . . . . . . . . 344
8.28 Atmospheric Compensation . . . . . . . . . . . . 349
8.28.1 Atmospheric compensation as part of
the measurement process . . . . . . . . 354
8.29 Straylight Correction . . . . . . . . . . . . . . . . . 357
8.29.1 Create new co rrecti on sp ectra . . . . . 3 59
8.29 .2 Corre ctio n A lgorithm . . . . . . . . . . . . 3 62
8.29.3 Straylight correction as part of the
measurement process . . . . . . . . . . . 364
8.30 Noise Generation . . . . . . . . . . . . . . . . . . . 367
8.31 M ovi ng Mea n . . . . . . . . . . . . . . . . . . . . . . 368
8.32 Make Mo notone . . . . . . . . . . . . . . . . . . . . 369
8.33 R ad i ometri c cal i b rati on . . . . . . . . . . . . . . . 371
8.33.1 Introduction . . . . . . . . . . . . . . . . . . 371
8.33.2 Theoretical background information . 373
8.33.3 Standard procedur e of radiometric
c a l i b ra t i o n . . . . . . . . . . . . . . . . . . . 3 76
8.33.4 Customizing Manipulat e menu . . . . . 3 76
8.33.5 Generating radiomet ric calibration file 377
8.33.6 Performing radiometri c calibr ation . . 380
8.33.7 Radiometric calibratio n n o t p a s s e d . . 383

9 Evaluate . . . . . . . . . . . . . . . . . . . . . . . . 385
9 .1 Curve Fi t . . . . . . . . . . . . . . . . . . . . . . . . . 386
9 . 1.1 Se tti ng up mo del . . . . . . . . . . . . . . . 3 88
9.1.2 Calculating Model . . . . . . . . . . . . . . 3 94
9.1.3 Saving Model . . . . . . . . . . . . . . . . . 396
9 . 1 . 4 Cu r v e F i t T h e o ry . . . . . . . . . . . . . . . 3 97
9.2 Integration . . . . . . . . . . . . . . . . . . . . . . . . 400

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9.2.1 Setting up integration method . . . . . 4 00

9.2.2 Interactive Method Setu p . . . . . . . . . 404
9 . 2 . 3 St a r t i n g I n t e g r a t i o n . . . . . . . . . . . . . 4 08
9.2.4 Printing Integration Re su l t . . . . . . . . 412
9.3 Se t u p Q U A N T M e t h o d . . . . . . . . . . . . . . . . 413
9 .4 QUA NT Builder (via OPUS wizar d) . . . . . . . 426
9.5 Qua n ti tati ve A na l ysi s . . . . . . . . . . . . . . . . 434
9.5.1 QUANT Analysis Theory . . . . . . . . . 437
9.6 Si g n a l -to -N o i se-R ati o . . . . . . . . . . . . . . . . 438
9.6.1 Theory on SN calculation . . . . . . . . . 443
9.7 Pe a k P i c k i n g . . . . . . . . . . . . . . . . . . . . . . 444
9.7.1 Interactive Peak Picki n g . . . . . . . . . 449
9.7.2 Theory of Peak Picking . . . . . . . . . . 451
9.8 Quick Identity Test . . . . . . . . . . . . . . . . . . 458
9.9 Qu a l i t y T e st . . . . . . . . . . . . . . . . . . . . . . . 462
9.9.1 Defining Parameters . . . . . . . . . . . . 465
9.10 M u l ti E va l ua ti on S e tu p . . . . . . . . . . . . . . . 469
9.10 .1 First ste ps . . . . . . . . . . . . . . . . . . . 4 71
9.10.2 Setting up an ME met hod . . . . . . . . . 472
9.10.3 Storing ME method . . . . . . . . . . . . . 4 92
9.11 Multi Evaluation . . . . . . . . . . . . . . . . . . . . 493
9.11.1 Input Variables . . . . . . . . . . . . . . . . 4 94
9 .12 Qui ck Co mpare . . . . . . . . . . . . . . . . . . . . 497
9.12.1 Theoretical background information . 497
9 . 12 .2 C re a ti ng meth od . . . . . . . . . . . . . . . 4 98
9.12.3 Performing quick compar e . . . . . . . . 506
9.12.4 Quick compare result . . . . . . . . . . . 5 08
9.12.5 Setting up template f o r a n a l y s i s r e p o r t 512
9.12.6 Generating analysis re p o rt . . . . . . . . 514
9.13 Layer Thickness . . . . . . . . . . . . . . . . . . . . 516
9.13.1 Theory of layer thickness deter-
mi na ti on . . . . . . . . . . . . . . . . . . . . 5 20
9.14 H18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 521
9.14.1 Theory . . . . . . . . . . . . . . . . . . . . . . 523
9.15 Spectrum Search . . . . . . . . . . . . . . . . . . . 525
9.16 Neuro Developer Classification . . . . . . . . . 538

10 Display . . . . . . . . . . . . . . . . . . . . . . . . . 539
1 0.1 Back /Forward . . . . . . . . . . . . . . . . . . . . . 540
1 0.2 Sta cked . . . . . . . . . . . . . . . . . . . . . . . . . . 540
1 0.3 Scale Al l /S cale Y . . . . . . . . . . . . . . . . . . . 542

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10.4 Page Back /Page Forward . . . . . . . . . . . . . 543

10.5 Zoom In /Zoom Out . . . . . . . . . . . . . . . . . . 544
1 0.6 Sing le Peak Pi ck . . . . . . . . . . . . . . . . . . . 544
10.7 Maximize All /Reset Maximi z e A l l . . . . . . . . 545
1 0.8 Shift Cu rve (w hole ) . . . . . . . . . . . . . . . . . . 546
10.9 Shift Curve (top) /Shi ft Curve (bottom) /Reset
S h i f t C u rv e . . . . . . . . . . . . . . . . . . . . . . . 547
1 0.10 Cursor (C rossha ir) /(Fo llo w D ata ) . . . . . . . 5 48

11 Print . . . . . . . . . . . . . . . . . . . . . . . . . . 549
1 1 . 1 P ri n t S p e ctra . . . . . . . . . . . . . . . . . . . . . . 550
11.2 Setup Analysis Report Templa t e . . . . . . . . 556
11.2.1 Dialog . . . . . . . . . . . . . . . . . . . . . . 5 57
1 1 . 2 . 2 Re p o r t T y p e s . . . . . . . . . . . . . . . . . 5 58
11.2.3 Setting options for report data . . . . . 558
1 1 . 2 . 4 Re p o r t S t r u c t u r e . . . . . . . . . . . . . . . 5 59
11.2.5 How to set up a templa t e ? . . . . . . . . 559
11.2.6 Examples of a single sample report
te mpl ate . . . . . . . . . . . . . . . . . . . . 5 62
11.2.7 Special features in case of a multi
sa mp l e rep o rt . . . . . . . . . . . . . . . . . 5 63
1 1 . 2 . 8 Mu l t i E v a l u a t i o n . . . . . . . . . . . . . . . 5 67
11.3 Generate Analysis Report . . . . . . . . . . . . . 568
11.3.1 Report Layout . . . . . . . . . . . . . . . . . 569
11.3.2 Standard Template . . . . . . . . . . . . . 570
1 1 .3 .3 Re p o rt O utp u t . . . . . . . . . . . . . . . . . 5 71
1 1.4 Qui ck Prin t . . . . . . . . . . . . . . . . . . . . . . . 572
1 1.5 New Layout . . . . . . . . . . . . . . . . . . . . . . . . 572
11.5.1 PLE View . . . . . . . . . . . . . . . . . . . . 5 73
1 1 . 5 . 2 Po p - u p men u . . . . . . . . . . . . . . . . . 5 78
11.5.3 Resizing Drawing Area . . . . . . . . . . 5 79
11.5.4 Adding elements, modifying spectrum
frame . . . . . . . . . . . . . . . . . . . . . . . 5 85
11.5.5 Adding text and modi f y i n g t e x t f ra m e 597
11.5.6 Adding table and modifying table
frame . . . . . . . . . . . . . . . . . . . . . . . 6 01
1 1 . 6 O p e n La yo u t . . . . . . . . . . . . . . . . . . . . . . . 605
1 1.7 Pri nt /Print P revi ew . . . . . . . . . . . . . . . . . . 606
1 1 . 8 P ri n t S etu p . . . . . . . . . . . . . . . . . . . . . . . . 606

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 Table of Contents

12 Macro . . . . . . . . . . . . . . . . . . . . . . . . . . 607
1 2 .1Sc ri p t Re c o rde d H is to ry . . . . . . . . . . . . . . 608
1 2.2 Insert MyInstru ment . . . . . . . . . . . . . . . . . 609
1 2.3 Macro C onverter . . . . . . . . . . . . . . . . . . . . 610
1 2.4 Run Macro . . . . . . . . . . . . . . . . . . . . . . . . 611
12.5 Macro Debuggen . . . . . . . . . . . . . . . . . . . 611
1 2.6 Edit Macro . . . . . . . . . . . . . . . . . . . . . . . . 612
12.6.1 Macro editor vie w . . . . . . . . . . . . . . 612
1 2 .6 .2 Co r re ct in g m a c ro s y n t a x e rr o rs . . . . 613
12.6.3 Adding special command lines . . . . . 613
12.6.4 Adding OPUS commands . . . . . . . . . 614
12.6.5 Adding variables . . . . . . . . . . . . . . . 6 15
12.6.6 Adding macros to the toolb ar . . . . . . 6 16
12.6.7 Adding macros to a m e n u . . . . . . . . 617
12.7 Compile Macro . . . . . . . . . . . . . . . . . . . . . 618
12.8 New Procedure . . . . . . . . . . . . . . . . . . . . . 618
1 2 . 8 . 1 Po p - u p men u . . . . . . . . . . . . . . . . . 6 25
12.9 Edit Procedure . . . . . . . . . . . . . . . . . . . . . 633
12.10 Run Procedure . . . . . . . . . . . . . . . . . . . . . 634

13 Validation . . . . . . . . . . . . . . . . . . . . . . 635
13.1 Setup OVP . . . . . . . . . . . . . . . . . . . . . . . . 6 3 7
13.1.1 Measure Laser Wavenumber . . . . . . 6 40
13.1.2 Setting up OVP tests . . . . . . . . . . . . 6 44
1 3.2 Run OV P Tests . . . . . . . . . . . . . . . . . . . . 676
13.2.1 Running OVP test using the Instrument
S t a t u s d i a l o g . . . . . . . . . . . . . . . . . 6 80
13.2.2 Start ing OVP tests for mul ti p l e tes t
channels sequentially . . . . . . . . . . . 6 8 3
13.3 Measuring with test channel-specific laser
w a ve n u mbe r . . . . . . . . . . . . . . . . . . . . . . . 684
1 3 . 4 O V P i n un a tte n d e d mode . . . . . . . . . . . . . . 686
13.5 OVP Trend Chart . . . . . . . . . . . . . . . . . . . 688
13.5.1 Displaying trend chart . . . . . . . . . . . 690
13.5.2 Pop-up menu in trend ch a rt . . . . . . . 6 9 3
13.6 Automatic Accessory Recogni t i o n . . . . . . . . 6 9 6
13.6.1 Activating automatic accessory re-
c o g n i t i o n . . . . . . . . . . . . . . . . . . . . 696
13.6.2 Registering new accesso ri es . . . . . . 6 97
13.6.3 Performing OVP tests . . . . . . . . . . . 7 00
13.6 .4 Automa ti c Pe forman ce Te st . . . . . . . 7 00

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 Table of Contents

13.6.5 Working with special types of

accessories . . . . . . . . . . . . . . . . . . 7 01
13.6.6 Resetting accessory in test channel . 706
13.6.7 Clearing accessory in bench . . . . . . 707
13.6.8 Setting up test ch annel for non-vali-
d a t e d a c c e s s o ry . . . . . . . . . . . . . . . 708

14 Setup . . . . . . . . . . . . . . . . . . . . . . . . . . 709
14.1 Logout . . . . . . . . . . . . . . . . . . . . . . . . . . . 710
1 4.2 Setup JCAMP <-> OPUS C onversion . . . . . 711
14.3 User Management . . . . . . . . . . . . . . . . . . . 713
14.4 Change User Passw o r d . . . . . . . . . . . . . . . 721
14.5 Setup User Macro List . . . . . . . . . . . . . . . . 724
1 4.6 Regi ster OPU S . . . . . . . . . . . . . . . . . . . . . 726
14.7 Customize Toolbars . . . . . . . . . . . . . . . . . . 728
1 4 . 7 . 1 Mo v i n g t o o l b a r . . . . . . . . . . . . . . . . 7 29
1 4 .7.2 Ad d i ng to o l ba r . . . . . . . . . . . . . . . . 7 29
1 4 . 7 . 3 De l e t i n g t o o l b a r . . . . . . . . . . . . . . . 7 29
14.7.4 Customizing toolbar . . . . . . . . . . . . 7 30
1 4 .7.5 Crea ti ng T oo l bar . . . . . . . . . . . . . . . 7 33
14.7.6 Adding or deleting icons . . . . . . . . . 736
14.7.7 Copying icons . . . . . . . . . . . . . . . . . 7 37
1 4 .7.8 De p i cti n g i co n s . . . . . . . . . . . . . . . . 7 37
14.7.9 Grouping icons in the toolbar . . . . . . 738
14.7.10 Creating user-defined icons . . . . . . . 739
14.8 Customize Menus . . . . . . . . . . . . . . . . . . . 741
14.8.1 Adding or deleting menu command s . 744
14.8.2 Moving or copying menu commands . 745
14.8.3 Moving or copying menus and men u
commands in toolbar . . . . . . . . . . . . 745
14.8.4 Creating sub-menus . . . . . . . . . . . . 7 45
14.8.5 Grouping menu commands . . . . . . . . 747
1 4.9 Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . 748
14.9.1 Assigning shortcuts . . . . . . . . . . . . . 7 48
14.9.2 Deleting shortcuts . . . . . . . . . . . . . . 7 50
14.9.3 Resetting shortcuts . . . . . . . . . . . . . 7 50
1 4 . 1 0 Us e r S e t t i n g s . . . . . . . . . . . . . . . . . . . . . . 751
14.10.1 Instrument Test (only in case of non-
OVP supported instruments) . . . . . . 761
1 4 . 1 1 Open P l a n n e r . . . . . . . . . . . . . . . . . . . . . . 766
14.1 1.1 V iew Opti ons . . . . . . . . . . . . . . . . . 7 67
14.11.2 Creating planner items . . . . . . . . . . 769

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14.11.3 Creating recurring ite m s . . . . . . . . . 771

14.11.4 Editing planner items . . . . . . . . . . . 772
14.11.5 Editing recurring planner items . . . . 773
1 4 . 1 2 Ne w W o rk s p a c e . . . . . . . . . . . . . . . . . . . . 774
14.13 Save Workspace As . . . . . . . . . . . . . . . . . . 775
1 4.14 Close Workspa ce . . . . . . . . . . . . . . . . . . . 775
14.15 Send Workspace . . . . . . . . . . . . . . . . . . . 776

15 Help . . . . . . . . . . . . . . . . . . . . . . . . . . . 777
1 5.1 Help Top ics . . . . . . . . . . . . . . . . . . . . . . . 777
1 5.2 Onl ine Docs . . . . . . . . . . . . . . . . . . . . . . . 777
15.3 F T-IR T u to ri al . . . . . . . . . . . . . . . . . . . . . . 778
15.4 A b o u t OP U S . . . . . . . . . . . . . . . . . . . . . . . 778

16 A p p e n di x A . . . . . . . . . . . . . . . . . . . . . 779

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xiv OPUS Reference Manual Bruker Optik GmbH

1 Sta r t i n g O P U S
Click the OPUS program icon from the Windows start menu.

Note: The icon is automatically displayed if the OPUS instal-

lation has been completed successfully.

Figure 1: Windows start menu

The OPUS Login dialog opens.

Bruker Optik GmbH OPUS Reference Manual 1

 Chapt. 1 Starting OPUS

B C

Figure 2: OPUS Login

A Select your User ID from the drop-down list. OPUS provides

an independent user account system which regulates the
access. Note: If you use OPUS for the very first time, the
User ID drop-down list includes the two pre-defined user
records Default and Administrator. Select either one of
them.
B Enter OPUS into the Password entry field. The password is
case sensitive. Note: Once you have assigned yourself a
user record in OPUS, it is possible to determine your own
User ID and Password.
C OPUS includes different accounts for operator and adminis-
trator rights. Users defined as Operator have limited access
rights compared to users defined as Administrator. The rights
depend on the User ID selected.
D Select the workspace desired, use the drop-down list. You
can always select those workspaces from the drop-down list
which have been defined for your User ID. Note: When you
use OPUS for the first time, we recommend to use the
standard Default.ows workspace. For further information
see chapter 2.2.
E Click Login.

2 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 1

The About OPUS window opens.

Figure 3: About OPUS

It shows the serial number of your OPUS copy and the registered
user name. The basic OPUS package integrates these additional
licensed packages as an all-in-one application.

Click OK to open the OPUS user interface.

Bruker Optik GmbH OPUS Reference Manual 3

 Chapt. 1 Starting OPUS

1.1 U ser Interface

The interface appearance depends on the screen settings and

operating system used. Thus, the screen display of the following
dialog boxes may not show exactly the screen contents displayed
on your screen.

BRUKER recommends a minimum graphic resolution of 800 x 600

pixel and True Color.

C
D

H G

I
Figure 4: OPUS user interface

A Pull-down menus
Allow access to all OPUS functions.
B Toolbar
Enables quick access to frequently used functions.
C Browser
Contains the spectrum file loaded together with the data
blocks.

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 User Interface Chapt. 1

D Spectrum window
Shows the spectrum loaded
E Overview window
Contains the full frequency range of the spectrum selected
F OPUS view
The OPUS view you work with is indicated by a tab:
Each tab
has a different color to be able to distinguish between them.
If several views are open simultaneously, click the respective
tab or use the buttons on the left and right to change
between the different views.
G Instrument status
Gray: no spectrometer connected
Green: spectrometer connected
Yellow: warning
Red: error
H Online help
The online help is context sensitive.
I Status bar
Indicates which background task is running.

Bruker Optik GmbH OPUS Reference Manual 5

 Chapt. 1 Starting OPUS

6 OPUS Reference Manual Bruker Optik GmbH

2 OPUS Basics
This chapter contains basic information about the most important
OPUS features and provides useful notes on how to work with the
OPUS tools.

2.1 B asic Software Features

Browser Contains the name and directory path of the spec-

trum file currently loaded. For further details refer to
chapter 2.6.

Dialog box The OPUS dialog boxes consist of different tabs.

Click these tabs to change between them. Buttons
and drop-down lists are only enabled, if they are dis-
played in black. Grayed buttons or other items are
disabled.

Drag & Drop OPUS supports drag & drop, a method to move
graphical elements by using the mouse. You can
drag single elements of a graphical user interface
from one particular position and drop them at a dif-
ferent position.

Drag & drop simplifies e.g. the Copy and Paste pro-
cess of files. In this case you have to select the file
first, press the left mouse button while moving the
file to the respective dialog box (or window). If you
release the mouse button, the file will be loaded into
the dialog box (or window) selected. Double clicking
the spectra file name allows to move spectra files to
a specific dialog.

Pop-up menu There are several pop-up menus in OPUS available.

To display a pop-up menu right click anywhere in a
window.

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 Chapt. 2 OPUS Basics

Shortcut OPUS supports shortcuts, i.e. a key sequence that

performs a pre-defined function by simultaneously
or successively clicking several keys in a particular
order.

The use of such sequences allow to send particular

control commands to the program, e.g. copy
(Ctrl+C), cut (Ctrl+X) and paste (Ctrl+V). To use
these shortcuts, you first have to select the text or
file you want to edit.

Toolbar OPUS provides toolbars which can be individually

configured to quickly access frequently-used func-
tions. By default, the OPUS interface contains one
single toolbar. For further details on toolbars refer to
chapter 14.10.

ToolTip Next to each icon context-sensitive tooltips pop up

when you position the cursor on that icon.

Wizard The OPUS wizard is an interactive help tool that

suggests a series of OPUS commands to perform a
particular application. For further details refer to
chapter 2.7.

2.2 Workspa ce

The following settings are stored in the OPUS workspace:

• User rights
• Configuration of toolbars and windows
• Parameter settings of all commands
• Configuration of menus and pop-up menu
• User name and password

These settings are stored in one file which has the extension *.ows.

Note: The workspaces available for you in OPUS depend

both on the user ID defined for you in the Login dia-
log (see figure 2 on page 2), and on the spectrometer
configuration.

The commands included in each OPUS menu correspond to the

workspace selected, i.e. a workspace designed for NIR (near infra-

8 OPUS Reference Manual Bruker Optik GmbH

 Workspace Chapt. 2

red) provides only those commands on each single menu which

are relevant for NIR. All the other commands are grayed, and thus
deactivated.

The following table includes the most important workspaces avail-

able in OPUS.

Workspace In connection with...

Alpha.ows ALPHA spectrometer

CONFOCHECK.ows protein analyses

default.ows OPUS default settings

full_access.ows all OPUS commands

HTS-XT.ows HTS-XT module

HYPERION1000.ows Hyperion 1000 microscope

HYPERION3000.ows Hyperion 3000 microscope

MIR_Advanced.ows OPUS commands for MIR (mid infrared),

customized view

MIR_FullAccess.ows all OPUS commands for MIR (mid infrared)

MIR_PROCESS.ows process control

MIR_R&D.ows R & D applications

MIR_Routine.ows routine MIR measurements

NIR_Advanced.ows OPUS commands for NIR (near infrared),

customized view

NIR_FullAccess.ows all OPUS commands for NIR (near infrared)

NIR_Routine.ows routine NIR measurements

To m o d i f y t h e w o r k s pa c e o r c r e a t e a n e w
one...

...you need the right to do so. On the Setup menu, click User Set-
tings. Activate the respective check boxes on the Rights tab.

Bruker Optik GmbH OPUS Reference Manual 9

 Chapt. 2 OPUS Basics

Figure 5: User workspace rights

Note: If you have modified the workspace, e.g. by re-posi-

tioning toolbars, these changes will be stored when
you exit OPUS.

If you have created a new workspace, a dialog pops

up requesting the name of this new workspace when
you exit OPUS.

For further information on user management and user settings

refer to chapter 14.7 and 14.10.

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 Access Control Chapt. 2

2.3 A ccess Control

OPUS has an access control mechanism which is shown in the

chart below:

Figure 6: OPUS access control chart

The OPUS User Database includes all User Records.

The User Records comprise:

• User ID
• Password
• Operator Name
• User Group (Administrator, Operator)
• Accessible Workspaces

The Workspaces comprise:

• Menu Contents
• Toolbar Contents
• Access Rights within OPUS
• Other Settings (e.g. file increment mode, display limits)

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 Chapt. 2 OPUS Basics

2.4 Paths and Directories

With OPUS 7.5 and higher the path structure of OPUS adapts to
the one used in Microsoft Windows. Chapter 2.4 describes the
default path structure used in OPUS.

The path structure can always be adapted to user-specific require-

ments. This, however, requires Administrator user rights.

Path name Path Directories/files included

User path

all users C:\Users\Public\Public Docu- • *\AAR_Dir

ments\Bruker\<OPUS_version> • *\Data
• *Macro
• *\ME_Basea
• *\Methods
• *\OpusLab
• *\ORADB
• *\OWSb
• *\Process
• *\SCRIPTS
• *\SEARCH
• *\straycorrc
• *\TANGO
• *\UserDataBase
• *\Validation
• *\VBSample
• *\Wizard Files
• *\WORK
• *\XPMd

user currently C:\Users\<User name>\My Doc- •*\DATA

logged in uments\Bruker\<OPUS_ver- • *\MEASe
sion> • *\WORK

Program path C:\Program Files\Bruker\ Program directories and pro-

<OPUS_version> gram files
a. Directory for multi evaluation files
b. Directory for workspace files
c. Directory for straylight correction files
d. Directory for experiment files
e. Directory for measuring data; generated after the measurement has finished;

12 OPUS Reference Manual Bruker Optik GmbH

 User Rights Chapt. 2

2.5 U ser Rights

OPUS distinguishes between three different types of users:

• Administrator
• LabManager
• Operator

The different user groups have the following user rights in OPUS:

User Group Workspaces User Settings

Administrator • Access to all • Complete access

• Right to modify all • Right to change them
• Right to create new ones

LabManager • Access to all No access

• Right to modify all
• Right to create new ones

Operator Access to the one(s) No access

assigned

The user rights are defined by the User settings command on the
OPUS Setup menu (see chapter 14.10). The Administrator has to
ensure that the Operator has only access to special commands
within the OPUS workspace assigned to the Operator.

2.6 B rowser

The OPUS browser shows the spectrum files together with the cor-
responding data blocks.

Note: If the browser is not displayed, make sure that the

Browser option is checked on the View menu.

By default, the browser is displayed on the left side of the OPUS

interface.

Bruker Optik GmbH OPUS Reference Manual 13

 Chapt. 2 OPUS Basics

Figure 7: Browser in OPUS

To e n l a r g e o r r e d u c e t h e s i z e o f t h e
b r o w s e r w i n d o w. . .

...click between browser and spectrum window. The cursor

changes to . Now, press the mouse button and drag the browser
window to the size desired.

To h a v e t h e b r o w s e r w i n d o w d i s p l a y e d a s
drop-down list

Left click the upper edge of the browser and draw it underneath the
toolbar. The OPUS browser window will be displayed as drop-down
list, including all the files loaded.

Figure 8: Browser as drop-down list

14 OPUS Reference Manual Bruker Optik GmbH

 Browser Chapt. 2

To undo this view click the upper edge of the drop-down list and
move the list to the original browser window position, i.e. to the left
side of the spectrum window.

When loading a spectrum file...

...it is displayed in the OPUS browser as follows:

Figure 9: Loaded spectrum file in the browser

A If you have opened several spectrum windows you can switch

between them. If you click the icon, the file name display will
be minimized.

B The blue document symbol indicates that the file has not yet
been manipulated. In case of manipulated files the docu-
ment symbol turns from blue to red.
The number next to the file name indicates the number of
copies made of the file loaded. You can load a file several
times into the OPUS browser window. In this case the copies
will be incremented accordingly.

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 Chapt. 2 OPUS Basics

C All data blocks which are part of the spectrum file are dis-
played. The data blocks displayed in figure 9 indicate a trans-
mission spectrum, single-channel spectrum, interferogram
and single-channel background spectrum.
Colored data block symbols indicate that the spectra or inter-
ferograms are displayed within the spectrum window. For fur-
ther information refer to chapter 2.12.

2.6.1 Make invisible

The icon allows to make the browser invisible. In this case the
browser is displayed as a blue bar below the toolbar on the left
side.

Figure 10: Hidden browser

To m a k e t h e b r o w s e r v i s i b l e a g a i n . . .

...position the cursor onto the blue bar below the toolbar. Now, the
icon points to the right. As soon as you move the cursor outside
the browser on the OPUS interface, the browser will be hidden
again.

To h a v e t h e b r o w s e r p e r m a n e n t l y d i s-
played again...

...click the icon as soon as you unhide the browser. To close

the browser click the icon

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 Browser Chapt. 2

2.6.2 Pop-up menus

Two different types of pop-up menus can be generated in the

browser:
• pop-up menu to edit spectrum data
• pop-up menu to change spectrum display

To e d i t s p e c t r u m d a ta o p e n t h e p o p - u p
menu...

...by right clicking the name of the spectrum file. The pop-up menu
contains the following options:

A
B

D
E

Figure 11: Pop-up menu - Editing spectrum data

A Changes made in a file are not automatically saved in the file

directory. Therefore, store these changes by using the Save
File command.
B The file is removed from the spectrum window, but is still
available in the file directory.
C Changes made in a file can be undone to restore the original
spectrum file.
D All pieces of information on data acquisition of a particular
spectrum file can be displayed.
E Both commands allow duplicating spectrum files. The differ-
ence between these two commands is that Copy Entry copies
a data file which has been edited. The Clone Original com-
mand copies the original spectrum file.

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 Chapt. 2 OPUS Basics

To c h a n g e t h e s p e c t r u m d i s p l a y o p e n t h e
pop-up menu...

...by right clicking one data block of the spectrum file. For further
details on this menu refer to chapter 2.8.4.

To a d a p t t h e O P U S i n t e r f a c e o p e n t h e p o p -
up menu...

...by right clicking somewhere within the browser. The pop-up

menu contains the following options:

Figure 12: Pop-up menu - OPUS interface

A If you select this command, the windows (browser, spectrum

and overview window) are displayed next to each other within
the OPUS interface. If you deactivate this command, you can
remove the browser window from the OPUS interface and
position it somewhere else on the Windows desktop.
B This command makes the browser window invisible. To undo
this setting, activate the Browser command on the View menu
again.

18 OPUS Reference Manual Bruker Optik GmbH

 Wizard Chapt. 2

2.7 Wiz a rd

The wizard is an interactive help tool to measure and edit spectra.

Certain OPUS commands are available which allow to manipulate
or evaluate spectra. These commands are either available as but-
tons, this concerns the most frequently and recently used ones, or
they are listed in a drop-down list.

Note: If the wizard is not displayed, make sure that the Wiz-
ard Bar option is checked on the View menu.

By default, the wizard is displayed on the left side of the OPUS

interface.

A C

Figure 13: OPUS Wizard

A The wizard contains a series of OPUS commands which can

be generally performed by a single click on the respective but-
ton.

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 Chapt. 2 OPUS Basics

B If you click the triangle, an additional menu pops up.

Use this menu to open the setup dialog for the command
selected as well as the online help.
C Up to 4 levels are available to edit spectra data.
D An instrument test to qualify the spectrometer performance
for daily routine work can be performed.
E This window contains a brief description of the OPUS com-
mand currently selected.

2.7.1 Make invisible

The icon allows to make the wizard invisible. If you click this
icon, the wizard is hidden in a blue bar below the toolbar.

Figure 14: Invisible wizard

To m a k e t h e w i z a r d v i s i b l e a g a i n . . .

...position the cursor on the blue bar below the toolbar. The
icon now points to the right. As soon as you move the cursor out-
side the wizard on the OPUS interface, the wizard will be hidden
again.

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 Wizard Chapt. 2

To h a v e t h e w i z a r d p e r m a n e n t l y d i s p l a y e d
again...

...click the icon as soon as the wizard is made visible. To close

the wizard click the icon.

2.7.2 Levels

Specific OPUS commands are available as buttons on the different

wizard levels (B in figure 13). Once you have performed one com-
mand you will automatically come to the next possible, and in this
particular context, reasonable level. To perform the single com-
mands just click the respective button.

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 Chapt. 2 OPUS Basics

Acquire

Figure 15: Wizard - Acquire

A On the first wizard level you either load a spectrum or...

B ...perform a measurement.
C It is recommended to perform an instrument test for the cur-
rent test channel within a specified period of time. Click Instru-
ment Test. For detailed information refer to chapter 13.

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 Wizard Chapt. 2

Manipulate

On the second wizard level you edit the spectrum file.

C
B

E D

Figure 16: Wizard - Manipulate

A The last 4 manipulation commands previously used are dis-

played as buttons. If you select a different manipulation com-
mand from the drop-down list (B), this command will be
displayed as button the next time you start OPUS.
B The drop-down list contains additional manipulation com-
mands.
C Click this button to start one of the manipulation commands
selected from the drop-down list.

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 Chapt. 2 OPUS Basics

D Click the triangle to open the respective dialog or the online

help of the command selected from the drop-down list.
E Start the next sample measurement. The Measurement dia-
log will be displayed.

Evaluate

On the third wizard level you evaluate the spectrum file.

C
B

E D

Figure 17: Wizard - Evaluate

A The last 4 evaluation commands previously used are dis-

played as buttons. If you select a different evaluation com-

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 Wizard Chapt. 2

mand from the drop-down list (B), this command will be

displayed as a button the next time you start OPUS.
B The drop-down list contains additional evaluation commands.
C Click this button to start one of the evaluation commands
selected from the drop-down list.
D Click the triangle to open the respective dialog or the online
help of the command selected from the drop-down list.
E Start the next sample measurement. The Measurement dia-
log will be displayed.

Report

Figure 18: Wizard - Report

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 Chapt. 2 OPUS Basics

A Activate the check box to store the spectrum file, and note the
following:
• If you load a spectrum file (by means of the wizard) from a
particular directory, this file will be stored into this directory.
• If you measure a spectrum by means of the wizard, this
spectrum will be stored into the C:\Users\<User name>\My
Documents\Bruker\OPUS_<version>\MEAS directory. This
directory is generated after a measurement has been per-
formed.
B Activate the check box to print the spectrum file.
C Activate the check box to unload the spectrum file, i.e. to
remove the spectrum from the spectrum window.
D Activate the check box to measure another sample.
E Click Go, to perform the options selected between A - D.

2.8 Spectrum Window

The spectrum window displays either the spectrum of a loaded

spectrum file, or the spectrum generated by a measurement.

Note: The default settings for the spectral range are from
4,000 to 400 wavenumbers and from 0 to 1.5 extinc-
tion units.

Figure 19: Spectrum window with spectrum and crosshair

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 Spectrum Window Chapt. 2

By default, the crosshair and the corresponding coordinates are

displayed in the spectrum window.

2.8.1 E n l a r g i n g o r r e d u c i n g t h e s p e c-
trum window
1 Position the cursor exactly between overview and spectrum
window.
➣The cursor changes to .
2 Now, re-size the spectrum window.

2.8.2 Fixing the size of the spectrum

window
1 Right click between spectrum window and overview window.
➣The Lock button is displayed.
2 Click the Lock button.
➣The size of the spectrum window is now permanently fixed.

2.8.2.1 Undo the fixed size of the

spectrum window
1 Right click between spectrum window and overview window.
➣ The Unlock button is displayed.
2 Click the Unlock button.
➣The size of the spectrum window is no longer fixed.

2.8.3 More than one spectrum in the

spectrum window

When working with more than one spectrum in the spectrum win-
dow simultaneously, it is recommended to activate on the Settings
menu On New File tab the Replace in current window option
button.

In this case the window currently loaded will not only be displayed
in the spectrum window but also in the browser (see
chapter 14.10).

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 Chapt. 2 OPUS Basics

2.8.4 Pop-up menu in the spectrum win-

dow

Right clicking a spectrum displayed in the spectrum window opens

a pop-up menu, which provides several setting options. The setting
options are described in the following chapters.

Figure 20: Pop-up menu in the spectrum window

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 Spectrum Window Chapt. 2

2.8.5 Zooming in a spectral range

☞ If a crosshair is displayed in the spectrum window, start with
step 3.

1 Right click the spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Zoom  Zoom
In command.
3 Draw a frame around the spectral range while pressing the
left mouse button.
4 Click the left mouse button to position this frame.
5 Click the left mouse button again to have the particular spec-
tral range displayed in the spectrum window.

Figure 21 exemplifies a zoomed-in spectral range in the spectrum

window.

Figure 21: Spectral range zoomed-in

The overview window below the spectrum window shows the com-
plete spectral range. The spectral range depicted on the white
background is exactly the one displayed in the spectrum window.

If you position the cursor on the white spectral range displayed in

the overview window, the cursor changes to . While pressing
the left mouse button, you can move this spectral range. If you
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 Chapt. 2 OPUS Basics

position the cursor on the interface line between white and gray
background, the cursor changes to . While pressing the left
mouse button, you can move the display limits of the spectral range
selected.

2.8.6 Zooming out a spectral range

☞ If a crosshair is displayed in the spectrum window, start with
step 3.

1 Right click the spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Zoom  Zoom
Out command.
3 Draw a frame around the spectral range while pressing the
left mouse button.
4 Click the left mouse button to position this frame.
5 Click the left mouse button again to have the particular spec-
tral range displayed in the spectrum window.

Figure 22 exemplifies a zoomed-out spectral range in the spectrum

window.

Figure 22: Spectral range zoomed-out

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 Spectrum Window Chapt. 2

2.8.7 Scaling all spectra

1 Right click any spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Scale All
Spectra command.
3 Click the Show Everything (XY) option.
➣The spectrum is displayed within the complete spectral
range.

2.8.8 Maximizing each spectrum

☞ If more than one spectrum is displayed in the spectrum win-
dow, you can maximize each one of them on the y axis simul-
taneously.

1 Right click any spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Scale All
Spectra command.
3 Click the Maximize Each Spectrum (Y) option.

2.8.8.1 Undo maximizing

1 Right click any spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Scale All
Spectra command.
3 Click the Reset Maximize (Y) option.

2.8.9 Scaling ordinate

The ordinate is a synonym for y axis.

1 Right click the spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Scale All
Spectra command.
3 Click the Scale Ordinate option.

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2.8.10 S h i ft i n g c u r v e

The Shift Curve command provides several options:

• Whole Curve: the complete spectrum curve is shifted
vertically
• Top: the spectrum curve is stretched to the top in y
direction
• Bottom: the spectrum curve is stretched to the bottom
in y direction.

To shift the curve proceed as follows:

1 Right click the spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Shift curve
command.
3 Select the option desired.
4 Click the spectrum.
➣The cursor changes to .
5 Press the left mouse button and shift the curve.

2.8.10.1 U n d o s h i ft c u r v e
1 Right click the spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Shift curve
command.
3 Select the Reset option.

2 . 8 . 11 Activating crosshair

By default, the crosshair is always displayed in the spectrum win-

dow. The Crosshair command contains two options:
• Cursor: the cursor is displayed as crosshair
• Follow Data: follows the data points of a spectrum. The
current crosshair position (e.g. wavelength or absorption
unit) is displayed in the upper right end of the spectrum
window. This allows to read out the x/y positions directly
from the spectrum.

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 Spectrum Window Chapt. 2

To activate the crosshair proceed as follows:

1 Right click the spectrum displayed in the spectrum window.

2 From the pop-up menu that opens, select the Crosshair
command.
3 Select the option desired.

2.8.12 Deactivating crosshair

☞ Right click the spectrum window to deactivate the crosshair.

2.8.13 Changing color of the spectrum

1 Right click the spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Change Color
command.
3 From the color palette displayed, select the color desired.

2.8.14 R e m o v i n g s p e c t r u m f r o m s p e c-
trum window
1 Right click the spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Remove from
Display command.
➣The spectrum window is only removed from the spectrum
window but not unloaded from the browser. By drag & drop
you can reload the spectrum file from the browser to the
spectrum window.

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2.8.15 A d d i n g a n n o ta t i o n s t o s p e c t r u m
1 Right click the particular position of the spectrum displayed
in the spectrum window.
2 From the pop-up menu that opens, select the Add Annota-
tion command.
➣By default, exactly at the cursor position an arrow is
inserted indicating the wavenumber of this data point. On
the browser, the data block is added to the spectrum
file.

Figure 23 exemplifies a spectrum with wavenumber annotations,

and the spectrum file with the data block added.

Figure 23: Spectrum with wavenumber annotations

➣If you position the cursor onto the arrow head of the anno-
tation, the cursor changes to . Press the left mouse but-
ton to move the arrow head.

2.8.15.1 E d i t i n g a n n o ta t i o n s
1 Right click the particular annotation.
2 From the pop-up menu that opens, select the Properties
command.
3 Enter the new text for the annotation.
4 If required, deactivate the Center text line or With arrow
checkboxes.
5 Click OK to confirm.
34 OPUS Reference Manual Bruker Optik GmbH
 Spectrum Window Chapt. 2

2.8.15.2 R e m o v i n g a n n o ta t i o n s
1 Right click the particular annotation.
2 From the pop-up menu that opens, select the Remove com-
mand.

2.8.16 Copying one spectrum

1 Right click the particular spectrum displayed in the spectrum
window.
2 From the pop-up menu that opens, select the Copy com-
mand.
3 From the Window menu, select the New Spectrum Window
command.
4 Right click into the new spectrum window.
5 From the pop-up menu that opens, select the Paste com-
mand.

2.8.17 Copying all spectra

1 Right click any spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Copy All com-
mand.
3 From the Window menu, select the New Spectrum Window
command.
4 Right click into the new spectrum window.
5 From the pop-up menu that opens, select the Paste com-
mand.

2.8.18 Performing single peak pick

1 Right click a particular spectrum displayed in the spectrum
window.
2 From the pop-up menu that opens, select the Single Peak
Pick command.

➣The cursor changes to .

3 Move the cursor to the desired position and click the peak.

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 Chapt. 2 OPUS Basics

➣The wavenumber of the generated peak is displayed.

Note: In case of equally large peaks only the peak
close to the cursor will be displayed.

Figure 24 exemplifies a spectrum with single peaks, and the spec-

trum file with the data block added.

Figure 24: Spectrum with single peaks

2.8.18.1 Deleting single peak

1 Right click the particular single peak displayed in the
spectrum window.
2 From the pop-up menu that opens, select the Delete peak
label command.

2.8.19 Settings of spectrum view

1 Right click a spectrum displayed in the spectrum window.
2 From the pop-up menu that opens, select the Properties
command.
3 Make the settings on the different tabs.
➣The tabs are described in the following chapters.
4 Click OK to confirm.

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 Spectrum Window Chapt. 2

2.8.19.1 Display settings

Figure 25: Display Settings - Display Limits

To change the display limits of the spectral range enter the values
into the particular entry field. If required, activate the Compressed
wavenumbers checkbox. The wavenumbers are displayed in a
more compressed manner in the spectrum window.

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 Chapt. 2 OPUS Basics

2.8.19.2 Axes

Figure 26: Display Settings - Axes

Each spectrum can be displayed with additional x and y axes on

top and on the right side of the spectrum window.

If the spectrum window contains more than one spectrum and the
spectra are displayed in stacked mode, you can define separate
axes for each spectrum if you select the X between option.

When activated the X checkbox, the drop-down lists are enabled.

Select the particular axe‘s labelling from the drop-down lists.

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 Spectrum Window Chapt. 2

2.8.19.3 General

Figure 27: Display Settings - General

The General tab allows to change the background color of the

spectrum and overview window, and to set the default height of the
overview window.

If you activate the Popup info check box and select an option, the
path and file name, or path name only, will be displayed as soon as
you position the cursor on the spectrum.

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 Chapt. 2 OPUS Basics

2.9 D efining Frequency Range

In case of some OPUS manipulation or evaluation commands you

have to define frequency limits first. There are several possibilities
to define a frequency range:

How to define a frequency range?

OPUS commands which require a defined frequency range contain

the Frequency Range tab. Use this tab to define the respective fre-
quency range. Figure 28 exemplifies the possibilities provided
according to the Normalize OPUS command.

Figure 28: Select frequency range

A If the check box is activated, the frequency range of the

spectrum shown in the spectrum window is used. The
other options on the tab will be disabled.
B Use this button to interactively select the frequency range.

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 Defining Frequency Range Chapt. 2

C The display limits of a particular part of the spectrum can

be used as frequency range. This makes sense if you have
zoomed a particular part of the spectrum before.
D Manually enter the values for the frequency range into the
entry fields.

How to interactively define a frequency

range?

1 Load the spectrum you want to manipulate or evaluate.

2 Select the respective OPUS command.
3 On the Frequency Range tab, click Interactive.
4 The Select Frequency Range(s) dialog opens and shows the
spectrum loaded.

Figure 29: Interactive frequency range selection

5 Position the cursor on the boundary between the white and

gray area, the cursor changes to . Press the left mouse
button and move the cursor either to the left or right side.

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 Chapt. 2 OPUS Basics

Figure 30: Select frequency range

6 Within the white section the cursor changes to . Press the

left mouse button to move the entire frequency range
selected.

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 Defining Frequency Range Chapt. 2

Figure 31: Move frequency range

7 Click OK to confirm the limits of the frequency range to be

used for data processing.

What does the interactive frequency range

view show?

• If both frequency ranges are within the display limits, the

area between the boundaries will be white, the back-
ground gray.
• If the complete frequency range displayed fits the dis-
play limits, the entire range will be white.
• If the display limits are either above or below the fre-
quency range displayed, the background will be com-
pletely gray. In this case, close the Select Frequency
Range(s) window, define reasonable frequency ranges
and start the interactive mode again.

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 Chapt. 2 OPUS Basics

2.10 Information View

The information view contains measurement parameters or evalua-

tion results of the spectrum file. This kind of data are stored in so-
called report data blocks, e.g. AB or TR.

Note: If the information view is not displayed, make sure

that the Information View option is checked on the
View menu.

By default, the permanent information view is displayed below the

spectrum window.

Figure 32: Information view

2.10.1 Make invisible

The icon allows to make the information view invisible. If you

click this icon, the information view is hidden in a blue bar on the
left side of the interface below the wizard.

Figure 33: Invisible information view

To m a k e t h e i n f o r m a t i o n v i e w v i s i b l e
again...

...position the cursor on the blue bar. The icon now points to
the right. As soon as you move the cursor outside the information
view on the OPUS interface, the view will be hidden again.

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 Information View Chapt. 2

To h a v e t h e i n f o r m a t i o n v i e w p e r m a n e n t l y
displayed again...

...click the icon as soon as the wizard is made visible. To close

the information view click the icon.

2.10.2 O p e n a s e pa r a t e r e p o r t w i n d o w

To open a separate report window double click the respective

report block in the browser. A separate report window will be dis-
played.

Figure 34: Report window

B

A Directory tree of the data included in the report block

If you select one item in the directory tree,...
B ...the specific data are displayed on the right. Click the column
title to sort the column data in ascending or descending order.
C The Datafile History directory contains any manipulation
made in the spectrum and changes performed in the mea-
surement parameters. These data are recorded in a non-edit-
able, non-deletable history datafile. Figure 35 shows such a
datafile history, including several spectrum manipulations.

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 Chapt. 2 OPUS Basics

Figure 35: Report window - Datafile history

D The first line of the datafile history indicates the operator as

well as the OPUS version and the name of the spectrum. All
manipulations and their parameters are listed below in the
order of their performance.
E All pieces of information are saved in the HISTORY data
block ( ) together with the edited spectrum in one spec-
trum file. This ensures that all data manipulations can be
reproduced, as every kind of manipulation as well as the
operator name are recorded.

To d i s p l a y t h e v i e w p r o p e r t i e s s e t . . .

...right click into the report window and select the Properties option
from the pop-up menu. The View Properties dialog box opens.

46 OPUS Reference Manual Bruker Optik GmbH

 Toolbar Chapt. 2

Figure 36: Information view - View Properties

The Header preferred check box is activated by default so that

each column is provided with a header. To specify the font and font
size click Printer Font.

2 . 11 Too l b a r

The OPUS toolbars can be individually configured to quickly

access frequently-used functions. For detailed information on how
to configure toolbars refer to chapter 14.7.

Context-sensitive tooltips pop up when you position the cursor on a

particular icon.

Figure 37: Icon with tooltip

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 Chapt. 2 OPUS Basics

2.12 Data Block

OPUS spectrum files can contain different kinds of spectra, evalua-

tion results or reports. This kind of data is depicted in data blocks in
the OPUS browser.

Note: To select a data block use the left mouse button. If

you press the CTRL key, you can select more than
one data block. Selected data blocks are always indi-
cated by a red frame.

The following table includes all data blocks available in OPUS.

Data block Abbreviation Definition

AB Absorption spectrum

ABARI Arithmetical result (absorbance)

TRARI Arithmetical result (transmission)

ANNO Annotation

ATR ATR spectrum

AVERAGE Average report

2CHN 2nd data channel

3CHN 3rd data channel

4CHN 4th data channel

CLASS Classification

CLUS Cluster analysis

CONF Conformity test

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 Data Block Chapt. 2

Data block Abbreviation Definition

1DER 1st derivative

2DER 2nd derivative

nDER nth derivative

3D 3D spectrum

EMIS Emission spectrum

FIT.REP Fit report

GEN.REP General report

GRAPH Video image(s)

HISTORY Protocol

IFG Interferogram

RIFG Reference interferogram

SIFG Sample interferogramm

INFO Information block

INTEG Integration report

INTERPR Interpretation

KM Kubelka-Munk spectrum

LIST Spectra file list

ME Multi Evaluation

METHOD Method

PAS Photoacoustic spectrum

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 Chapt. 2 OPUS Basics

Data block Abbreviation Definition

PEAKS Peak table

RPH Reference phase spectrum

SPH Sample phase spectrum

RPOW Reference power spectrum

SPOW Sample power spectrum

QUANT QUANT report

QC Quick Compare

QTEST Quality test

RAM Raman spectrum

REFL Reflectance spectrum

LREFL Logarithm of reflectance

REPORT Result view of an IDENT analysis

RSC Single-channel spectrum, reference

SSC Single-channel spectrum, sample

SEARCH Search result

SIGNAT. Signature

STR Molecular structure

SUBTR. Subtraction report

TR Transmittance spectrum

TRC Trace

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 Decimals Chapt. 2

Data block Abbreviation Definition

... Unknown data block

??? Unknown data block

? Unknown spectrum type

2.13 Decimals

In principle, always use a decimal point in OPUS when entering

decimals. This applies to all OPUS commands without distinction.

2.14 Connecting to Spectrome-

ter

1 On the OPUS Measure menu, click Optic Setup and Service.

2 Click the Optical Bench tab.
3 Select the spectrometer type from the Configuration drop-
down list.
4 Click Save Settings.

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 Chapt. 2 OPUS Basics

Figure 38: Optic Setup and Service - Basic

For further details on this dialog refer to chapter 7.7.1.

2.15 Instrument Status

The instrument status is shown by the status light ( ) at the right

end of the OPUS interface. The status is based on the currently
active channel or measurement experiment loaded.

The OPUS status light can have the following colors: green, gray
yellow and red. The following table explains the meaning of these
colors.

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 File Name Extensions Chapt. 2

Color Meaning Measuring

Green • spectrometer connected possible

• spectrometer works properly

Gray • no spectrometer connected not possible

• spectrometer switched off

Yellow • a warning is displayed (e.g. IR source possible

has not yet reached its operating tem-
perature, the validity period of the
instrument test has expired, the air
humidity content inside the instrument
is too high etc.)

Red • spectrometer malfunction not possible

• defective spectrometer component
• instrument test failed

If you click the instrument status light, the Diagnosis dialog pops
up. This dialog shows the status of the single hardware compo-
nents in the upper icon row.

The second and third row refer to the possible active test channels.
For further information on this subject refer to chapter 7.8 and 13.

2.16 File Name Extensions

The following table includes the file name extensions used in the
OPUS software.

Extension Definition

*.CLA Cluster analysis method

*.CLG Scan/find OPUS file

*.CON Conformity test method

*.DAT Pirouette file, used by InStep software

*.DX JCAMP file, also DX1, DX2

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 Chapt. 2 OPUS Basics

Extension Definition

*.FAA IDENT method

*.INT Integration method

*.MAC Macro file

*.MOL Chemical structure in MOLFILE format

*.MTB Macro file

*.MTD Method file for user library

*.NNN OPUS spectrum file (any numerical extension,

between 1 to 3 digits)

*.NTI Optical bench configuration file

*.OBS Visual basic scripts

*.OWS OPUS workspace

*.PCT Parameter correlation table used for JCAMP-DX

*.PLE Printing template

*.PLT Printing template

*.Q1 QUANT 1 method

*.Q2 QUANT 2 method

*.QCM Quick Compare method

*.QT Quality test

*.RED OPUS help file

*.S01 Spectrum library, also S02, S03...

*.SNT NeuroDeveloper file

*.SPC GALACTIC spectrum library

*.TRS TRS experiment

*.TXD Information mask

*.VAL Validation report

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 Command Line Parameters Chapt. 2

Extension Definition

*.XPM Experiment file

*.XY List of XY measuring positions

2.17 Command Line Parameters

The following table contains command line parameters which can

be used with OPUS.

Parameter Description Parameter Example of entry

value

/CHECKWINAD- Only Windows ON /CHECKWINADMIN=ON

MIN administrators are
OPUS administra-
tors as well (for
compatibility rea-
sons)

/COMMAND- Any command pos- any OPUS com- /COMMANDLINE=MeasureRef-

LINE sible that can be mand erence (0, {});
executed in an
OPUS VBScript via
ExecuteCommand-
Line(); See OPUS
PROGRAMMING
manual for details

/DIAGTIMER (For AQP instru- Minutes /DIAGTIMER=5

ments only) Time
interval to update
the instrument sta-
tus lamp in OPUS

/DIRECTLOGIN- Allows to get rid of UserID@pass- /DIRECTLOGINPASS-

PASSWORD the OPUS login dia- word WORD=XYZ@geheim
log.

/DSN Source for ODBC- Name of OBDC /DSN=odbc

database connec- database
tions (refers to:
OPUS DATABASE)

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 Chapt. 2 OPUS Basics

Parameter Description Parameter Example of entry

value

/DSN_PWD Password for Password /DSN=password

ODBC database
connection (refers
to: OPUS DATA-
BASE)

/DSN_UID User ID for ODBC User ID /DSN=JOHNSON

database connec-
tion (refers to:
OPUS/DATABASE)

/HIDEEXTSYNC Start of measure- ON /HIDEEXTSYNC=ON

ment is not trig-
gered by OPUS
dialog, but by the
hardware.

/LANGUAGE Defines the lan- ENGLISH, /LANGUAGE=GERMAN

guage in which GERMAN,
OPUS is displayed FRENCH,
KOREAN,
SPANISH, POL-
ISH, CHINESE,
RUSSIAN, JAP-
ANESE, HUN-
GARIAN

/LOADFILE Loads a spectrum OPUS file /LOADFILE=d:\data\spectrum.0

immediately after
OPUS start

/NO_VIEW- New OPUS views ON /NO_VIEWMAXIMIZE =ON

MAXIMIZE are not automati-
cally displayed in
full size, which
allows to have mul-
tiple views shown in
OPUS

/OPUSPIPE Allows other hard- ON /OPUSPIPE=ON

ware (e.g. TGA
instruments from
NETZSCH) to com-
municate with
OPUS

56 OPUS Reference Manual Bruker Optik GmbH

 Command Line Parameters Chapt. 2

Parameter Description Parameter Example of entry

value

/QUIT Closes OPUS after ON /QUIT=ON

the last thread
ended. Makes
sense together with
/COMMANDLINE
and /SHOHWIN-
DOW. OPUS can
be used as a batch
process which exe-
cutes a tasks and
ends without show-
ing a screen.

/RDMERRORS To be compatible ON /RDMERRORS=ON

with older OPUS
versions, regarding
some error mes-
sages with OPUS
search libraries

/SCRIPT Run an OPUS Name of /SCRIPT=d:\Scripts\run.obs

VBSript after OPUS VBScript
start

/SERVER Name of server to Name of server /SERVER=WS330

be used if we are
client (refers to:
OPUS/SERVER)

/SHOWWIN- Specifies the MINIMIZE, MIN- /SHOWWINDOW=HIDE

DOW appearance of NOACTIVE,
OPUS after start- SHOWMINI-
ing. E.g., if you MIZED, SHOW-
want to start OPUS MAXIMIZED,
as a batch process HIDE, NOACTI-
and you do not VATE
want to have the
OPUS user inter-
face displayed.

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 Chapt. 2 OPUS Basics

Parameter Description Parameter Example of entry

value

/SINGLE_CLICK Single click on a ON /SINGLE_CLICK=ON

toolbar icon exe-
cutes the OPUS
command immedi-
ately, double click
shows the dialog (in
contrast to default
behavior)

/SPOTLIGHT Some graphic cards ON /SPOTLIGHT=ON

need this parameter
to display the 3D
files correctly.

/WIZARD- Shows the specified Name of /WIZARDSCRIPT=d:\Scripts\opus.obs

SCRIPT script in the ALPHA VBScript
wizard, instead of
the default ALPHA
wizard.

/WIZMLFILE Starts another Name of xml file /WIZXMLFILE=d:\data\applica-

ALPHA wizard user tion.xml
interface, instead of
the default GOS-
Wizard.xml.

/WSPATH Looks for work- Path name /WSPATH=p:\server\temp

spaces in the
defined path, not in
the OPUS directory

UDBPATH Uses the specified Path /UDBPATH=d:\differentLoca-

path instead of: tion\Userdatabase
OPUS\UserData-
Base for the user-
database.dat file

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 Command Line Parameters Chapt. 2

H o w t o s e t u p c o m m a n d l i n e pa r a m e t e r s ?

1 Click the Windows Start button and right click the OPUS
icon.
2 A menu appears. Select Properties. The following dialog
opens:

Figure 39: Command line parameter

Depending on your Windows version this dialog may look

slightly different.
3 Add the command line parameter into the Target entry field
on the Shortcut tab. Make sure that you always type the
parameters in capital letters, and that there is always a
blank between the single parameters.
4 To confirm the setting click OK.

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 Chapt. 2 OPUS Basics

2.18 Changing OPUS Language

OPUS is available in the following languages:

• Chinese
• English
• French
• German
• Japanese
• Korean
• Polish
• Russian
• Spanish

The language originally installed can be changed as follows:

1 Click the Windows Start button and right click the OPUS
icon.
2 A menu appears. Select Properties. The following dialog
opens:

Figure 40: Language parameter

Depending on your Windows version this dialog may look

slightly different.
3 Add the correct language parameter into the Target entry
field on the Shortcut tab. Make sure that you always type
the parameter in English and in capital letters. If the

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 Changing OPUS Language Chapt. 2

parameter is not recognized, OPUS will use the default lan-

guage, i.e. English.
4 To confirm the setting click OK.

Note: The language setting will be transferred to OPUS as

parameter when starting the program next time.

Parameters for OPUS languages:

Language Parameter

Chinese /LANGUAGE=CHINESE

English /LANGUAGE=ENGLISH

French /LANGUAGE=FRENCH

German /LANGUAGE=GERMAN

Japanese /LANGUAGE=JAPANESE

Korean /LANGUAGE=KOREAN

Polish /LANGUAGE=POLISH

Russian /LANGUAGE=RUSSIAN

Spanish /LANGUAGE=SPANISH

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 Chapt. 2 OPUS Basics

2.19 Abort OPUS

If OPUS hangs for quite some time and cannot be closed by the
icon, you can abort the program by using the Windows Task Man-
ager. Data not stored before aborting the program will be lost.
This also applies to the workspace settings made during the pro-
gram run (e.g. toolbar configuration, directory name etc.)

1 To open the Task Manager simultaneously press the Alt, Ctrl

and Del keys on the PC keyboard. The Windows Task
Manager will be displayed.
2 On the Applications tab, select OPUS.
3 Click End Task. OPUS will terminate without saving any
data.

2.20 Run OPUS from CD

It is possible to copy OPUS directories (even write-protected ones)

on CD and run OPUS from CD without installing OPUS on your
system.

Note that in this case possible changes made, e.g. in the work-
space, are only stored temporarily. They will not be available when
restarting OPUS from CD.

62 OPUS Reference Manual Bruker Optik GmbH

3 File
The File menu includes features required for your data file man-
agement.

Figure 41: File menu

Bruker Optik GmbH OPUS Reference Manual 63

 Chapt. 3 File

3.1 Load File

This command is used to load a spectrum file into the spectrum

window. If you select this command from the menu, the following
dialog opens:

A B C D E F G

Figure 42: Load Spectrum

A Title bar: shows the directory in which the file is stored.

B Includes directory paths to search for spectra files.
C To return to the last selection.
D To return to the parent directory.
E To create a new directory.
F Various options to display the file list.
G Preview window: displays a small spectral range without
indicating the axes. Data blocks are displayed on top of the
preview window. They include additional information on the
spectrum file.

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 Unload File Chapt. 3

H File list of the path selected.

I The name of the file you want to load can be manually typed
into this entry field.
J It is also possible to load spectra of different formats, e.g.
JCAMP-DX or GRAMS.SPC files. These files will be con-
verted into the OPUS file format.
K Parameters are additional information appended to the OPUS
file. Sometimes not all parameters to be selected by each
drop-down list will be defined for each spectrum file. This
means that some parameter fields may remain empty.

To open the online help click the F1 key.

3.2 U n load File

Definition The Unload File command removes files from the

OPUS browser and spectrum window. Note: When
unloading files they will not be automatically
deleted from hard disk.

Principle • Load the spectrum file and select the Unload File
command.
• If required, drag & drop the spectrum file into the
File(s) to unload selection field.
• Click Unload.

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 Chapt. 3 File

3.3 Unload All Files

Definition The Unload All Files command removes all files from
the OPUS browser and spectrum window.

Principle • If you have loaded several spectrum files and you

want to remove them all at once, select the Unload
All Files command.
• If required, drag & drop the spectrum file into the
File(s) to unload selection field.
• Click Unload.

3.4 Sa ve File /S ave File As

Definition The two commands are used to save spectrum files.

Principle • The Save File command saves the spectrum file

and changes made into the appropriate directory.
• If you use the Save File As command you can
change the directory path of the spectrum file to be
saved, or export OPUS data.

If you select the Save File command, the following dialog opens:

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 Save File /Save File As Chapt. 3

Figure 43: Save File

A The name of the spectrum file lately used is shown in the

File(s) to save selection field.
B Click Save to save the spectrum file.

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 Chapt. 3 File

If you select the Save File As command, the following dialog

opens:

C
D

Figure 44: Save File As - Select File

A The name of the spectrum file lately used is shown in the File
to save selection field.
B In this entry field you enter the appropriate file name.
C You change the path shown either manually or by using the
Change Path button.
D If you activate the Overwrite check box, existing files with the
same file names will be replaced by new files. Note: This
option cannot be used when working in GLP1 mode.
E To save the spectrum file click Save.

1.GLP = Good Laboratory Practice; regulations for laboratories and producers on

how to plan, perform and control tests and measurements.

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 Save File /Save File As Chapt. 3

The Mode tab allows to set up the output format for the spectrum
data to be saved.

Figure 45: Save File As - Mode

A Apart from the OPUS and Data Point Table format there are
also other formats available, e.g. GRAMS1 (Galactic), InStep2
(Pirouette) or JCAMP.DX as an additional ASCII format. The
spectrum can also be saved in the XML format.
B Additional saving options are available, provided you have
checked the OPUS format option button first. If you check the
Save all option button, all data blocks will be saved. You can
also move the original spectrum file, or remove all copies of
the spectrum file.
C Click Save to save the spectrum file.

1. GRAMS is a registered trademark of Galactic Industries Corporation

2. InStep is a registered trademark of Infometrix Inc.

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 Chapt. 3 File

The Data Point Table tab allows to define the structure of the out-
put file.

Figure 46: Save File As - Data Point Table

A You enter the number format for x and y values, the number
of decimals as well as the separator format into these entry
fields. If you activate the Separator is TAB check box, the col-
umns will be separated by tabs.
B You can limit the output file size to 64KB by checking the
Max. 64KB option button.
C This group field is enabled if you have activated the XML
option button on the Mode tab. Two types of data format are
available for converting the binary area of a spectrum:
The Base 64 data format converts the binary spectrum area
into coded text. Advantage: as the data are more compressed
than in case of the X/Y Table format, less storage capacity is
required.
The X/Y Table data format converts the binary spectrum area
into a data table. This format is more readable than the
Base 64 format.
D To save the spectrum file click Save.
70 OPUS Reference Manual Bruker Optik GmbH
 Undo Changes Chapt. 3

3.5 Undo Changes

Definition This command undoes all changes made in a spec-

trum file since it has been saved for the last time. The
original data will be restored, but the History report
which includes all the previous manipulations will not
be reset.

Principle • Load the spectrum file and select the Undo

Changes command.
• If required, drag & drop the spectrum file into the
File(s) to undo changes selection field.
• Click Undo.

Figure 47: Undo changes

A The red document symbol indicates that the spectrum file has
been edited.
B As soon as you click Undo, the color of the document symbol
changes from red to bright blue in the browser.

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 Chapt. 3 File

3.6 Send File

Definition OPUS spectrum files can also be sent by e-mail.

Principle • Load the spectrum file and select the Send File
command.
• If required, drag & drop the spectrum file into the
File(s) to send selection field.
• Click Send.

Figure 48: Send File

A Name of spectrum file

B Sending options available to send the whole file or particular
data blocks only.
C Clicking the Send button transfers the data to the Windows
mail program. You can specify an address and write a com-
ment.

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 Send File to GRAMS Chapt. 3

Note: If you use the mail program for the first time, you will
be prompted to configure it. The data will be sent as
attachment. If the addressee uses an appropriate mail
program, it is possible to drag and drop the attach-
ment from this program directly to the OPUS spec-
trum window.

3.7 Send File to GRAMS

Definition You can export a spectrum to GRAMS, which has

been loaded or measured by OPUS.

Principle • Load the spectrum file and select the Send File to
GRAMS command.
• If required, drag & drop the spectrum file into the
File(s) to send selection field.
• Click SendToGrams.

Figure 49: Send File

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 Chapt. 3 File

A Name of spectrum file

B To start an existing macro, enter the name of this macro into
the entry field or select the macro using the Browse button.
C As soon as you click Send, the data will be transferred to
GRAMS via DDE (Dynamic Data Exchange) Note: Make
sure that the GRAMS program has been started on the
same computer.

3.8 Send File to InStep

Analog to Send File to GRAMS (chapter 3.7) you can also send a
file to the InStep program.

3.9 Delete Data Blocks

Definition A spectrum file can consist of several data blocks,

which you can delete separately.

Note: If you work in GLP mode, data blocks will

not be deleted (see also chapter 14.10).

Principle • Load the spectrum file and select the Delete Data
Blocks command.
• If required, drag & drop the spectrum file into the
File(s) to delete data blocks selection field.
• Click Delete.

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 Delete Data Blocks Chapt. 3

Figure 50: Delete Data Blocks

A Selected data block which has to be deleted. If you want to

delete several data blocks belonging to one particular spec-
trum file, drag & drop the data block from the browser to the
selection field. Note: Peak tables, integration results and
other data blocks belonging to this file will also be
deleted.
B If you click Delete, the data blocks deleted will not be dis-
played in the browser any more.

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 Chapt. 3 File

3.10 External Program

Definition External programs, e.g. data evaluation programs,

can also be started from OPUS.

External programs are always employed if you

encounter tasks which cannot be handled by OPUS,
or if dedicated programs for special problem solutions
do already exist.

Therefore, external programs used in OPUS are sub-

divided into:

• Programs designed by the user to perform specific

calculations or evaluations, and which are able to
exchange data and communicate with OPUS.
• Any other external program which can be started
from and controlled by OPUS.

Principle • Click the External Program command.

• Start the program by clicking Execute.

Basic Features

You can only start external programs which run on Windows as the
appropriate system functions will directly be activated when start-
ing the program. You can also use batch files which can be identi-
fied by the following extensions:
•*.exe
•*.com
•*.bat

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 External Program Chapt. 3

Selecting Program

Figure 51: External Program - Select File(s)/Program

A Defines the type of data communication between OPUS and

the external program:
• Dynamic Data Exchange (DDE): this interface allows to
control external programs by sending DDE commands to
the external program. If you use the DDE interface, OPUS
acts as target (client) and the external program as source
(server). This communication type has to be selected, even
if no data exchange is planned.
• Pipe: the communication via a pipe is restricted to programs
which have particularly been designed to serve as a client to
OPUS. This interface ensures fast data transfer between
OPUS and the external program. In this particular case
OPUS can be controlled by commands.
• Start Program: if this check box has not been activated, the
program start can be suppressed. This makes sense if the
functionality to call DDE commands should be repeatedly
used by the same server, without starting a new instance of
the server already running.

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 Chapt. 3 File

B This group field defines the name and parameters of the

external program.
• Name: enter the name (including the path) of the program to
be started. The drop-down list contains the names of the
programs started during earlier sessions. Note: After
installing OPUS the list will generally be empty. The
entries will be added to the list any time you start a new
program. Alternatively, use the Browse button to open a
Load File dialog.
• Parameter: additional parameters to be used with the exter-
nal programs can be specified in this entry field. A lot of pro-
grams accept parameters such as the name of a file which
should be processed. These parameters will be forwarded
to the external program as command line arguments. The
entries can be accessed by the external program using the
READ_FROM_ENTRY command.
C Drag & drop the data blocks to be processed by the external
program into this entry field.
D To execute the program click this button.

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 External Program Chapt. 3

Defining Program Settings

Additional parameters to control the external program can be set

on the Program Settings tab.

Figure 52: External Program - Program Settings

A Usually, each program runs in its own window. The size and
type of this window can be defined, according to the following
options:
• Normal: the program runs in a window of standard size.
• Maximized: the program runs in a window of maximum size.
• Minimized: the program runs in a minimized window, i.e. the
window is reduced in size and can be enlarged by selecting
the respective icon on the task bar.
• Hidden: the program starts without any visible window and
must be made visible, if desired, by using special com-
mands.
• Run as private VDM (for 16 bit applications only): if you acti-
vate this check box, you allocate a separate VDM Virtual
DOS Machine) to the external program. This may cause
increased administrative costs for the systems, but will also

Bruker Optik GmbH OPUS Reference Manual 79

 Chapt. 3 File

enhance overall stability due to the independence of the pro-

grams.
B If you activate this check box, OPUS will completely terminate
all connections to the external program after the program
starts. Both OPUS and the external program will run in paral-
lel (but asynchronously).
C If you activate this check box, OPUS will wait before execut-
ing further processing steps until the external program has
been terminated. This is especially useful for macros and
scripts, as they can wait for the end of a calculation, and also
have the possibility to evaluate any result or return value.

DDE Command

On this tab you can make settings which are called via the DDE
interface. This can apply to a server program which has to be
started or which has already been started.

Figure 53: External Program - DDE Command

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 External Program Chapt. 3

A The Execute DDE transaction check box determines whether

the DDE server has to execute a command sequence. If you
have activated this check box, you have to select which type
of DDE transaction should be performed:
• Poke: this option sends binary data to the server via the
XTYP_POKE transaction.
• Execute: a server command will be executed via the
XTYP_EXECUTE transaction. In this case the external pro-
gram does not return any data.
• Request: a server command will be executed via the
XTYP_REQUEST transaction. The external program
returns the result.
B Define the server name which has been used by the DDE
server to register with the system.
C Topic in DDE nomenclature defines the category which the
command belongs to. The topic depends on the external pro-
gram and the command to be executed. For details on the
values to be entered refer to the documentation of the exter-
nal program used.
D Item in DDE nomenclature specifies the command which will
be executed. The value depends on the program and com-
mand executed. For details on the values to be entered refer
to the documentation of the external program used.
E This entry field is only relevant, if Poke has been selected as
DDE transaction type.
Enter the binary data which will be forwarded to the server. All
data will be coded in string format, for example 65 0x0A
0x0D.
If the data are a character string, they are to be enclosed in
inverted commas, e.g. “hallo”. In this case, the respective
ASCII codes, including a terminating 0 will be entered as well.
A special prefix (i = int, l = long, d = double, f = float) is used to
classify the following data to be of the given numerical type. Z
in combination with a figure n is used to add n zeros.

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 Chapt. 3 File

3.11 Visu alBasic Script

Definition VisualBasic Scripts can be started from OPUS.

OPUS provides an interface to the Microsoft Scripting
Engine, which is able to process sequences and cal-
culations described by different scripting languages.

Principle • Load the spectrum file with the appropriate data

blocks for the script.
• Click the VisualBasic Script command.
• If required, drag & drop the spectrum file into the
File(s) for VisualBasic script selection field.
• Start the script by clicking Execute.

A
C
B

Figure 54: VisualBasic Script

A Enter the name (including the path) of the script to be exe-

cuted into the Script entry field. The drop-down list contains
the names of scripts which have previously been started.
Thus, frequently-used scripts with special parameters can
easily be started. If you click the Browse button and select a

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 VisualBasic Script Chapt. 3

script from the dialog that opens, the script name will be dis-
played in the Script entry field, but not started until you click
Execute.
Note: Directly after the OPUS installation the drop-down
list will be empty. Entries will be added to the list at the
beginning of a new program selection.
B If you activate this check box, OPUS waits for the script to ter-
minate after starting the script. This is useful if you activate
this function from within macros and scripts and you have to
wait for the end of the script loaded, or have to retrieve return
parameters.
C If you activate this check box, the script will run in the back-
ground instead of being displayed when starting the script.
D Additional parameters to be used in combination with the
script can be specified in this entry field. They will be
exchanged in string format.
E Drag & drop the spectrum data blocks from the browser to the
entry field. Make sure that the data blocks can be processed
by the script.

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 Chapt. 3 File

3 .12 L o ad Data Po in t Tab le

Definition The Load Data Point Table command enables to read

in ASCII data tables. In addition to the standard load
data commands, it is possible to

• identify the table columns,

• specify the data block type and
• limit the number of data points.

Make sure that you know the type of data point table
(type of spectra, configuration of x and y values). You
can select the data range directly from the table by
either numeric entry or interactive mode. The preview
window displays the data as spectrum.

Principle • Click the Load Data Point Table command and click
the respective file in the dialog that opens.
• Click Open after you have optionally made the set-
tings described in Definition.

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 Scan OPUS Files Chapt. 3

3.13 Scan OPUS Files

Definition This command allows to scan saved spectra selec-

tively for character strings and text.

Principle • Before you can use this search command, you have
to create a database.
• To do so click the Scan OPUS Files command. The
following dialog opens.

Figure 55: Scan OPUS Files - Path to Scan

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 Chapt. 3 File

To c r e a t e a d a ta b a s e . . .

1 ...select the drive on which the spectrum files are saved.

Activate the respective check box on the Path to Scan tab.
Note: Generally, you should select all drives which
contain spectrum files.
2 Click the Parameter Evaluation tab to limit the information
stored in the database by selecting the parameters you want
to add or remove. Note: The smaller the number of
parameters, the smaller the database.

Figure 56: Scan OPUS Files - Parameter Evaluation

3 Click the Scan Files button after the settings have been
made. Note: Depending on the number of spectrum files
being stored, the scanning can take a while. During scan-
ning, the status bar indicates this background task by Scan
OPUS Files.

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 Find OPUS Files Chapt. 3

3.14 Find OPUS Files

Definition This command allows to selectively find particular

spectrum files.

Principle • Click the Find OPUS Files command.

• Make the settings required.

Figure 57: Find OPUS Files - Parameter Evaluation

A If you want to find text in files, activate the check box. Enter
the text to be searched for into the entry field. You can specify
whether to find Exact wording only, any word, or All words
you have entered.
B You can even further narrow down the search by activating
the Find in period check box. Specify the date and select
between after, before or between this date to narrow down
your search.

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 Chapt. 3 File

C As soon as a database has been generated you can search

for file names, text strings in files or file parameters. In case
you added spectra to your hard drive after the database has
already been generated, it is recommended to update the
database. Click the Update Database now button prior to a
search run. The date and time of the last update is displayed
to the left of this button.
D You start the query by clicking the Find in Database button.
E All spectrum files found are displayed in the Select file(s) to
load selection box. If you point the cursor on a spectrum, the
selected parameters and information from the info block are
listed on the right side of the dialog.
F This button is used to load the files selected in (E). If you have
selected too many files, you will be informed that the list has
been shortened.

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 Clone Entry /Clone Original Chapt. 3

3.15 Clone Entry / Clo ne

Original

Definition The Clone Entry and Clone Original commands are

used to duplicate spectrum files. The Clone Entry
command makes a copy of a data file that has been
manipulated (e.g. by baseline correction). The Clone
Original command creates a copy of the original data
file (manipulations made will not be stored).

Principle • In either case load the spectrum file and select the
respective command.
• If required, drag & drop the spectrum file into the
File(s) to clone selection field.
• Click Clone.

Figure 58: Clone Entry - Select Files

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 Chapt. 3 File

Note: When storing the changes made in a cloned file you

have to use the Save File As command if you do not
want the original file to be overwritten by these
changes, and use a different file name for the cloned
file.

3.16 Add Comment

Definition This command allows to add a comment to the audit

trail of a spectrum file.

Principle • Load the spectrum file and select the Add Comment
command.
• If required, drag & drop the spectrum file into the
File(s) to comment selection field.
• Enter the respective comment into the Comment
text entry field.
• Click Add.

Figure 59: Add Comment - Select Files

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 RS 232 Communication Chapt. 3

The comment is stored...

...in the data block of the spectrum file. This data block is
added to the spectrum file in the OPUS browser.

To h a v e t h e c o m m e n t d i s p l a y e d

Right click on the data block and select the Show Report
option. The report view of the data block is displayed, including the
comment(s) added.

Figure 60: Comments added and displayed in the history data block

3.17 RS 232 Communication

Definition This command allows to communicate with external

devices via the serial port(s) of the PC (COM1,
COM2, etc.).

Note: In general, it is recommended not to use

this command interactively, but in combination
with a macro or VB-Script. The interactive mode
can be used to test the communication.

Principle If you start the command interactively, the following

dialog window will be displayed

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 Chapt. 3 File

A
G

B H

C
I
D

E
J

F
K

L M

Figure 61: RS 232 Communication - Write/Read

A This check box enables or disables the Write command.

B Indicates the status of the Write command (e.g. Writing...,
Time-out etc.)
C You enter the text line(s) which are to be written to the exter-
nal device. If you enter more than one line, each line will be
optionally terminated by the specified end-of-line character. If
you want to send single special characters to RS 232, which
cannot be used as strings as they are reserved for special
purposes e.g. ’ (single quote),{} (braces) etc., enter @(#) fol-
lowed by the three digit ASCII code of this special character.
Example: ABC@(#)039DEF will be sent as ABC'DEF
D In this group field you specify the type of line separator for the
Write command. Whenever the specified line separator is
detected the lines will be separated accordingly. Carriage
Return (CR) and Line Feed (LF) are already pre-defined.

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 RS 232 Communication Chapt. 3

If you need a different kind of line separator, check the Other

option button and enter the ASCII code of the desired line
separator into the entry field next to the option button. If no
line separator is to be used, check the None option button.
E In this group field you specify which type of terminator is to be
sent after the last character has been entered. Either select
None, if no character, or Other if a different character should
be sent. In the latter case you have to enter the ASCII code of
the terminator into the entry field next to the option button.
F If you click the Write button, the text entered in (C) will be sent
to the RS 232 interface.
G This check box enables or disables the Read command.
H The status of the Read command is indicated here (e.g.
Reading, Time-out etc.).
I The answer sent by the external device is displayed in this
entry field.
J These options are used to specify the kind of terminator for
the Read command. Whenever this terminator is detected the
Read command will stop. Carriage Return (CR) and Line
Feed (LF) are already pre-defined.
If you need a different kind of terminator, check the Other
option button and enter the ASCII code of the desired termi-
nator into the entry field next to the option button. If you check
the None option button, the Read command waits for answers
until the time-out has been reached.
K If you click the Read button, you activate the read command
only.
L By means of this button you exit the RS 232 Communication
command and store the current settings. No write or read
activity is started.
M By means of this button you cancel the RS 232 Communica-
tion command without saving the current settings.
N Clicking this button opens the online help.

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 Chapt. 3 File

The RS 232 Settings tab allows to set the different options for the
serial interface.

A
G

B H

I
C

Figure 62: RS 232 Communication - Settings

A The drop-down list includes all serial interfaces currently

available. If a serial interface is not available (e.g. if the
mouse is connected to COM1) this interface will not be
included in the drop-down list.
B The current interface settings are displayed in this area.
C Enter an appropriate time-out value in milliseconds.
D If you activate this check box, the interface will be configured
with a Mode string. For details on the Mode command, refer
to the operating system manual. If the check box is deacti-
vated, (E) and (F) will be disabled.
E Enter the Mode string to be used for configuration (without
specifying the serial port) into this entry field.

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 RS 232 Communication Chapt. 3

F If you click this button, the current settings according to the

Mode string. The settings will be shown in (B).
G This button allows to reads the current settings which have
been specified in the operating system as default.
H This button allows to activate the setup dialog of the operating
system (see figure 63).
I This button allows to overwrite the operating system settings
by the current settings made.

Clicking the Change Settings button (H in figure 62) opens the fol-
lowing dialog:

Figure 63: RS 232 Communication - COM1 Properties

This dialog allows to specify the following communication parame-

ters:
• Bits per second
• Data bits

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 Chapt. 3 File

• Parity
• Stop bits
• Flow control

The same dialog opens if you set up the parameters of the serial
interface by using the System Settings command of the operating
system.

3.18 Copy Data Block

Definition This command allows to copy single data blocks from

one OPUS file to another. This, however, is only pos-
sible when using definite block types, e.g. INFO.

Principle • Load the spectrum file and select the Copy Data
Block command.
• If required, drag & drop the data block(s) to be cop-
ied into the Block(s) to copy selection field.
• Define the file where to copy the data blocks in the
Destination file field.
• Click Copy Block.

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 Change Data Block Type Chapt. 3

Figure 64: Copy Data Block

3.19 Change Data Block Ty pe

Definition This command allows to change the data block type.

Changing the data block type is not required very
often. Macros, however, may need a definite data
block type. Note: If you select the Change Data
Block Type command, the data block type will
only be renamed. The data, however, will not be
changed.

Principle • Load the spectrum file and select the Change Data
Block command.
• If required, drag & drop the data block(s) to be
changed in to the Block(s) to change selection field.
• On the Choose block type drop-down list, select the
block type. It may be possible that not all data block
types are included in the drop-down list.
• Click Change Block Type.

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 Chapt. 3 File

Figure 65: Change Data Block Type

3.20 Compare Parameters

Definition This command allows to compare paramaters of two

spectrum files, e.g. OPUS spectrum or experiment
files.

Principle • Load the spectrum files you want to compare with

each other and select the Compare Parameters
command.
• If required, drag & drop the spectrum files into the
respective selection fields.
• Click Compare.

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 Compare Parameters Chapt. 3

Figure 66: Compare Parameters

A ft e r c o m pa r i n g . . .

...the result is displayed in a special view. This kind of view con-

tains different parameters, e.g. sample or measuring parameters.

Besides, the result view shows those parameters which are either
available in one spectrum file only, or in both files with different val-
ues (see figure 67).

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 Chapt. 3 File

Figure 67: Result view of parameter comparison

3.21 LabJournal

Definition This command allows to run a lab journal. This auto-

matically-generated lab journal records what kind of
evaluations or measurements have been performed
in OPUS, how and when. The evaluation and mea-
surement data stored are displayed in a special view.

The lab journal data are sorted by the:

• name of the spectra file

• type of evaluation or measurement
• date

Lab journals are files with the *.lbj extension, which

are stored in the OPUS directory. The lab journal file
name contains the name of the user who created the
lab journal, and who is assigned to the journal.

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 LabJournal Chapt. 3

To c r e a t e a l a b j o u r n a l . . .

1 ...click the User Settings command from the Setup menu.

Click the Basic Settings tab.
2 Activate the Run a lab journal check box (A in figure 68), oth-
erwise it will not be possible to create a lab journal.

Figure 68: User Settings - Run a lab journal

3 On the File menu, click LabJournal. If no lab journal can be

assigned to you, you will be asked whether a new journal
has to be created. Confirm the dialog that pops up by click-
ing Yes. OPUS creates a lab journal with your user name.

Note: If you have Administrator or Labmanager user rights,

the Open dialog will first be displayed. Select the
respective lab journal from this dialog.

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 Chapt. 3 File

D e p e n d i n g o n t h e u s e r r i g h ts . . .

...defined (see chapter 2.5) you either have limited or full access to
the lab journals in OPUS.
• Operator: you can only access the lab journal assigned
to your account.
• Administrator or Labmanager: you can access the lab
journals of other users as well.

3.21.1 Lab journal view

A B

Figure 69: LabJournal View

A This window shows a list of spectra file names as well as the

date of different evaluations or measurements performed.
These evaluations or measurements performed are indicated
in the Block column as follows:
• INTEG: Integration
• PEAK: Peak Picking
• QCMP: Quick Compare
• QUANT: Quantitative analysis
• MEAS: Measurement

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 LabJournal Chapt. 3

Note: The lab journal does not contain all evaluation

commands available in OPUS but only the ones men-
tioned above.
B You can have the evaluation or measurement results dis-
played on the right side by clicking the spectra file name.

Double clicking a spectrum file name opens the spectrum window

and displays the spectrum selected, together with the evaluation or
measurement results.

Figure 70: Spectrum window view

Lab journal entries

One single lab journal contains up to 1000 entries. If the number of

entries exceeds the limit of 1000, the lab journal will be renamed
and copied into a sub-folder for archiving purposes.

When renaming, the date of the first and last entry are added to the
previous file name. Thus, the new file name indicates the time
period of the different entries. The following format applies to the
new file name:

YYYYMMDD: YYYY = year, MM = month, DD = day

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 Chapt. 3 File

Example: LabJournal_Default_2006-03-15_2006-04-10

If the previous journal has been archived, OPUS creates a new

journal using the LabJournal_Default.lbj name.

The lab journal can also be printed with each lab journal entry
being on a separate page. On the File menu, click Print.

When sorting lab journal entries...

...in ascending or descending order click the particular column

title.You can sort the lab journal entries displayed on the left
according to
• spectra file name
• block
• date

Clicking again the particular column title restores the original sort-
ing order.

When sorting by date...

...you have the possibility to limit the entries to a certain period of

time.

1 Double click the Date column to open the following dialog:

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 LabJournal Chapt. 3

Figure 71: LabJournal - Select Time Span

2 Activate the Restrict time span check box.

3 Determine the period of time using the drop-down lists.

Confirm the settings made by clicking OK. The list will be sorted
again, considering only those evaluations or measurements
selected within the defined period of time.

To undo this setting double click again the Date column. Deactivate
the Restrict time span check box and click OK.

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 Chapt. 3 File

3.22 New/Open

Definition The New command allows to select different OPUS

views, e.g.:

• OPUS
• PLE
• VBScript
• GMacro

The Open command allows access to the OPUS

workspaces available.

Principle • Click the New command to open the respective

OPUS view.
• Click the Open command and select the respective
workspace from the dialog shown.

3.23 Print

Definition The Print command allows to print reports.

Principle The report data are either printed on the printer or

into a different file.

3.24 Print Preview

Definition The Print Preview command allows to view several

pages of a report in reduced size. Note: This com-
mand is only available if a report window is dis-
played.

Principle If you have selected this command, you can individu-

ally edit the report before printing it.

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 Print Setup Chapt. 3

3.25 Print Setup

Definition The Print Setup command allows to define printer

settings.

Principle You can define the paper size and print-out format.
These settings will be standard for all OPUS print-
outs.

3.26 Exit

If you click the Exit command, the OPUS program will close.

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 Chapt. 3 File

108 OPUS Reference Manual Bruker Optik GmbH

4 Edit
The Edit menu includes features for information input, options to
edit structures as well as the standard Windows commands Copy
and Paste.

Figure 72: Edit menu

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 Chapt. 4 Edit

4.1 E d i t P arameter

Definition The Edit Parameter command allows to edit the most

important sample parameters, e.g. sample name,
sample form, operator name and sample number.
Note: When working in GLP modea you will not be
able to change these parameters.

Principle • Load the spectrum file and select the Edit Parame-
ter command.
• If required, drag & drop the spectrum file into the
Select file selection field.
• Make the changes required.
• Click Change.
a. GLP = Good Laboratory Practice; regulations for laboratories and
producers on how to plan, perform and control tests and measure-
ments.

Figure 73: Edit Parameter - Parameter

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 Edit Parameter Chapt. 4

The Axes Labels tab allows to edit the axes labeling of the spectra,
and set a scaling factor for the axes. The settings made are consid-
ered when printing the spectrum file.

Figure 74: Edit Parameter - Axes Labels

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 Chapt. 4 Edit

4.2 Replay

Definition When working in GLP modea a copy of the original

spectrum is saved together with the corresponding
data.

On the basis of this original spectrum, you can repeat

some of the manipulations performed.

Principle • Load the spectrum file and select the Replay com-
mand.
• If required, drag & drop the spectrum file into the
File to replay selection field.
• Select the appropriate editing command.
• Click Replay.
a. GLP = Good Laboratory Practice; regulations for laboratories and
producers on how to plan, perform and control tests and measure-
ments.

Figure 75: Edit Parameter - Axes Labels

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 Attach Video Image Chapt. 4

If you select e.g. the Delete DataBlock command, as exemplified in

figure 75, the Restore and Calculate commands will be performed
on the original spectrum, but not the Baseline command.

4.3 Attac h Vid eo I m a g e

Definition The Attach Video Image command allows to attach a

video image to a spectrum file (2D or 3D). The video
image requires the jpg or bmp data format.

Principle • Load the spectrum file and select the Attach Video
Image command.
• If required, drag & drop the spectrum file into the
Select OPUS spectrum selection field.
• Click the Browse button to select the respective
video image. The image is displayed as preview.
• Optionally, make further settings on the Options tab.
• Click Attach Video Image.

Figure 76: Attach Video Image to OPUS File

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 Chapt. 4 Edit

4.3.1 Further setting options

The Options tab allows further image settings to be made.

Figure 77: Attach Video Image - Options

A Define whether the scaling refers to a single pixel of the video

image, or to the complete video image. Define the size of the
pixel or image in x and y direction1.
B If you activate the checkbox, the measurement position is
marked by a red cross in the video image preview.

After the video image has been attached, the measurement

position is stored in the datablock as annotation. This

1. If you attach the video image to a 3D-MAP file, you can define the position of the
video image in relation to the chemical image. In this case, the x and y position
coordinates defined refer to the lower left end of the chemical image.
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 Attach Video Image Chapt. 4

data block is attached to the spectrum file in the explorer. To

show the data block parameters right click the data block and
select the Show Report option.
C If you activate the checkbox, the detector area is marked by a
red circle in the video image preview. Define the circle diame-
ter manually.

After the video image has been attached, the detector area is
stored in the datablock as annotation. This data block is
attached to the spectrum file in the explorer. To show the data
block parameters right click the data block and select the
Show Report option.

Loading Configuration

To load a previously created video image configuration proceed as

follows:

1 Click the Load Configuration button.

2 Select the respective configuration from the dialog that
opens.
3 Click the Load button.

Saving Configuration

The parameter settings of the current video image can be saved as

configuration to be able to reuse it later.

1 Click the Save Configuration button. A dialog opens.

2 Right click and then left click the New option.

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 Chapt. 4 Edit

Figure 78: Attach Video Image - Save Con-

figuration

3 Specify a name for the configuration.

4 Click the Save button.

4.3.2 Sp e c t r u m f i l e i n t h e b r o w s e r

After clicking Attach Video Image the image is attached to the

spectrum file in the form of a graph data block ( ). This data
block is displayed in the browser, and contains the specific image
data and the bitmap.

Additionally, if you have set the measurement position and the

detector area, an annotation data block ( ) is attached to the
spectrum file (see chapter 4.3.1).

4.3.3 R e p o r t v i e w o f g r a p h d a ta b l o c k

If you right click the graph data block ( ) attached to the spec-
trum file and displayed in the browser, the Show Report option
pops up. Select this option to open the report view.

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 Add Information Chapt. 4

Figure 79: Report view of graph data block

4.4 Add Information

Definition The Add Information command allows to save addi-

tional information apart from OPUS parameters. This
kind of information will be saved in a separate infor-
mation data block ( ), and can be integrated both
into a report window and in a plot.

If you want to save spectra in your own search librar-

ies, information input is mandatory. The so-called
information mask (see chapter 4.5) includes the
descriptions of up to 99 lines which can be saved in
one information data block. You can define this info
mask according to your individual needs.

First-time information input

1 Load a spectrum file and select the Add Information

command.
2 The respective dialog opens which contains the name of the
spectrum file in the selection field on the upper left side.
3 Enter the parameters and click Add.

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 Chapt. 4 Edit

A F

G
B

Figure 80: Add Information

A This field contains the spectrum file selected.

B Instead of attaching an information data block to an existing
OPUS file you can also create a new file, which only consists
of one information data block. In this case activate the New
File check box. A new file will be created with INFOx.0 as file
name. In this case x is either a single or multi-digit number.
C The name of the current information mask used is displayed
in the Text definition field. This file has the extension *.TXD.
D Enter the requested information. You do not need to fill in all
the lines.
E Clicking Add creates or modifies the information data block
for the file selected. Note: This new data block is attached
to your spectrum file and displayed in the OPUS browser
window. If you right click this data block, a menu pops up. On
this menu, select the Show Report command. The report win-
dow only contains data which have been filled into the lines of
the Add Information dialog.

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 Add Information Chapt. 4

Figure 81: Report window with text information

F To use a different information mask, click this button. The

Load Info Text Mask dialog pops up which you can select a
different information mask from.
G If you have deleted or overwritten entry fields by accident,
click the Restore Original button to read the original data
again.

E d i t i n g i n f o r m a t i o n d a ta b l o c k

If you load a spectrum file which already contains an information

data block, the information added to this data block will be dis-
played in the Add Information dialog together with the appropriate
information mask (see figure 80).

It may occur that the appropriate information mask cannot be found

on your data structure. Maybe the mask is based on a different
data structure or you have copied the information mask into a dif-
ferent directory, or even deleted it. In this case the information
mask reference will be highlighted in red in the Text definition field
(B in figure 80).

Edit the existing data or add new data. Alternatively, you can select
a different kind of information mask. In this case all inputs made so
far will be deleted in the dialog.

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 Chapt. 4 Edit

D i s p l a y i n g a n d p r i n t i n g i n f o r m a t i o n d a ta
block

The information data block can be displayed in a report window.

When printing the information data block each single data line of
the block can be addressed as OPUS parameter, using the param-
eter name Inn, with nn being the line number (e. g. I01 = first line,
I12 = twelfth line).

You can also include information mask texts into the plot, by using
Tnn as parameter name (e.g. T01 = text in first line, T12 = text in
twelfth line).

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 Setup Information Mask Chapt. 4

4.5 Setup Information Mask

Definition When creating an information mask you define the

kind of information available for information input.

Depending on the field of application you can create

different kinds of information masks. The contents
and file name of the information mask will be saved
during information input. This enables all data to be
displayed even on data systems which do not contain
the appropriate information mask.

Principle If you select the Setup Information Mask command, a

dialog opens which will be described in the following.

Figure 82: Setup Information Mask

A The information mask recently loaded will always be dis-

played automatically.
B To load and edit a different information mask click this button.
Bruker Optik GmbH OPUS Reference Manual 121
 Chapt. 4 Edit

C Changes on the information mask can be restored by using

this button.
D Depending on the number of lines up to 7 pages can be dis-
played.
E To save the information mask click this button. Note: If an
information mask with the same name already exists, you
will be asked whether you wish to overwrite the existing
mask.

Creating new information mask

1 Click the Clear All button (see figure 82).

2 All entries will be deleted and only the first page is available.
The entry fields will all be highlighted in red.

Figure 83: Setup Information Mask - Define new entries

3 As soon as you have started to enter data, the entry field

color will change to white. Note: When entering data, make
sure that the entry fields are filled in one after the other.
Be careful not to skip a line.
122 OPUS Reference Manual Bruker Optik GmbH
 Setup Information Mask Chapt. 4

Figure 84: Setup Information Mask - Lines with new entries

4 You have to define all entry fields on the first page before
being able to open a new page by the Next Page button.
5 Save the information mask after you have filled in all lines.

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 Chapt. 4 Edit

4.6 I mport St ructure

Definition The Import Structure command allows to load chemi-

cal structure formulae, which have been created
using different structure editors, into the OPUS
browser.

Make sure that the structure files to be imported

to OPUS have been created in Molfile format.
These files must have the extension *.MOL.

Principle • Select the Import Structure command.

• A dialog opens. Use this dialog to load the structure
file from the respective directory.

For more detailed information refer to the OPUS STRUCTURE

manual.

124 OPUS Reference Manual Bruker Optik GmbH

 Edit/Create Structure Chapt. 4

4.7 Edit/Create Structure

Definition The Edit/Create Structure command allows to edit

existing chemical structure or create completely new
ones.

Principle • Select the Edit/Create Structure command.

• A dialog opens.

Creating new structure

1 Select the Edit/Create Structure command and click the Edit

Structure tab.

Figure 85: Edit/Create Structure - Edit Structure

2 Activate the New structure file check box. The path and file
name definition are displayed by default. If required, change
these data accordingly.

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 Chapt. 4 Edit

Figure 86: Defining path and file name

3 As soon as you click the Edit/Create Structure button the

structure editor interface is displayed. Use this interface to
create a chemical structure. For more detailed information
on how to create a structure refer to the OPUS STRUC-
TURE manual.

Editing existing structure

1 Load the structure file into the browser.

2 Select the Edit/Create Structure command.
3 If required, drag & drop the structure from the browser into
the respective entry field.

Figure 87: Selected structure data block

4 Click the Edit/Create Structure button. The structure editor

interface is displayed which contains the structure of the
data block selected. For more detailed information on how to
edit a structure refer to the OPUS STRUCTURE manual.

126 OPUS Reference Manual Bruker Optik GmbH

 Edit/Create Structure Chapt. 4

Sta r t i n g s t r u c t u r e e d i t o r

1 Select the Edit/Create Structure command.

2 Click the Choose Editor tab.

Figure 88: Edit/Create Structure - Choose Editor

3 Select the Mol2d.exe file from the C:\Program

Files\Bruker\OPUS_<version> directory using the Browse
button.
4 Click the Edit/Create Structure button to open the structure
editor interface.

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 Chapt. 4 Edit

Figure 89: Interface of OPUS structure editor

The Windows-based menus include, apart from standard com-

mands (e.g. Copy and Paste), specific editing commands used to
create molecular structures. The most frequently used commands
can be found in the icon bar.

• Drawing/Editing bonds:

• Scaling bonds:

• Arranging bonds:

• Refining/Rotating bonds:

On the left side you find the abbreviations of the most important
atoms. If you click PSE, the periodic table of elements opens.

For more detailed information refer to the OPUS STRUCTURE

manual.

128 OPUS Reference Manual Bruker Optik GmbH

 Attach Structure Chapt. 4

4.8 Atta ch St ru cture

Definition The Attach Structure command allows to attach struc-

tures, created in Molfile format (MOL), to an OPUS
spectrum file. The structural formula is converted into
the OPUS format.

Principle • Load the spectrum file which you want to attach a

structure to and select the Attach Structure com-
mand.
• If required, drag & drop the spectrum file into the
Select OPUS Spectrum selection field.
• Select the appropriate structure file using the
Browse button.
• Click Attach Structure.

Figure 90: Attach Structure

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 Chapt. 4 Edit

4.9 Convert 3-D Jcamp

Definition The Convert 3-D Jcamp command allows to convert

JCAMP spectra files into the OPUS format. A JCAMP
file can consist of several spectra.

Principle • Select the Convert 3-D Jcamp command.

• A dialog opens which is described in more detail in
the following.

Basic features

Each spectrum of a JCAMP file has to have a specific format. The

following file extract exemplifies such a format:

##TITLE=Butanoic acid
...
...
##CAS REGISTRY NO=107-92-6
...
450.0 637 638 621 624 638 665 702 723 741 798
490.0 839 862 888 935 928 967 1021 1000 996 1098
530.0 1133 1222 1328 1382 1488 1531 1571 1558 1559 1570
570.0 1572 1637 1678 1756 1802 1942 1924 1905 1927 1920
...

The "..." characters represent additional information lines, all start-

ing with "##" (exceptions see below), or additional lines of data
points.

For further details on how to convert information lines into OPUS

parameters, refer to chapter 14.2.

The information line for the CAS registry number is obligatory if a

structure formula JCAMP file is allocated to the spectrum JCAMP
file, as the allocation of the spectrum to the molecular structure is
based on the CAS number. The structure of this spectrum is avail-
able in OPUS in the form of the structure data block ( ).
130 OPUS Reference Manual Bruker Optik GmbH
 Convert 3-D Jcamp Chapt. 4

Sta r t i n g c o n v e r s i o n

1 Select the Convert 3-D Jcamp command. The following

dialog opens:

Figure 91: Convert 3-D Jcamp Files - Select File(s)

2 Enter the name of the 3-D JCAMP file into the 3-D JCAMP
file entry field. Either type in the file name manually with the
complete path, or click the Browse button to select the file in
the respective directory.
3 Optionally, you can enter the file name of the molecule struc-
ture file. Observe the additional information below. Note: If
you skip the Molecule structure file entry field, the OPUS
spectra created will not include a structure data block.
4 Define the OPUS format which the JCAMP spectra have to
be converted to. Observe the additional information below.
5 Activate the X Units check box. JCAMP files with x units
being indicated in wavelengths (i.e. nm or µm) cannot be
used in OPUS without converting the x units into wavenum-
bers (cm-1).
6 Click the Convert button to start the conversion. The conver-
sion progress will be indicated by the status bar on the bot-
tom right. Note: If one of the information lines includes
the sum formula, the molecular mass will be calculated

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 Chapt. 4 Edit

from this formula, indicated in atomic units and entered

in the information data block of the respective spectrum.

Format of JCAMP structure formulae

The format of a molecular structure may be as follows:

c:75014
C2H3Cl
2:(303,155,320,165;2)(337,156,320,165;1)
1:(3,Cl)
0:

The first line includes the CAS number followed by the sum for-
mula, bonding data and the names of foreign atoms.

You can also add the melting and boiling points of the different sub-
stances to the information data block of the OPUS file. Make sure
that you add the data at the end of the JCAMP structure file, line by
line as follows:

,CAS_NO,MELTINGPOINT,BOILINGPOINT,

Example:

,1571864,75.0,263.0,

Note: Always write a comma at the beginning and at the end

of the lines.

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 Convert 3-D Jcamp Chapt. 4

OPUS format of the JCAMP spectrum file

In the Target group field (figure 91) you specify the OPUS format
which the JCAMP spectra have to be converted to. You can select
between three option buttons:
• 1-D OPUS files:
Each JCAMP spectrum is stored separately as OPUS
spectrum. The file name is a combination of the TITLE
and CAS REGISTRY NO information lines used in the
JCAMP file. If you activate the 1-D OPUS files option
button, you also have to specify the target path. Either
type in the target path name manually or click the
Browse button to select the path from the directory
structure.
• 3-D OPUS files:
The 3D JCAMP file is converted into a 3D OPUS file.
This is useful if the spectra have been acquired by chro-
matography, or if all spectra are a compound of always
the same substance which comes in different concentra-
tions. You can also define this substance concentration
in the information line for each spectrum. The format in
the JCAMP file must be as follows:
##CONCENTRATIONS= (NCU)
(<Glucose>, 2.100, %)
(<Lnvisco104>, 1.131, %)
In this case the substance name, quantity and quantity
unit will be specified in a text file (in table format) which
will be created apart from the OPUS file, and with the
same file name. This is helpful if the data are used to
perform a QUANT analysis. In this case the concentra-
tion data can be used from the text file using the clip-
board.
Either type in the target path name manually or click the
Browse button to select the path from the directory.
Specify the OPUS target file name without any exten-
sion. Note: If a 3D OPUS file already exists with this
name, it will not be overwritten, but the name will be
incremented.

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 Chapt. 4 Edit

• OPUS library
All spectra are stored in an OPUS library, including
spectra information and possible structure data blocks.
Either type in the target path name manually or click the
Browse button to select the path from the directory.
Specify the OPUS target file name without any exten-
sion. Note: If the OPUS library already exists with
this name, it will be overwritten.

4.10 Create Spectrum from

Structure

Definition The Create Spectra from Structure command calcu-

lates a theoretical IR spectrum resulting from a chem-
ical structure. In this case the structural formula is
searched for chemical groups which create charac-
teristic bands within IR spectra. The information
extracted from these bands is used to calculate a
spectrum.

Principle • Load a spectrum file which contains a structure data

block ( ) and select the Create Spectrum from
Structure command.
• If required, drag & drop the spectrum file into the
Structures used to create specra selection field.
• Click Create to start the calculation.

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 Create Spectrum from Structure Chapt. 4

Figure 92: Create Spectra from Structure - Select Structures

The result output will be depicted as an absorbance spectrum, and

stored in the absorption data block ( ). If there has already
been a ratio spectrum (AB, TR etc.) in the file selected, this spec-
trum will be overwritten.

The additional interpretation data block ( ) will be created and

attached to the file. This data block contains all pieces of band
information as text, which serve as a basis to calculate the spec-
trum. This kind of band information may comprise:
• Name of chemical group
• Consecutive numbers of atoms included in the group
• Band position and band height

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 Chapt. 4 Edit

I f t h e i n t e r p r e ta t i o n d a ta a r e n o t d i s p l a y e d
a u t o m a t i c a l l y, . . .

...right click the interpretation ( ) data block in the browser. A

small menu pops up, click Show Report. Figure 93 exemplifies a
structure interpretation.

Figure 93: Structure interpretation report

4.11 Setup Filelist

Definition The Setup Filelist command allows to combine sev-

eral spectra of a particular spectrum type into one file
list, and edited as one single spectrum. The list which
consists of different spectra is stored in the list data
block ( ) and displayed when selecting this data
block.

All OPUS commands available for manipulating and

evaluating spectra data can be used for the complete
spectra file list in the same way as being used for sin-
gle spectra files.

Principle • Select the Setup Filelist command.

• A dialog opens. Select the spectra to be used for the
file list.
• Save the file list.

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 Setup Filelist Chapt. 4

A B C D

Figure 94: Setup Filelist

A To load the respective spectra click this button. The spectra

will be displayed as follows:

B To load an already existing file list click this button.

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 Chapt. 4 Edit

C By default, the path and file name of each spectrum is dis-

played in a table. This table can be customized, i.e. enlarged
by as many columns as you like, e.g. to be able to store
parameters and input values required for evaluation func-
tions.
Enter the name of the column into the entry field below the
Add Row button. If you click this button, the new column will
be added to the table.
D To store the spectra file list click this button. Define a specific
name for the list. Spectra file lists are stored as reports in the
OPUS format. The file extension of the list may be incre-
mented, i.e. increased by 1. This is especially helpful if you
want to use the same name for different spectra file lists.

To e v a l u a t e s i n g l e s p e c t r a . . .

...you can also add specific parameter values to the table in the
form of a column. Make sure that you always enter the right param-
eter code for the specific value into the entry field. The parameter
code can be obtained from the Macro Editor, for more information
see the OPUS Programming manual.

Example:

If you want to add, e.g. the Mahalanobis distance in case of a

QUANT evaluation, or the outlier identification for each single spec-
trum from the QUANT report to the spectra file list, you first have to
create an information data block (see also chapter 4.4).

Select the Add Information command. Enter the following data into
the Compound name line (see figure 95):
• name of the OPUS function (A)
• result data block (B) as well as the
• corresponding element from the QUANT report (C), i.e.
main report number, sub-report number, line, column.

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 Setup Filelist Chapt. 4

A B C

Figure 95: Example of information input

E v a l u a t i o n r e s u l ts f o r f i l e s w i t h i n t h e
spectrum file list...

...are stored in the trace data block ( ) which is attached to the

list. The data block gives a survey about the results of all single
spectra.

When loading a spectrum file which contains a trace data block the
results are displayed within separate columns. Figure 96 exempli-
fies the results of an integration recently performed.

Figure 96: File list with integration results

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 Chapt. 4 Edit

4.12 Cut

If you cut a selected object, it will be removed from the

interface and stored in the clipboard.

4.13 Copy /Paste

If you copy a selected object, it will be stored in the clipboard.

To insert the data of the clipboard into the active file or
window click the Paste icon in the toolbar, or select the Paste
command from the menu.

4.14 Copy to Image File

Definition The command Copy To Image File allows to store the

current OPUS view as image file, with the following
formats being available:

• *.bmp (Bitmap)
• *.pdf (Portable Data Format)
• *.emf (Enhanced Metafile)

Principle If you select the command, a dialog opens in which

you define the file name and path as well as the file
format.

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5 Vi e w
The View menu allows to configure the OPUS user interface. You
can define the toolbars, hide or unhide the status bar, browser or
wizard window as well as the permanent information view.

Figure 97: View menu

5 .1 To o l b ars

Definition For each OPUS menu a toolbar is available which

can be individually customized. Generally, the tool-
bars include icons of frequently-used commands.

Principle • If you click the Toolbars command, the Customize

dialog opens.
• The options provided allow to customize toolbars
and configure single icons. For further details on this
subject refer to chapter 14.7.

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 Chapt. 5 View

5.2 Stat u s B a r

Definition The status bar informs about the background tasks of

programs running in OPUS, and displays their current
status.

Principle To activate or deactivate the status bar, check or

uncheck the Status Bar command (see figure 4 on
page 4).

5.3 B rowser

Definition The browser contains the spectrum files with the cor-
responding data blocks.

Principle To activate or deactivate the status bar, check or

uncheck the Browser command. For further informa-
tion on the browser refer to chapter 2.6.

5.4 Wizard Bar

Definition The OPUS wizard is an interactive help tool which

facilitates the measuring of samples, as well as
manipulation and evaluation of spectra.

Principle To activate or deactivate the status bar, check or

uncheck the Wizard Bar command. For further details
on the wizard refer to chapter 2.7.

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 Information View Chapt. 5

5.5 I nformation Vi ew

Definition The information view on the lower OPUS interface

shows the data parameters, manipulation and evalua-
tion results of a particular spectrum file.

When loading a spectrum file either the contents of

the existing report or the spectrum parameters are
shown.

Principle To activate or deactivate the information view, check

or uncheck the Information View command. For fur-
ther details on the information view refer to
chapter 2.10.

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 Chapt. 5 View

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6 Win d o w
The Window menu allows to open new windows and customize
their position and appearance. If you load a file, OPUS automati-
cally opens the appropriate window to this file.

Figure 98: Window menu

6.1 N e w Spe c t r u m Win d o w

Definition The New Spectrum Window command opens a new

spectrum window.

Principle • Select the New Spectrum Window command.

• Load a spectrum file.

Note: It is possible to have several spectrum win-

dows open simultaneously.

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 Chapt. 6 Window

6.2 N ew 3D Window

Definition The New 3D Window command is used to create the

standard window type for displaying 3D spectrum
files.

Note: Displaying, editing and evaluating three-

dimensional spectrum files requires the OPUS/3D
software package.

Principle • Load a 3D spectrum file.

• The 3D window opens and displays the spectrum
file accordingly.

For any further information on this subject refer to the

OPUS/3D manual.

6.3 N e w R e p o r t Win d o w

Definition The New Report Window command opens a new

report window. A report window contains the corre-
sponding data parameters of a spectrum file as well
as evaluation results.

Principle • Select the New Report Window command.

• Drag the respective data block from the browser into
the left column of the report window (see figure 99)
while pressing the left mouse button.
• As soon as you drop the data block the parameters
will be displayed in the right column of the report
window (see figure 100).

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 New Report Window Chapt. 6

Figure 99: Dragging report data block into report window

Figure 100: Parameters displayed in report window

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 Chapt. 6 Window

6.4 N ew Registered Wi ndow

If you click the New Registered Window command, a drop-down

list opens which contains all types of OPUS windows available.
You can open any type of blank window by selecting the particular
window from this list.

Window To display...

3d, 3d+ three-dimensional spectra files

Chemical Imaging mapping files, in connection with OPUS/3D

ChromPostrun spectra files created by OPUS/CHROM

Cluster Analysis dendrograms or histograms

CorrelChart band assignment chart

Display a new spectrum window

EvalResults evaluation results

Factor3d score plot window

FPA Measurement measurements made by means of the FPA detector

GridReport grid report window

Library libraries

Live+Overview spectrum files created by OPUS/VIDEO

Macro macro editor interface

Map+Spec measuring result produced by OPUS/MAP

OldReport reports in the OPUS format

Online measuring result produced by OPUS/CHROM

Process Control standard trend chart by OPUS/PROCESS

QCompResult quick compare results

Report OPUS reports

SearchResults search results

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 New Registered Window Chapt. 6

Window To display...

SingleReport OPUS reports without tree structure

Structure molecular structures created by using a structure

editor

Substance search results in connection with the Mobile-IR

spectrometer

TextView window to manually enter text or copy text files

TRS Postrun time-resolved spectra files

6.4.1 Te x t Vi e w

To enter text select the TextView window type from the drop-down
list, which is indicated by the tab. There are
three possibilities to enter text:

1 Keyboard
Position the cursor into the window and enter text using your
keyboard.
2 Copy and Paste
It is possible to copy and paste text by using the shortcuts
CTRL+C and CTRL+V.
3 Drag & Drop a text file
Drag and drop a text file into the TextView window. You can
only drag one single file into the TextView window. If there
has already been a text file in the TextView window, this file
will be replaced and the text overwritten unless you press
the CTRL key during drag & drop. In this case the text of the
dragged file is appended to the content of the file which has
already been displayed in the window.

To s e l e c t t e x t

1 Move the cursor to the relevant text passage and press the
left mouse button.
2 You can also use the Shift and an arrow key to select a text
passage.

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 Chapt. 6 Window

To d e l e t e t e x t

1 Either use the Backspace () or Delete key.

2 You can also select the text and use the CTRL+X shortcut to
delete it. It is also possible to use the Cut command from the
Edit menu.

To s a v e t e x t

1 Right click into the TextView window.

2 Select the Save option from the pop-up menu.

6.5 C ascade

Definition The Cascade command allows to arrange the win-

dows like a cascade. The name of each single win-
dow is shown in the window title bar.

Principle • Select the Cascade command.

• The window types currently open are cascaded.

Figure 101: Cascaded windows

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 Tile Chapt. 6

6.6 Ti l e

Definition The Tile command allows to arrange the windows like

tiles. The windows are reduced and repositioned.

Principle • Select the Tile command.

• The windows types currently open are tiled.

Figure 102: Tiled windows

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 Chapt. 6 Window

6.7 A rrange Icons

Definition If you have minimized several spectrum or report win-

dows, they are displayed as small icons. You can
have these minimized icons re-arranged by drag &
drop. By default, the icons are located at the bottom
of the OPUS user interface.

Principle • Minimize the window views.

• Select the Arrange Icons command.
• Move the icons to the position desired while press-
ing the left mouse button.

Figure 103: Window views arranged as icons

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7 Measure
The Measure menu allows to start measurements, optionally using
the pre-defined parameters, as well as define, save and load mea-
surement experiments.

Apart from the spectrometer you can control additional external

spectroscopic devices by this OPUS menu, and have the data
acquisition triggered by external signals.

Note: If an Ethernet interface is used to communicate with

the spectrometer, you have to install the Microsoft
Internet Explorer 8 or higher.

Figure 104: Measure menu

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 Chapt. 7 Measure

General Measuring Procedure

The general measuring procedure can be subdivided into the fol-

lowing steps:

1 Measuring background spectrum

2 Measuring sample spectrum
3 Saving interferogram peak
4 Manipulating sample spectrum, if required
5 Saving and/or printing manipulated sample spectrum

Note: Measurements can both be started by the OPUS menu

commands as well as by the wizard. For information
on the wizard refer to chapter 2.7.

Measuring Modes

Basically, two types of measurement modes are available in

OPUS:
• Advanced Measurement
• Routine Measurement

The difference between these two modes is the number of parame-

ters predefined or to be set up. The Advanced Measurement mode
provides access to all parameters, the Routine Measurement mode
provides a pre-selection of parameters appropriate for the spec-
trometer.

Note: To be able to switch between these two measuring

modes administrator rights are required.

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 Chapt. 7

Measurement Parameters

It is recommended to perform a measurement using the parameter

settings predefined in OPUS. By default, these parameters are
stored in the so-called experiment files in the C:\Users\Public\Pub-
lic Documents\Bruker\OPUS_<version>\XPM directory, with the
*.XPM file extension.

There are OPUS experiment files available for each spectrometer

configuration for NIR, MIR and Raman. It is also possible to adapt
these measurement parameter settings (e.g. the Scan Time
parameter) to your individual requirements (see chapter 7.2).

Predefined Parameters

This kind of parameters use values which are predefined by

default. To perform measurements by using predefined parameters
require the Enforce Predefined Measurement Parameters check-
box (see chapter 7.7) to be activated.

Activating or deactivating the checkbox Enforce Predefined Mea-

surement Parameters has the following impacts on the Measure
dialog:

Enforce Predefined Meaning

Measurement Parame-
ters

Activated The values of those parameters only which are

visible in the Measure dialog can be defined by
the user. All the other parameters remain invisi-
ble, and their values are predefined.

Note: In this case the options provided in

the advanced measurement dialog are iden-
tical to those in the routine measurement
dialog (see chapter 7.3).

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 Chapt. 7 Measure

Enforce Predefined Meaning

Measurement Parame-
ters

Deactivated The values of those parameters only which are

visible in the Measure dialog can be defined by
the user. All the other parameters remain invisi-
ble, and their values are predefined.

The values of some parameters can be defined

by the user. The remaining parameters contain
the values defined in the experiment file.

If the parameter values defined for a user-specific experiment differ

from the values specified by Bruker, the following error message
pops up:

Figure 105: Warning displayed when changing parameter settings

This may occur in case of loading existing experiments. Measure-

ments using non-conforming parameters are not possible, by
default.

Note: Before storing the experiment file with the new

parameters a backup is made of the original file
(*.xpm.bak). If you work in validated mode, you have
to sign the experiment once again after the experi-
ment file has been stored.

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 Advanced Measurement Chapt. 7

7.1 Advanced Measurement

Definition This command allows to perform a background and

sample measurement.

Principle • Select this command.

• Click the Basic tab and then the respective button to
perform the right measurement. The dialog is only
available if you have selected the corresponding
spectrometer configuration before. To do so, select
the Optic Setup and Service command (see
chapter 7.7).
• Click Save and Exit. All default parameter settings
are stored, except the interferogram peak position
(see chapter 7.1.8).

Note: If you start OPUS, the parameters pre-

defined or used for the last OPUS experiment will
be loaded by default. If you do not want to work
with this kind of parameters, you have to load a
different experiment or create a new one (see
chapter 7.2).

If measuring has been completed, the parameters

are stored together with the measuring results.

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 Chapt. 7 Measure

W h e n d o y o u p e r f o r m w h i c h k i n d o f m e a-
surement?

1. Background measurement (reference measurement)

A background measurement is performed without any sample in

the sample compartment (transmission) or on the crystal (ATR).
This kind of measurement is also called reference measurement. A
background measurement is always to be performed before a
sample measurement.

2. Sample measurement

During sample measurement a sample is measured which has

been positioned into the sample compartment (transmission) or on
the crystal (ATR). A sample measurement is always to be per-
formed after a background measurement. In case of a measure-
ment series, however, it is not necessary to always perform a
background measurement before each single sample measure-
ment.

If the measurement runs...

...the progress is indicated by the status bar at the bottom of the

OPUS workspace, below the spectrum window.

Figure 106: Measuring progress

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 Advanced Measurement Chapt. 7

Aborting running measurement

Right clicking the status bar (figure 106) opens a pop-up menu
which you can use to abort the measurement.

Figure 107: Pop-up menu to stop tasks

A A running measurement is interrupted (a repeated measure-

ment will be continued by the next spectrum).
B A repeated measurement is completely aborted.
C If you click the Task Window command, an additional menu
pops up including the current OPUS tasks running.

Figure 108: OPUS task list

Select the corresponding task from the list and click the Stop Task
or Abort Task button. If the measurement has been completed, the
No Active Task message is displayed in the status bar.

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 Chapt. 7 Measure

If measurement has been completed,...

• ...the sample spectrum measured will be displayed in

the OPUS spectrum window.
• ...the measurement parameters are stored in the
data block together with the results.
• ...by using the parameter settings predefined, the sam-
ple spectrum is stored in the C:\Users\<User name>\My
Documents\Bruker\OPUS_<version>\MEAS directory,
by default.
• ...the file name is identical to the sample name which
you have specified in the Measure dialog (see
figure 96). If you do not change the sample name, the
file name will be incremented in case of any further mea-
surement.

In the following only those tabs of the Advanced Measurement

command are described which are relevant to perform a measure-
ment by using predefined measurement parameters. All the other
tabs are explained in detail in chapter 7.2.

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 Advanced Measurement Chapt. 7

7.1.1 Basic

Figure 109: Measurement - Basic

A Clicking Load allows to load an experiment file from the

C:\Users\Public\Public Documents\Bruker\OPUS_<ver-
sion>\XPM directory.
B The information on the sample name and sample form is
optional and will be stored in the information data block of the
spectrum file (see chapter 4.4). Note: If the measurement
parameters differ from the parameters used in the loaded
experiment, the experiment name is displayed in yellow.
Define the sample name and sample form either manually or
use automated parameters by clicking the Auto button. For
details see below.
C To perform a background measurement click this button.
D To perform a sample measurement click this button.
E By clicking this button you save all parameter settings made
in the Measurement dialog, except the interferogram peak.
The peak position has to be saved separately by clicking the
Save Peak Position button on the Check Signal tab (see
figure 114).
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 Chapt. 7 Measure

To w o r k w i t h a u t o m a t e d pa r a m e t e r s . . .

1 ...click the Auto button (see figure 109) to open the following
dialog:

Figure 110: Automated parameters

Note: The list always includes the same automated parame-

ters, whether you define the sample name, sample
form or path.
2 Select the parameter desired.

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 Advanced Measurement Chapt. 7

3 The parameter selected is shown in full below the list.

4 Click the Add at cursor position button. The entry field con-
tains the parameter in pointed brackets. Below the expanded
value is shown in full.

5 You can add several parameters, one behind the other, to

one single sample name or sample form. In this case pro-
ceed as described above.

6 To save the settings made click OK.

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 Chapt. 7 Measure

7.1.2 Advanced

The settings which can be made on this tab are not essential for
the actual measuring procedure. This tab is identical to the one of
the Setup Measurements Parameters command (see
chapter 7.2.2).

On the Advanced tab you specify further measurement parame-

ters.

Figure 111: Measurement - Advanced

A You can specify the directory path, and the data file name of
the spectra file to be saved. Starting with the second mea-
surement, the data file name will be incremented, indicating
the current number of measurements. Enter the path either

manually or by using the button. To add automated

parameters click the Auto button (see chapter 7.1.1).

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 Advanced Measurement Chapt. 7

B In these entry fields you define the resolution and spectral

range. Besides, you can determine the number of scans per
spectrum, or the total acquisition time for sample and back-
ground measurement. Note: The resolution should not be
higher than necessary to minimize the total acquisition
time.
Improving the resolution, e.g. by a factor of 2, requires a four-
times higher acquisition time at a constant signal-to-noise
ratio of the spectrum. This is due to the fact that the sig-
nal-to-noise ratio is proportional to the square root of the
acquisition time.
C In these entry fields you define the wavenumber range to be
measured.
D The optic configuration provides possible result spectrum
types. Select one of the following types available from the
drop-down list:
- Transmittance
- Absorbance
- Kubelka Munk
- Reflectance
- Log Reflectance
- ATR Spectrum
- PAS Spectrum
E Activate the check box if you want to perform additional data
treatment, e.g. straylight correction, during measurement. For
detailed information on straylight correction as part of the
measurement refer to chapter 8.29.3.
F Activate the check box if you want to perform atmospheric
compensation. If the sample measurement has been suc-
cessful, atmospheric compensation will immediately be per-
formed after the measurement. For details on atmospheric
compensation as part of the measurement refer to
chapter 8.28.1.
G All parameters defined can be saved in an experiment file
(see also chapter 7.2.2).

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 Chapt. 7 Measure

7.1.3 Optic

The settings which can be made on this tab are not essential for
the actual measuring procedure. Which kind of settings you can
make depends on whether you work with predefined parameters
(see introduction to chapter 7).

This tab is identical to the one of the Setup Measurements Param-

eters command (see chapter 7.2.3).

7.1.4 Acquisition

Whether this tab is displayed depends on the spectrometer config-

uration. The settings which can be made on this tab are not essen-
tial for the actual measuring procedure. This tab is identical to the
one of the Setup Measurements Parameters command (see
chapter 7.2.4).

7.1.5 FT

Whether this tab is displayed depends on the spectrometer config-

uration. The settings which can be made on this tab are not essen-
tial for the actual measuring procedure. This tab is identical to the
one of the Setup Measurements Parameters command (see
chapter 7.2.5).

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 Advanced Measurement Chapt. 7

7.1.6 Display

On the Display tab you define the axes settings for the spectrum
display during measurement.

Figure 112: Measurement - Display

A If you activate this check box, the spectrum will be calculated

by single scans and displayed, before the actual measure-
ment starts. The actual data acquisition is performed as soon
as the operator starts measuring.
B To display intermediate results during measurements, acti-
vate this check box.
C It is possible to manually define upper and lower limits for the
x- and y-axis. Click into the respective entry field and enter
the value desired.

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 Chapt. 7 Measure

7.1.7 Background

The Background tab is used to save a background spectrum cre-

ated, or load an existing one.

Note: It is recommended to acquire a new background

spectrum at the beginning of a new measurement
series, or after a certain validity period has expired.

Figure 113: Measurement - Background

A To load an existing background spectrum click this button.

The name and path of the spectrum file will be displayed in
the entry field below.
B To save a background spectrum previously measured click
this button.
C To delete a background spectrum loaded click this button.

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 Advanced Measurement Chapt. 7

7.1.8 Check Signal

To determine and save the exact interferogram peak position you

have to open the Check Signal tab at least once after you have
installed your spectrometer.

The purpose of checking the signal is to either achieve a maximum

interferogram signal or optimize the shape of the single-channel
spectrum.

The appearance of the Check Signal tab depends on the spectrom-

eter configuration. Besides the options and commands displayed in
figure 114 you may have additional functions available for your sys-
tem.

To z o o m i n t o a s p e c i f i c s i g n a l r a n g e . . .

1 ...right click into the interferogram display and select the

Zoom In option.
2 A crosshair appears.
3 Press the left mouse button and draw a frame around the
signal range.
4 Click the left mouse button to reposition the frame.
5 Click the left mouse button again to resize the signal range
to the interferogram display.
6 Click the left mouse button to remove the crosshair.

To z o o m o u t a s p e c i f i c s i g n a l r a n g e . . .

1 ...right click into the interferogram display and select the

Zoom Out option.
2 A crosshair appears.
3 Perform the same steps as described for the Zoom out pro-
cedure.

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 Chapt. 7 Measure

C
D
E
F
G

Figure 114: Measurement - Check Signal

A If the peak position is constant, save it by clicking the Save

Peak Position button.
B To undo a former signal range zooming click the Scale Dis-
play button, and the interferogram will be scaled on the inten-
sity axis.

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 Advanced Measurement Chapt. 7

Figure 115: Interferogram zoomed-in

C If the maximum interferogram value is not displayed, move

the range by clicking the arrow buttons.
D Activate the check box if the display mode should be stored.
E If the option button is checked, the interferogram will be dis-
played graphically.
F If the option button is checked, the interferogram is Fourier
transformed during adjustment and displayed as single-chan-
nel spectrum.
G If the option button is checked, the amplitude and zero-cross-
ing position are displayed.

Figure 116: Numerical display of ADC count

H To have the complete scan displayed click this button.

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 Chapt. 7 Measure

St e p p e r M o t o r A d j u s t m e n t

In case of spectrometers (e.g. IFS 125HR, VERTEX 80V, IFS 66V)

providing a software-controlled adjustment of the interferometer by
using stepper motors, the motor control panel is displayed at the
top on the left.

Figure 117: Menu to adjust stepper motors

A To start an automatic adjustment click this button.

B Use this button to correct minor misalignments within the near
range of the current xy-coordinates. Note: This is especially
recommended if you measure spectral regions of higher
frequency (NIR to UV). The Fine Auto Align command pro-
duces the same result as the Auto Align command, however,
it performs faster than Auto Align as it covers a smaller fre-
quency range.
C The motors can be controlled manually by using the arrow
buttons ( ). To restore the motor position to 0 click the
Restore button.

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7.1.9 Beam Path

Whether the Beam Path tab is available or not depends on the

spectrometer type.

Figure 118: Measurement - Beam Path (TENSOR 27)

Use the Beam Path tab to graphically visualize the spectrometer

beam path which is based on the parameters defined on the Optic
tab.

If you position the cursor on a beam path component, e.g. source,

the component description pops up. Double click the source com-
ponent to have the beam path displayed.

Figure 118 shows a TENSOR 27 beam path. If an accessory is

inserted in the spectrometer sample compartment, this kind of
accessory is also graphically displayed.

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C h a n g i n g o p t i c pa r a m e t e r s

Depending on the spectrometer type used it is also possible to

interactively change the optic parameters (e.g. source, detector,
measurement channel) on the Beam Path tab.

1 Left click one of the beam path components to activate or

deactivate it.
2 All the changes made will be stored on the Optic tab.

7.1.10 Spectral Range Selection

The Spectral Range Selection tab is only available with spectrome-

ters which support the graphical beam path (e.g. TENSOR, VER-
TEX). The tab allows to interactively select the spectral range1 for
measurement, and to optimally adapt it to the spectral range of the
optical components.

In this case the white area (figure 119) representing the currently
selected spectral range should not be larger than the filled area of
the colored bars.

1.The spectral range in which the spectrometer can select an IR signal depends on
the optical components (source, beamsplitter, detector etc.) used. To achieve
good measuring results make sure that the spectral range interactively defined
for measurement is not larger than the spectral range covered by the optical
components.

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 Advanced Measurement Chapt. 7

Figure 119: Measurement - Spectral Range Selection

Selecting spectral range

1 Position the cursor on the red line between the white and
gray area. The cursor changes to .
2 Press the left mouse button and move the line to the position
desired. If required, perform step 1 and 2 for both red lines.

Moving spectral range

1 Position the cursor to the white area.

2 Press the left mouse button and move the spectral range to
the position desired.

Note: The limits selected interactively on the Spectral

Range Selection tab are automatically entered into
the Save data from...to entry fields on the Advanced
tab.

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Zooming-in spectral range

1 To enlarge a range right click a particular frequency range.

2 Select the Zoom command from the pop-up menu.

O p t i c a l c o m p o n e n ts

The optical components best suited for the currently selected spec-
tral range of the spectrometer connected are indicated below the
graphics (A in figure 120).

A B

Figure 120: Example of best (A) and additional (B) optical components

The components shown on the right (B in figure 120) are a selec-

tion of further components which can additionally be used with the
spectrometer connected.

Note: It may be necessary that you have to replace single

spectrometer components to ensure that these com-
ponents optimally cover the spectral range selected
for measurement. For details on how to replace opti-
cal components refer to the spectrometer user man-
ual.

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7 . 1 . 11 R a m a n M e a s u r e m e n ts
• Laser power
In case of Raman measurements you can also specify
the laser power on the Basic tab.
In the standard configuration the laser will automatically
be switched off after each measurement. For some
applications, e.g. series measurements, you can deacti-
vate this laser option. Uncheck the Auto Laser OFF
check box.
The laser power can be set using the slider on the
Check Signal tab, i.e. the actual performance will be dis-
played.
• Frequency Range
On the Advanced tab the frequency range for data stor-
age will be displayed in relation to the laser excitation
frequency.
• Acquisition
On the Acquisition tab all frequencies are displayed in
relation to the laser excitation energy.

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7.2 Setup Measurement

Parameters

Definition This command allows to set up, edit and load param-
eters for a measurement experiment.

Principle Define the setting options on the respective tabs

which are described in the following.

Configuration errors are...

...indicated by colored entry fields, and warning symbols on the

particular tab. Errors during measurement may be caused by:
• an experiment which has been loaded and is not com-
patible with the spectrometer configuration.
• a parameter value which is beyond the allowed limit.

The warning symbols and their meaning are described in the fol-
lowing table:

Symbol Meaning What has to be done?

The measurement parameters • Position the cursor on the red entry

do not fit with the existing hard- field. An error message pops up.
ware. No measurement pos- • Select one option suggested by
sible! OPUS from the drop-down list.

The entry field of the measure-

ment parameter is marked in
red in this case.

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Symbol Meaning What has to be done?

The value of a measurement • Position the cursor on the red entry

parameter is beyond the limits. field. A help text pops up indicating
No measurement possible! the cause of the error.

The entry field of the measure-

ment parameter is marked in
red in this case.
• Enter an appropriate value.

The value of an experiment • Position the cursor on the yellow entry

measurement parameter has field. A help text pops up indicating
been changed. Measurement the cause of the error.
possible!

The entry field of the measure-

ment parameter is marked in • Enter an appropriate value.
yellow in this case.

One measurement parameter • Either create a new measurement

is wrong and cannot be cor- experiment or
rected. No measurement pos- • change the user settings accordingly
sible! (see chapter 14.10). Note that you
need administrator rights to be able to
A warning symbol is shown if do so.
the experiment contains a
wrong parameter, and if the
operator is not allowed to
change parameters of a mea-
surement experiment.

In the following only those tabs of the Setup Measurement Experi-

ments command are described which are relevant to perform a
measurement by using predefined measurement parameters. All
the other tabs are explained in detail in chapter 7.1.

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7.2.1 Basic

This tab allows to load measurement experiments already existing.

Figure 121: Setup Measurement Experiments - Basic

A To load an already existing measurement click this button. By

default, the measurement experiments are stored in the
C:\Users\Public\Public Documents\Bruker\OPUS_<version>\
XPM directory.
B Use these entry fields to define the sample name as well as
the sample description. For a detailed description on working
with automated parameters by using the Auto button refer to
chapter 7.1.1.

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7.2.2 A d v a n c ed

On the Advanced tab you define further parameters.

Figure 122: Setup Measurement Experiments - Advanced

A You can specify the directory path, and the data file name of
the experiment file to be saved. Enter the path either manu-

ally or by using the button. To add automated parame-

ters click the Auto button (see chapter 7.1.1).
B In these entry fields you define the resolution and spectral
range. Alternatively, you can determine the number of scans
per spectrum, or the total time of all scans for sample and
background measurement. Note: The resolution should not
be higher than necessary to minimize the total acquisi-
tion time.
Improving the resolution, e.g. by a factor of 2, requires a four-
times higher acquisition time at a constant signal-to-noise
ratio of the spectrum. This is due to the fact that the sig-

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 Chapt. 7 Measure

nal-to-noise ratio is proportional to the square root of the

acquisition time.
C In these entry fields you define the wavenumber range to be
measured.
D The optic configuration provides possible result spectrum
types. Select the appropriate spectrum from these result
spectra.
E Activate the check box if you want to perform additional data
treatment, e.g. straylight correction, during measurement (see
also chapter 7.1.2).
F Activate the check box if you want to perform atmospheric
compensation (see also chapter 7.1.2).
G The Data blocks to be saved group field is only displayed if
the Enforce Predefined Measurement Parameters checkbox
(chapter 7.7.2) of the Optic Setup and Service command is
NOT activated. By default, the checkbox is activated.
Depending on the result spectrum selected, a checkmark is
set by default in front of the appropriate data block
(figure 122). To save more data blocks activate the particular
checkbox.
H Clicking this button opens the Setup Experiment Filename
dialog. Enter an appropriate name for the measurement
experiment defined and save this name. All parameters
defined are now saved by the file name specified.

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7.2.3 O p t ic

Depending on the spectrometer configuration the number of entry

fields displayed in figure 123 may be different. Which kind of set-
tings you can make depends on whether you work with predefined
parameters (see introduction to chapter 7).

Select the optic parameters from the respective drop-down list.

Figure 123: Setup Measurement Experiments - Optic

A With external synchronisation the measurement experiment

can be triggered externally. External synchronisation
requires the E516/B or E517/Z (S510) accessory with the
E525/Z trigger connector box. The following settings are pos-
sible:
- Off: external trigger signals are ignored
- On: the next measurement (or optionally one measurement
of a sequence of measurements) starts with the next trigger
signal. In case of measurement sequences, the related trig-
ger signal is waited for before starting a measurement.

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 Chapt. 7 Measure

- Trigger measurement: see the On option

- Trigger sequence: measurement starts with the next trigger
signal. In case of measurement sequences, the trigger sig-
nal is not waited for before starting a measurement.
B Depending on the spectrometer configuration there are sev-
eral different measurement channels. The drop-down list con-
tains the measurement channels available for the respective
configuration.
C Some spectrometers are equipped with several different
detector types. The drop-down list contains detector types
available for the respective configuration.
D The scanner velocity depends on the detector type installed
and the current experiment used. Note: Select a slow scan-
ner velocity (<10 kHz) for photoacoustic experiments. For
DTGS detectors and photodiodes 10 kHz are adequate,
while you should use a higher velocity (>10 kHz) if your
spectrometer is equipped with MCT or InSb detectors.
E It is recommended to set the Sample signal gain and Back-
ground signal gain values to Automatic. The optimal gain is
determined by a separate short scan before the measurement
starts, to ensure that the complete dynamic ADC range will be
covered.
The preamplifier amplifies the electronic detector signal.
Depending on the spectrometer used, the drop-down list con-
tains different preamplifier gains. The most important pream-
plifier gains are described in the following:
- A: standard gain1
- B: mean gain (with low signals)2
- C: high gain (with very low signals)3
- Ref: lowest gain for reference measurements4
- Standard: basic gain for particular detector types5

1.The gain is x1 per definition, with "x" meaning multiplied by.

2.Typically, the gain is x4 to x10 in comparison with the standard gain (A or Stan-
dard); with "x" meaning multiplied by.
3.Typically, the gain is x16 to x100 in comparison with the standard gain (A or Stan-
dard); with "x" meaning multiplied by.
4.Typically, the gain is x0.25 to x0.4 in comparison with the standard gain (A or
Standard); with "x" meaning multiplied by.
5.Some detector types, e.g. DTGS, have only one gain, i.e. the basic gain Stan-
dard. The gain is x1 per definition, with "x" meaning multiplied by.

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 Setup Measurement Parameters Chapt. 7

F You can define time intervals before each measurement start

or device change. Enter the respective time intervals in sec-
onds into the Delay after device change or Delay before mea-
surement entry fields.
The Delay after device change option will only be performed if
certain parameters (e.g. sample changer position, detector,
measurement channel) have been changed to avoid prob-
lems especially in case of slow detectors (DTGS). A Delay
before measurement avoids detector saturation in case of
slow detectors if certain parameters (e.g. detector, measure-
ment channel) have been changed.

In case of different configurations the Aperture parameter may be

available. This option is used to set the spectrometer aperture. The
aperture size defines the spectral resolution. An aperture diameter
A causes a spectral peak broadening1  at a wavenumber  (pro-
vided a fixed focal length F of the collimated mirror in front of the
interferometer is given):
A2
  --------2-  
8F
A further optic parameter is the switch gain. The switch gain allows
to amplify the interferogram by 2N within the spectral ranges which
are quite off the centerburst. This has almost the same effect as if
you enhance the ADC dynamic from, e.g. 16 to (16 + N) bit, which
reduces digital noise.

This aspect is important for data acquisition in high resolution when

using a broad-band source. The window width around the center-
burst can be specified in the Window in points field.

7.2.4 A c q u i s i t io n

Whether this tab is displayed depends on the spectrometer config-

uration. Depending on the spectrometer configuration the number
of entry fields displayed in figure 124 may be different.

1. More precisely, a convolution with a delta function of a width

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 Chapt. 7 Measure

Select the acquisition parameters from the respective drop-down

list. The most important parameters are described in the following.

Figure 124: Setup Measurement Experiments - Acquisition

A When defining the upper and lower frequency limit the result-
ing actual frequency limits calculated may deviate from the
values defined and are therefore displayed next to the
Wanted high or low frequency limit entry field on the right.
Note: Restricting the sampling bandwidth reduces the
amount of data and may be useful when recording high
resolution spectra. However, electronic and/or optical filters
have to be used to ensure that signal intensity is 0 beyond the
selected frequency limits. Otherwise, the signals may be con-
voluted or folded to the selected range, and may adulterate
the intensity.
B The High pass filter limits the bandwidth within the high fre-
quency ranges. If you select On from the drop-down list, you
activate the filter. If you select Open, you deactivate the filter.
Note: This electronic filter is not available for all spec-
trometers.

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 Setup Measurement Parameters Chapt. 7

The Low pass filter limits the bandwidth in the low frequency
ranges. As the mapping of IR wavenumbers to frequencies in
the low frequency range is proportional to the scanner veloc-
ity v, the fixed cut-off frequency f of the filter (in Hz) corre-
sponds to a wavenumber  which depends on v as follows:
  cm – 1  = f  Hz   v  cms –1 

C The acquisition mode defines whether one or both sides of

the interferogram is measured, while the correlation mode
checks the data integrity.
As the interferometer mirror continuously moves, all fre-
quency components of the IR spectrum are depicted in a
detector-response spectrum. This kind of spectrum is located
in a lower frequency range, its bandwidth can be limited by
using electronic filters.

Acquisition Mode

You can select between different types of acquisition modes:

Mode Definition

Single Sided This option allows the measurement of

one-sided interferograms, and data acquisi-
tion is performed only during the forward-mir-
ror movement.

Double Sided The interferogram is measured on both sides,

and data acquisition is performed during the
forward-mirror movement. In this mode the
time resolution amounts to half the value
achieved in Single Sided mode. The sig-
nal-to-noise ratio shows an improvement of
2 , and the ordinate accuracy is higher com-
pared to the Single Sided mode. Note: The
Double Sided acquisition mode is suitable
for Raman, emission, phase correction
measurements and high-resolution quanti-
tative measurements.

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 Chapt. 7 Measure

Mode Definition

Forward/Back- Data acquisition is performed during the for-

ward ward and backward mirror movement. For-
ward and backward scans are separately
co-added, calculated and added. This option
reduces dead time, improves the sig-
nal-to-noise ratio, but requires twice as much
computation time.

Fast Return This mode offers a fast mirror retrace without

data acquisition. This causes less dead time
and a better signal-to-noise ratio.

Fast Return and Forward/Backward modes are not available for all
types of spectrometers. On condition that the measurement times
are identical, the signal-to-noise ratio improves in the following
order:

S/N (no Fast Return) < S/N (Fast Return) < S/N (Forward/Back-
ward)

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 Setup Measurement Parameters Chapt. 7

Correlation Mode

The correlation mode determines whether a data integrity check is

performed during data acquisition. Depending on the spectrometer
type OPUS provides different correlation modes.

Spectrometer Type Mode Definition

AQP instruments No No data check

Around Peak, This mode is only available, if several scans

Low are averaged. Each new interferogram is
compared to the first one within a range
around the centerburst. If the deviation
exceeds the threshold, the interferogram will
be rejected. Otherwise, the interferogram will
be used for averaging

Around Peak, Same as Around Peak Low, but the limit is

High more sensitive to minor changes (e.g. caused
by thermal drift in case of long-term measure-
ments).

AQP instruments Full Igram Length All interferogram data points are compared to
with Raman each other. An interferogram is rejected if the
points contain more than 10 defective areas
or if the number of defective points exceeds
one eighth of the total number of interfero-
gram points.

TENSOR, MATRIX, OFF No data check

MPA, VERTEX,
IFS 125HR

ON This mode is always a combination of the fol-

lowing three modes: ADS FS, Vel,
IFG_Length_Diff

ADC FS (Full The complete scan is rejected if the interfero-

Scale) gram amplitude is greater than 80%. If this
mode is activated, acquisition and co-addition
of overloaded signals is avoided.

Vel (Velocity) Rejects all scans which velocity deviation is

greater than the specified limit during data
acquisition. The default deviation limit is set to
>2% and can be customized.

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 Chapt. 7 Measure

Spectrometer Type Mode Definition

IFG_Length_ Dif- The number of interferogram data points is

ference not identical to the nominal number. This
mode should be activated in case of non-fre-
quent and intense mechanical disturbances to
have the scan automatically rejected.

Signal Amplitude Scans of a particular interferogram amplitude

Limits range are used only. The range can be cus-
tomized.

Start on Signal The measurement starts only if one scan is

Amplitude Limits within the defined amplitude limit. Thus, the
measurement is triggered by intensity. Exam-
ple: sample inserted, measurement
starts

Note: In case of this mode you have to

enter a fixed value for the Signal gain
parameter on the Optic tab (see
chapter 7.2.3), i.e. do not select Automatic.

Stop on Signal The measurement stops if a scan is beyond

Amplitude Limits the defined amplitude limit. Example: sample
removed, measurement stops

Note: In case of this mode you have to

enter a fixed value for the Signal gain
parameter on the Optic tab (see
chapter 7.2.3), i.e. do not select Automatic.

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 Setup Measurement Parameters Chapt. 7

Spectrometer Type Mode Definition

Gate Scans CTR This mode rejects all scans during the time
when the DI1/Pin11 inlet is not connected to
mass Pin1. Scans during which the signal
changes are also rejected.
The measurement continues until the desired
number of scans is reached. No time-out nor
any maximum number of rejected scans are
part of this mode. You can interrupt measure-
ment as often as you like by gate periods.
Note: To feed the gate signal a trigger box
with BNC connectors has to be connected
to the spectrometer (Bruker part no:
E525/Z).
If this mode is not automatically selectable
from the drop-down list, you first have to
define it.
• On the Measure menu, click the Optic Setup
and Service command.
• Click the Devices/Options tab.
• Click the Setup button next to Correlation
mode.
• Click the Add New Item button in the dialog
that opens. Enter the following parameter:
512=Gate Scans CTR.

• Click the Setup button.

• Confirm the entries by OK.

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 Chapt. 7 Measure

Spectrometer Type Mode Definition

Gate Scans SCT This mode rejects all scans during the time
when the probe trigger is not activated, or if at
least 5V are not applied at the trigger cable
(E516/B). Scans during which the signal
changes are also rejected.
The measurement continues until the desired
number of scans is reached. No time-out nor
any maximum number of rejected scans are
part of this mode. You can interrupt measure-
ment as often as you like by gate periods.
Note: To feed the gate signal a trigger
cable with BNC connectors has to be con-
nected to the spectrometer (Bruker part
no: E516/B).
If this mode is not automatically selectable
from the drop-down list, you first have to
define it.
• On the Measure menu, click the Optic Setup
and Service command.
• Click the Devices/Options tab.
• Click the Setup button next to Correlation
mode.
• Click the Add New Item button in the dialog
that opens. Enter the following parameter:
1024=Gate Scans SCT.

• Click the Setup button.

• Confirm the entries by OK.

Raman Detects Raman spikes in the interferogram

and substitutes them by other scans of the
same measurement. If more than 10% of the
interferogram data points have to be substi-
tuted, the scan will be rejected.

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 Setup Measurement Parameters Chapt. 7

7.2.5 FT

Whether this tab is displayed depends on the spectrometer config-

uration. On the FT tab you define phase resolution.

Figure 125: Setup Measurement Experiments - FT

A Set the phase resolution in such a way that the number of

phase interferogram points amounts to at least 250.
B Phase correction increases the interferogram symmetry.
Phase correction is always necessary as the interferogram
measured is never perfectly symmetric. For details on the
phase correction method refer to chapter 8.15.

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 Chapt. 7 Measure

C Apodization function allows to suppress artificial side lobes on

spectral bands (see also chapter 8.15).
D The zerofilling factor value has to be of 2n order within the
range between 1 and 512.

7.2.6 Display

The settings which can be made on this tab are identical to the one
of the Advanced Measurement command (see chapter 7.1.6).

7.2.7 Background

The settings which can be made on this tab are identical to the one
of the Advanced Measurement command (see chapter 7.1.7).

7.2.8 Check Signal

The settings which can be made on this tab are not essential for
the actual procedure of setting up measurement experiments. This
tab is identical to the one of the Advanced Measurement command
(see chapter 7.1.8).

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 Routine Measurement Chapt. 7

7.3 Routine Measurement

Definition This command allows to perform a background and

sample measurement. Routine measurement pro-
vides only a pre-selection of measurement parame-
ters, i.e. not all OPUS measurement parameters
described in chapter 7.1 are available.

Principle • Select this command.

• Click the Basic tab and then the respective button to
perform the right measurement. The dialog is only
available if you have selected the corresponding
spectrometer configuration before. To do so, select
the Optic Setup and Service command (see
chapter 7.7).
• Click Save and Exit. All default parameter settings
are stored, except the interferogram peak position
(see chapter 7.1.8).

In case of routine measurement it is also possible to work with

pre-defined measurement parameters. To be able to do so make
sure that the Enforce Predefined Measurement Parameters check-
box is activated on the Devices/Options tab of the Optic Setup and
Service command (see chapter 7.7.2).

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 Chapt. 7 Measure

7.4 Repeated Measurements

Definition This command allows to define a measurement

series to automate data acquisition.

Principle • Select this command.

• Define the number of measurements.
• Click the Basic tab and then the respective button to
perform the right measurement. The dialog is only
available if you have selected the corresponding
spectrometer configuration before. To do so, select
the Optic Setup and Service command (see
chapter 7.7).
• Click Save and Exit. All default parameter settings
are stored, except the interferogram peak position
(see chapter 7.1.8).

Figure 126: Repeated Measurements - Basic

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 Repeated Measurements Chapt. 7

A This entry field allows to define the total number of measure-

ments.
B This entry field allows to define the delay between single
measurements. If you enter a value of =0 seconds, the mea-
suring data are stored in the internal spectrometer buffer, until
this buffer is full. Only then, will the spectra be displayed in
the OPUS spectrum window.
In this case, data acquisition is of high priority to minimize the
interval of idle time between the single spectra. Whether the
spectrum is displayed in the spectrum window, depends on
the spectral acquisition bandwidth and resolution. Therefore,
it may occur that 50 spectra must have been measured,
before the spectral data are displayed in the spectrum win-
dow. Besides, the entire repeated measuring cyle must have
been completed before you can use the spectra for further
manipulation.
If you enter a value of >0 seconds, the first spectrum mea-
sured is immediately displayed in the spectrum window. The
spectra, which have already been measured, can be
accessed directly.

The Options included on the other tabs are identical to those of the
Advanced Measurement command (see chapter 7.1).

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 Chapt. 7 Measure

7.5 R a p id S ca n Ti me R e so l ved
Measurement

Definition This command allows to acquire spectra in quick suc-

cession.

Typically, time-resolved measurements (TRS) are

performed to record sample changes or environmen-
tal fluctuations, to achieve an absolute time resolution
(i.e. maximum possible number of measurements) or
to repeat measurements with high time constant.

The result of this kind of measurement is stored in a

3D file which contains all spectra measured.

Principle The command is available for VERTEX 70 and

VERTEX 80. A detailed description on this command
in connection with spectrometers of the VERTEX
series is available in a separate document, on
request.

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 Direct Command Entry Chapt. 7

7.6 Direct Command Entry

Definition This command is used to directly send specific com-

mands to the optics which determines the structure of
the syntax.

By default, the command recently sent to the optics

will be displayed in the respective entry field (A in
figure 127).

Principle • Select this command.

• Commands sent to the optics will be logged and dis-
played on the screen.
• If you click a certain line in the entry field next to the
Send Command button, this command line can be
repeated.
• The answers sent by the optics are displayed in the
field below.

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 Chapt. 7 Measure

Figure 127: Direct Command Entry

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 Optic Setup and Service Chapt. 7

7.7 O ptic Setup and Service

Definition This command allows to configure the optics and

retrieve diagnostic results and statistics of specific
spectrometer data.

Principle Each tab of this command contains different optics

features. Define these features and save them.

The different tabs are described in the following.

Note: Depending on the spectrometer configuration not all

tabs described will be displayed on the screen.

7.7.1 Optical Bench

This tab is used to realize the connection between OPUS and the
spectrometer.

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 Chapt. 7 Measure

Figure 128: Optic Setup and Service - Basic

A The spectrometer configuration is selected from this

drop-down list. If there is no connection between OPUS and
the spectrometer, the No optical bench connected option is
displayed in the entry field.
B The URL (Uniform Resource Locator) of the spectrometer
connected is displayed as soon as you have selected the
respective spectrometer configuration in (A). This URL can be
used to access the instrument diagnostic pages via an inter-
net browser.
C The name of the optical bench (spectrometer) is displayed as
soon as you have selected the respective spectrometer con-
figuration in (A).
D The name of the firmware is displayed as soon as the respec-
tive spectrometer configuration in (A) has been selected.

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7.7.2 Devices/Options

The Devices/Options tab allows to set up certain spectrometer

components, and specify measurement parameters.

In case of spectrometers which can be connected to a network

cable all non-OPUS configurable parameters are deactivated.

Note: The setup of single spectrometer components or

options requires Administrator user rights in OPUS.

Figure 129: Optic Setup and Service - Devices/Options

A To set up the result spectrum click this button (see detailed

description below).
B If you activate this checkbox, specific parameters are
pre-defined, and interferograms will be stored. The Bruker
standard experiments have been adapted to this mode.
Note: The Enforce Predefined Measurement Parameter
checkbox is automatically activated if OPUS is installed
for the first time to perform measurements by using MPA

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 Chapt. 7 Measure

or TENSOR spectrometers. To deactivate the mode

remove the check mark, which requires Administrator
rights in OPUS.

Configuring options

All available options and components are configured by using the

Setup button. Basically, the procedure is the same for each compo-
nent or option.

The following example shows the setup procedure on the basis of

the result spectrum.

Example: Configuring correlation mode

Step 1:
Next to Correlation mode, click the
Setup button.

Step 2:
• Select the 64=Signal Amplitude Lim-
its.

The Setup button is displayed.

• Click the Setup button.

Step 3:
• Enter a lower and upper limit for the
signal amplitude.
• Confirm the entry by OK.

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 Optic Setup and Service Chapt. 7

Step 4:
Click the Add New Item button.

Step 5:
• Enter a figure.
• Then, click the Setup button.

Step 6:
• Select Start... and Stop on Signal
Amplitude Limit.
• If necessary, modify the limits.
• Confirm the entry by OK.

Step 7:
The new entry is numbered and dis-
played.

• Click the entry and enter an appropri-

ate name.

Step 8:
The new correlation mode needs to be
selectable on the Measure menu, click-
ing the Acquisition tab.

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7.7.3 Optic Communication

The Optic Communication tab allows to monitor the optics commu-

nication and contains the appropriate URLs.

Figure 130: Optic Setup and Service - Optic Communication

A Activate this checkbox if you want the list to automatically

scroll (in case of long lists).

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 Optic Setup and Service Chapt. 7

7.7.4 Interferometer/AQP

This tab is only displayed in case of spectrometers with AQP.

Figure 131: Optic Setup and Service - Interferometer/AQP

A You have to experimentally evaluate the absolute peak posi-

tion by using the Check Signal tab of the Measurement dia-
log. This value has to be re-adjusted if the detector or laser
have been replaced, or if the optics has been completely
re-adjusted. In this case enter the new value into the Absolute
peak position entry field.
B In case of multi-channel measurements, the laser wavenum-
ber can be specified individually for each channel if a chan-
nel-specific IT test is possible.

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7.7.5 Export Options

Whether this tab is displayed depends on the spectrometer config-

uration.

Figure 132: Optic Setup and Service - Export Options

A The option button is checked by default, i. e. data output will

be in compact OPUS format.
B Optionally, you can also export the data to GRAMS format. To
be able to do so make sure that the GRAMS software runs on
the main memory of your computer, together with OPUS,
while exporting data. If you activate this option button, you
can select between the following options:

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7.7.6 Service

This tab includes the OPUS diagnostic functions, i.e. diagnostic

results and statistics of spectrometers with AQP. The buttons on
the right allow to reset different parameters.

Figure 133: Optic Setup and Service - Export Options

A These two buttons refer to the HeNe laser parameters. Some

lasers show sporadic power fluctuations during operation,
which influence the interferometer control. These fluctuations
are recorded by an internal counter. The fluctuation value
should always be 0, other values would indicate an error. If
the fluctuations increase, you have to replace the laser. Use
the Reset Laser Dropouts button to reset this counter to 0.
If you have replaced the laser, you can set the laser operating
time meter to 0 by using the Laser Replaced (Reset Parame-
ters) button. At the same time, the value of the laser start
intensity is read again.

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 Chapt. 7 Measure

B This button resets both the counter of the total source operat-
ing time and the counter of the on/off source cycles after
replacing the source.
C To update the parameters of all motors click this button.

The remaining buttons determine the control parameters of the dif-

ferent spectrometer stepper motors. The number and position of
stepper motors depend on the spectrometer type. These buttons
allow to read one of the following motor status:

Update Aperture Motor Table motor to control the aperture

Update Channel Motor Table motor to switch beam ports

Update Detector Motor Table motor to switch detectors

Update Source Motor Table motor to switch sources

Update Calibration Filter Motor motor to control the calibration filter

Table

Update Polarizer Motor Table motor to control the polarizer

Update Sample Changer Motor motor to move the sample wheel

Table

Update Flaps Motor Table motor to control the flaps

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 Optic Setup and Service Chapt. 7

7.7.7 C o n tr o l P a n e l

The options available on this tab apply to the IFS 125HR spectrom-
eter only and are described in the IFS 125HR user manual.

Figure 134: Optic Setup and Service - Control Panel

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7.8 Optics Diagnostics

Definition This command allows to retrieve the status of single

spectrometer hardware components, and have the
result of the last instrument test for the current test
channel displayed.

Note: The dialog is only available if you have

selected the corresponding spectrometer config-
uration before. To do so, select the Optic Setup
and Service command (see chapter 7.7).

Principle see the following description

Figure 135: Instrument Status

A The status of the hardware components, e.g. source, laser,

interferometer etc. is displayed in the upper icon line. The sta-
tus can be as follows, exemplified on the source component:

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 Optics Diagnostics Chapt. 7

OK (green):
Component is okay

WARNING (yellow):
The exact meaning of a warning depends
on the specific component. In case of the
source a warning means:

• end of the specified component lifetime

of the component is nearly reached. In
this case, measuring is still possible.
• the source is still warming-up. In this
case, measuring is not possible.

ERROR (red):
Component is defective. In this case mea-
suring is not possible.

B The second row of icons refers to the possible active test

channel and indicates the result of the last instrument test
performed. The results can be as follows:

INACTIVE (yellow):
The single tests of the particular test cat-
egory are disabled.

PASSED (green):
Instrument test configured or passed.
Test still valid.

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 Chapt. 7 Measure

EXPIRED (light blue):

Instrument test validity period has
expired.

FAILED (red):
Last instrument test failed.

C The instrument status report, i.e. a report about the current

spectrometer status, can be sent to Bruker by e-mail. If you
click the Send Report button, the report will be sent to opusre-
[email protected]. Note: This function requires an
e-mail program installed on your computer and a set-up
mail account. Additionally, the spectrometer needs to be
connected to a network or network computer.
Different sending options are available. You can define when
the instrument report has to be sent, e.g. on a daily basis or
as soon as errors occur in the report.

For details on test channels in case of spectrometers which do not

support OVP refer to chapter 14.10.1.

To p e r f o r m f a u l t d i a g n o s t i c s o f a pa r t i c u -
lar spectrometer component

1 Click the spectrometer component icon which indicates an

error or warning.
2 The Instrument Status Message dialog opens. Figure 136
exemplifies an error message for the source component.

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 Optics Diagnostics Chapt. 7

Figure 136: Instrument Status Message

3 Click the Service Info button (A in figure 136). The spectrom-

eter component diagnostics page opens. Figure 137 shows
the diagnostics page of the MATRIX-F source. This page
contains all relevant information about the current operating
status of the respective spectrometer component.

Figure 137: Source diagnostics page of MATRIX-F

4 Depending on the type of error indicated on the diagnostics

page, clicking the RESET button may solve the problem.

Note: You can also send these diagnostics pages as full

report to the Bruker service by e-mail allowing the
technician a first remote fault diagnostics.

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 Chapt. 7 Measure

I n s t r u m e n t Te s t R e s u l t

The result of the instrument test (see figure 135) refers to the active
test channel. Each time you load an experiment file, the corre-
sponding channel is set as active channel. The status of this new

active channel is tested and indicated by the status light (see

chapter 2.15). The active test channel refers to an IT channel posi-
tion defined in the OVP Setup dialog (see also chapter 13).

7.8.1 Sta t u s d i s p l a y f o r n o n - E t h e r n e t
based spectrometers

The status light and icons are especially intended to be used in

connection with Bruker Ethernet-based spectrometers. In case of
previous spectrometer types and research spectrometers the func-
tionality is different.

In this case you have to define an additional command using the

OPUS Properties dialog, and to specify a time (in minutes) that
OPUS should use to poll the current status of the active channel.
Once during each interval, the particular status is polled, and the
status light is updated.

Enter the command line as follows:

1 Right click the OPUS icon from the Windows Start menu.
2 Select the Properties command and click the Shortcut tab.
3 Enter the command line into the Target entry field. In
figure 138 the /DIAGTIMER=5 command polls the status
once every 5 minutes.

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 Optics Diagnostics Chapt. 7

Figure 138: OVP command line

Note: The status is not updated when loading an experi-

ment file, it is only updated if the time interval has
expired and the assigned program polled.

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 Chapt. 7 Measure

7.9 Te mperature Con trol

Definition This command allows to operate and control external

equipment, e.g. temperature-controlled stage.

Principle • Select this command.

• Define the basic settings.
• Click Save Settings.

Figure 139: Temperature Control - Basic

A This drop-down list allows to select the respective serial port

which the stage is connected to.
B This drop-down list allows to specify the type of thermo-sen-
sor.
C If you activate this check box, the default port parameters will
be set as specified in the operating system.
D Clicking this button, makes the current stage temperature to
be read.

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 Temperature Control Chapt. 7

E To set the required temperature click this button.

F If macros are used to control the temperature, click this button
to stop the makros until the required temperature has been
achieved.

The Extended Commands tab allows direct command input. For

details on the corresponding commands, refer to the control unit
manual. The following syntax applies to command input:
• To read a command: R <command>
• To write a command: W <command>

C
A
B

Figure 140: Temperature Control - Extended Command

A To enter the respective command use this entry field.

B The command will only be transmitted if you press this button.
C Clicking this button provides a blank entry field again.
D To save your command sequence click this button.

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 Chapt. 7 Measure

7.10 Interleaved Time Resolved

Measurement

Definition This command has been developed for spectrome-

ters which use an acquisition processor (AQP), e.g.
IFS 66v.

The electronics of these Bruker spectrometers can

generate up to 16 data points (equidistant in time) per
standard interferogram data point. This can be used
to analyze the kinetics of rapid processes which are
completely reproducible with as many as 16 time
intervals. If the time required to digitize n time inter-
vals is higher than the time available between two
normal interferogram data points, the time intervals
can be distributed over several scans (interleave fac-
tor >1).

Principle • Select this command.

• The dialog, which includes tabs which are quite sim-
ilar to the ones already described in the Measure
dialogs, is only available if you have selected the
corresponding spectrometer configuration before.
To do so, select the Optic Setup and Service com-
mand (see chapter 7.7).
• Define all parameters desired for this kind of mea-
surement on the Timing/Interleave tab.
• Click Exit to save the settings made.

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 Interleaved Time Resolved Measurement Chapt. 7

Figure 141: Interleaved Time Resolved Measurement - Timing/Interleave

A Time resolution is the distance between two time slices in

microseconds.
B The number of n time slices which are to be measured for
each normal interferogram data point are defined in this entry
field. Values between 1 and 16 are possible. n time slices will
create n spectra.
C The delay between the trigger of a normal data point and the
digitalization of the first time slice in microseconds are defined
in this entry field.
D The maximum measurement repetition rate is defined in this
entry field. The actual repetition rate will be displayed below
this value.

Note: After the measurement, the data are sorted into n

interferograms which are assigned to the respective
time slices. If desired, the corresponding single-
channel spectra are calculated. Similar to TRS-mea-
surements the results are stored in a 3D data file.

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 Chapt. 7 Measure

7.11 Sample Wheel

Measurement

Definition This command allows to perform measurements by

using a sample wheel. Note: This command can
only be used in connection with spectrometers
which are equipped with a sample wheel of up to
32 positions.

Principle • Select this command.

• Create a setup file by means of the Setup tab.
• Save the settings made.
• Load the setup file created.
• Start background measurement and then sample
measurement (see the descriptions below).

1 s t Ste p : C r e a t i n g S e t u p F i l e

On the so-called setup file you define the single sample wheel posi-
tions. For each sample wheel position to be measured you can
define a separate experiment method file, a user-defined file name
and path to save the spectra files measured.

Note: A setup file created to measure samples by using a

sample wheel has the file extension *.ini.

Click the Setup tab to open the following dialog:

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 Sample Wheel Measurement Chapt. 7

A
B

Figure 142: Sample Wheel Measurement - Setup

1 Define the sample wheel positions to be measured. Left click

any position (A in figure 142) in the list on the right. A
selected position is displayed by a blue marking. Note: It is
not obligatory to consecutively fill in the sample
positions, you can also skip positions.
2 Enter a comment for the position selected into the Comment
entry field (B).

As soon as you select the next position the comment written

for the last position will be displayed in the respective Com-
ment entry field.

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 Chapt. 7 Measure

Note: If you enter a comment for a specific sample

wheel position, the comment is written to the sample
name of the spectra saved during measurement.
3 Activate the Use this position check box (C in figure 142) to
ensure that the position selected is really used during mea-
surement. Otherwise, the position will not be considered dur-
ing measurement. The parameters set, however, will remain.
If you click the Clear Position button, only the settings
defined for the respective sample position will be deleted.
The position itself still remains.
4 Select a spectrum file for each sample position. Either use
the Select button to select an already existing spectrum file
or enter the path and name of the spectrum file which will be
created for the respective position after measurement. Note:
If you do not fill in this entry field (D in figure 142), OPUS
reads the path and file name of the spectrum file in the
experiment.
5 Select an experiment file for each sample position. Either
use the Select button to select an already existing experi-
ment file or enter the path and name of the experiment file
into the entry field (E in figure 142). For information on how
to create experiment files refer to chapter 7.2. Note: It is
also possible to use a global experiment file (see the fol-
lowing description.
6 Save the settings made by clicking either the Save or Save
As button. Enter an appropriate file name. The name and
path of the setup file created will be displayed (see A in
figure 143).

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 Sample Wheel Measurement Chapt. 7

Figure 143: Sample Wheel Measurement - Example of a setup file

Global Experiment File

A global experiment file applies to all sample wheel positions. In

this case the experiment file individually assigned to each sample
wheel position will not be considered to be valid.

1 Activate the Use global experiment file check box (F in

figure 142).
2 Either type in the path and file name manually or load them
from the respective directory by clicking the Select button.

This kind of settings performs one single reference measurement

to be used for all sample wheel positions.

Note: If you want to perform an additional reference mea-

surement before each sample measurement, you
have to activate the Background before each mea-
surement check box on the Measurement tab as well.

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 Chapt. 7 Measure

2 n d St e p : M e a s u r e m e n t / R e f e r e n c e

Start measuring by using the setup file created.

1 Click the Measurement tab. By default, the single sample

wheel positions on the graphic display are gray. As soon as
you have loaded a setup file, all positions defined in this file
will turn to light-green (see figure 144).

Figure 144: Sample Wheel Measurement - Measurement

2 Click the Start Measuring button. During measurement the

button becomes deactivated.

First, OPUS moves the sample wheel...

...to the reference position ( ) and performs the reference

(background) measurement(s), either using the global experiment
file or the experiment file defined for the first sample wheel position.
Note: The terms Reference and Background Measurement are
used as synonyms in the following.

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 Sample Wheel Measurement Chapt. 7

If you use a global experiment file...

...the Background before each measurement check box is dis-

played.

If you activate this check box, a background (reference) measure-

ment will be performed before each single sample is measured.

Example: R - S - R - S - R - S; (R = reference measurement, S =

sample measurement)

If you deactivate the check box, only one single background mea-
surement will be performed before each sample measurement.

Example: R - S - S - S - S - S; (R = reference measurement, S =

sample measurement)

If you do not use any global experiment file...,

...a background measurement will always be performed before

each sample measurement. This is due to the fact that the experi-
ment file used may be different for each sample position.

If the reference measurement(s) has been completed...,

...OPUS moves the sample wheel to the position selected and

measures the sample. Then, the remaining sample or reference
measurements are performed according to the settings in the setup
file.

During measurement...

...the current sample wheel position is always displayed in the Cur-

rent Position group field, as well as the spectrum file and experi-
ment file defined for this particular position. If a comment has been
defined, this comment will also be displayed.

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 Chapt. 7 Measure

Figure 145: Example of current sample wheel position

It is possible to selectively move the sample wheel to any desired

position when a sample run is not active. First, enter the number of
the target position into the corresponding entry field, and then click
the Go to Position button to move to the position defined.

Figure 146: Example of target sample wheel position

After measurement...

...all spectra measured will be saved, using the file name and path
indicated in the setup file. If the setup file does not contain any file
name and path, OPUS reads the two parameters from the experi-
ment.

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 Twister Control/Calibration Chapt. 7

3 r d St e p : E d i t i n g S e t u p F i l e

The settings of a setup file created can always be edited.

1 Load the particular setup file. Click the Load button on the
Setup tab.
2 To edit single sample wheel positions left click the corre-
sponding position (A in figure 142). The settings defined for
the position selected are displayed on the left. Edit these set-
tings, as desired.
3 To delete the settings made for all positions and the global
experiment file entry click the Clear All button.

If you have edited a loaded setup file and you click the Measure
tab, you will be asked whether these changes made are to be
stored. If you click Yes, the changes will be stored and become
effective during measurement.

7.12 Tw iste r C ontrol/Calibra -

tion

Definition This command allows to control and calibrate the

Twister stacker.

Note: This command is only available if the spec-

trometera is connected to the Twister stacker
which allows to automatically measure several
microtiter plates.

Principle To control and calibrate the stacker follow the user

instructions described in chapter 7.12.1 and 7.12.2.
a. In most cases the HTS-XT module is used.

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 Chapt. 7 Measure

General Features

Before the initial use the Twister stacker has to be calibrated. For
calibration you need a microtiter plate which you have to place into
the respective position to be calibrated.

The calibration purpose is to detect the different positions (input

and output stack, HTS-XT drawer) to be accessed by the stacker.
Each position has to be selected by the OPUS software, and cali-
brated separately.

Note: The Twister stacker is only ready-to-operate if all

positions have been calibrated.

7.12.1 C a l i b r a t i n g Tw i s t e r

Select the Twister Control/Calibration command. Click the Twister

calibration tab. The standard stacker array is displayed.

Figure 147: Twister Calibration - Standard stacker array

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 Twister Control/Calibration Chapt. 7

1 Select position for calibration:

Start to calibrate position 0, activate the respective option
button. Position the microtiter plate onto the primary
position 0.
2 Adjust rotary control:
Move the gripper above position 0. To do so use the
up/down arrow buttons, or enter the number manually.
Adjust the position as precisely as possible. Click the Set
button.
3 Adjust vertical position:
To calibrate the vertical position click the Find plate button.
As soon as the gripper has detected the microtiter plate, it
stops somewhat above the plate.
Make a fine alignment for position 0. Use the arrow buttons
in the Adjust rotary control group field.
4 Save calibrated position:
Save the settings for position 0 by clicking the Save position
button.
5 Back to vertical home:
To measure position 2 and 4 click the Vertical home button.
This causes the gripper to be removed from the previous
position.
Perform the steps 1 - 4 as described above for position 2
and 4.

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 Chapt. 7 Measure

7.12.2 C o n t r o l l i n g Tw i s t e r

There are several different possibilities to configure the stacker

control on the Twister control tab.

Figure 148: Twister Control

1 Define the source for the microtiter plate. Activate the

respective option button.
2 Select the operation mode which will be performed after
clicking the Start Twister button. Activate the respective
option button.
3 The number of plates in the destination stack has to be 0 at
the beginning. If you remove plates from the destination
stack during operation, you have to write the number of the
remaining plates into the entry field.

Additionally, you have the possibility to reset the Twister control or

to access the vertical home.

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 Twister Control/Calibration Chapt. 7

Control by macro

The ready-to-operate Twister stacker can also be controlled by

macros. The following parameters are available:

Parameter Definition

TCP = Twister Communi- Parameter which defines the communication

cation Port port, valid terms: 1 or 2

TMC = Twister (Opera- Parameter which defines the operation mode

tion) Mode/Control

TSS = Twister (Destina- Parameter which defines the number of

tion) Stack Size microtiter plates in the destination stack

TPT = Twister Plate Thick- Internal parameter which stores the microtiter
ness plate thickness measured

TPL = Twister Last Vertical Internal parameter which identifies the posi-
Stack tion from which the plate has been picked up

TPS = Twister Source Parameter which defines the source position

Position of microtiter plate, valid terms: 0, 2, 4

TDP = Twister Destination Parameter which defines the destination posi-

Position tion of the microtiter plate after measurement,
valid terms: 0, 2, 4

1 On the Macro menu, click the Edit Menu command. The

macro editor view opens. Leave the view open.
2 On the Measure menu, click the Twister Control/Calibration
command.
3 Click the command execute button. The Assign Macro Vari-
ables to Function Parameters dialog appears.

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 Chapt. 7 Measure

Figure 149: Macro variables for Twister control

4 Set the parameters.

5 Click OK to confirm the settings made.
6 The macro line must now be displayed in the macro editor.

Figure 150: Macro editor with Twister command lines

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 Pump Control Chapt. 7

7.13 Pump Control

Definition This command is only available in connection with

spectrometers which use a pump for the automatic
measurement of liquids. The OPUS command allows
to control this pump.

General Features

Before using the pump for the very first time, the pump has to be
calibrated which cannot be done by the OPUS software.

Detailed information on how to calibrate the pump has to be pro-

vided by the pump manufacturer.

W h a t k i n d o f p u m ps a r e s u p p o r t e d b y t h i s
OPUS command?

• AIM3000
• ISMATEC REGLO Digital
• Metrohm 838
• Sapphire VFP17

P u m p Vo l u m e

Depending on the kind of pump used, the actually pumped volume

can slightly differ (0.5% to 1%) from the specified volume.

The deviation is due to the fact that the pump control rounds off the
volume to complete cam steps. For further details refer to the docu-
mentation provided by the pump manufacturer.

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 Chapt. 7 Measure

7.13.1 Control the pump

1 Select the Pump Control command. The following dialog
opens:

Figure 151: Pump Control

2 Select the pump type from the Device selection drop-down

list.
3 Select the communication port used in connection with the
pump.
4 Define the operation mode and the pump direction.
5 Click the Start Pump button.

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 Pump Control Chapt. 7

Operation Mode

There are two types of operation mode available:

• Flow rate: this mode defines the pump time and the
speed (flow rate)
• Volume: this mode defines the volume and the speed
(flow rate)

7.13.2 Control the pump by using a

macro

The ready-to-operate pump can also be controlled by a macro. The

following parameters are available:

Set the amount of fluid MPF e.g. 0.1ml

Set the speed of fluid MPS e.g 2ml/sec.

Set the pump direction MPD 0 or 1

Set the pump control device MPV 0 = Ismatec

Set the COM port MPC 1 = COM1; 2 = COM2

Set the pump operation mode MPM 0 = Flowrate

1 = Volume

1 On the Macro menu, click the Edit Menu command. The

macro editor view opens. Leave the view open.
2 On the Measure menu, click the Pump Control command.
3 Click the command execute button. The Assign Macro Vari-
ables to Function Parameters dialog appears.

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 Chapt. 7 Measure

Figure 152: Macro variables for pump control

4 Set the parameters.

5 Click OK to confirm the settings made.
6 The macro line must now be displayed in the macro editor.

Figure 153: Pump control macro lines in the macro editor

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 Auto Sampler Configuration Chapt. 7

7.14 Auto Sampler Configura -

tion

Definition This command can only be used in connection with

an application-specific and automated procedure
(macro). An auto sampler allows to set up and per-
form a measurement sequence. The measurement
sequence is stored as configuration file with the
extension *.ini.

The auto sampler is controlled via the RS 232 inter-

face. OPUS supports the AIM3000 and Metrohm 838
auto sampler.

Principle • Select the Auto Sampler Configuration command.

• Make the settings for each single sample on the
Sample Table Setup tab.
• Define the serial interface on the Auto Sampler
Setup tab. Observe the additional information given
on this tab.
• Load a measuring experiment on the Sample Table
Setup tab. Click the Select Experiment button.
• Click the Save Sample Table button to store the set-
tings made.

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 Chapt. 7 Measure

Figure 154: Auto Sampler Configuration - Example of a sample table

Figure 155: Auto Sampler Configuration - Auto Sampler Setup

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 Measure with Auto Sampler Chapt. 7

7.15 Measure with Auto Sam-

pler

Definition This command can only be used in connection with

an application-specific and automated procedure
(macro).

Different sample positions, which are configured on

an auto sampler, are accessed and measured. The
auto sampler is controlled via the RS 232 interface.
OPUS supports the AIM3000 and Metrohm 838 auto
sampler.

7.16 Val v e Con tr ol

Definition This command can only be used in connection with

VALCO valves. This command allows to control the
single valve positions.

Principle • Select the Valve Control command.

• Define the serial interface.
• Define the valve position.
• Click the Start Valve Control button.

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 Chapt. 7 Measure

Figure 156: Valve control

7.17 Cleanness Test Setup

Definition This command is only available if the spectrometer

connected is equipped with an ATR measurement
module.

This command allows to perform a reference mea-

surement of the ATR crystal, and defines the maxi-
mum allowed limit of crystal contamination.

Principle To perform a reference measurement observe the

instructions described in chapter 7.17.1.

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 Cleanness Test Setup Chapt. 7

7.17.1 R e f e r e n c e m e a s u r e m e n t o f ATR
c r y s ta l
1 Select the Cleanness Test Setup command. The following
dialog opens:

Figure 157: Cleanness Test Setup

2 Click the Reference Measurement button.

Note: When measuring a reference spectrum make sure

that the ATR crystal is not contaminated.

As soon as the reference measurement starts, it will be indi-

cated as follows.

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 Chapt. 7 Measure

Figure 158: Reference measurement runs

If the reference measurement has been finished, the refer-

ence spectrum is stored.
3 Define the maximum allowed contamination level. Enter the
corresponding value into the entry field.

Figure 159: Defining contamination level

4 Click the OK button.

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7.18 Cleanness Test

Definition This command is only available if the spectrometer

connected is equipped with an ATR measurement
module.

Based on the maximum contamination level defined,

the cleanness test checks whether the ATR crystal is
clean. The wave number range is between 2800 and
3050cm-1 (absorption).

Principle To perform a reference measurement observe the

instructions described in chapter 7.18.1.

7.18.1 Performing cleanness test

1 Select the Cleanness Test command. The following dialog
opens:

Figure 160: Cleanness test

2 Click the Measure button. The cleanness test starts.

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 Chapt. 7 Measure

7.18.2 Te s t r e s u l t

The test result always shows the contamination level measured,

and compares it with the maximum allowed level.

Test result Meaning

Crystal is clean, i.e. the defined maximum

contamination level has not been
exceeded.

Crystal is contaminated, i.e. the defined

maximum contamination level has been
exceeded.

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8 Manipulate
This chapter describes OPUS data manipulation options. The term
Manipulate involves all arithmetic methods which modify or create
new spectral data of a spectrum acquired.

Manipulating spectra...

...primarily serves to increase the information content of the spec-

trum and to reduce the amount of interferences reflected in the
spectrum. There are, of course, esthetic aspects to be considered
as well.

T h e m a n i p u l a t i o n r e s u l ts . . .

...are only temporary files (work files). Therefore, you need to

directly save them using the Save File command from the File
menu.

If you exit OPUS without saving these work files, the data gener-
ated during manipulation get lost. Normally, a warning pops up
when you want to exit OPUS indicating the existence of data which
have not yet been saved.

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 Chapt. 8 Manipulate

Figure 161: Manipulate menu

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 Baseline Correction Chapt. 8

8.1 Baseline Correction

Definition If the spectrum baseline is not at 0, a baseline correc-

tion can be advisable.

Note: A baseline correction is to be performed if

the spectrum baseline deviates too much from a
theoretical horizontal line, which may be due to
sample scattering losses.

Principle This kind of correction subtracts a baseline from a

spectrum, which allows to get a spectrum with band
edges of up to the theoretical baseline. In case of
absorption spectra this corresponds to a theoretical
baseline of 0 and of 100% in case of transmission
spectra.

How to perform a baseline correction?

OPUS allows to perform a standard baseline correction. With this

kind of correction the baseline is calculated using a rubberband
correction with 64 baseline points.

It is also possible to perform the baseline correction interactively,

i.e. by manually setting baseline points. Additionally, you can select
between several baseline correction methods. The different proce-
dures are described in the following.

8.1.1 Sta n d a r d B a s e l i n e C o r r e c t i o n
1 On the File menu, click Load File. Load the spectrum file.
2 On the Manipulate menu, click Baseline Correction. The fol-
lowing dialog is displayed:

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Figure 162: Baseline Correction - Select Files

Note: The file name will be displayed in the File(s) to correct

selection field. If not, drag and drop the spectrum
file(s) from the OPUS browser window into the
respective selection field.
3 Click the Correct button to perform baseline correction, i.e. to
subtract the baseline from the spectrum.
4 The corrected spectrum is displayed in the spectrum win-
dow, without being immediately stored. If you want to undo
the baseline correction, select Undo Changes from the File
menu.

Figure 163 shows the original spectrum as well as the corrected

spectrum.

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 Baseline Correction Chapt. 8

Figure 163: Top: original spectrum; Bottom: corrected spectrum

You can perform a baseline correction for several spectra at the

same time. First, load the spectrum file(s) you want to correct. On
the File menu, click Load File. Then, select the Manipulate menu
and click Baseline Correction.

8.1.2 In t e r a c t i v e B a s e l i n e C o r r e c t i o n

In case of interactive baseline correction the baseline points are set

manually.

1 On the File menu, click Load File. Select the respective

spectrum file.
2 On the Manipulate menu, click Baseline Correction. The
name of the spectrum file is displayed accordingly (see
figure 162).
3 Click the Start Interactive Mode button (figure 162).
4 A separate view opens (figure 164) which shows the original
spectrum on top and the result spectrum at the bottom.
5 If all the settings have been made, click Store.

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Figure 164: Baseline Correction - Interactive mode

A Using the Straight lines or Polynomes option button you

decide whether to adjust straight lines or polynomes as the
baseline to the original spectrum.
B You can perform a concave rubberband correction (see
chapter 8.1.3). The slider position determines the number of
iterations in the algorithm. Therefore, the result spectrum will
be the original spectrum less the baseline points manually set
(if they have been set at all) and less a subsequent concave
rubberband correction (if the number of iterations is greater
than 0).

S e t t i n g B a s e l i n e P o i n ts

1 Position the cursor in the window with the original spectrum.

The cursor changes to .
2 Double click the position desired in the original spectrum.
Note: Local maxima are selected in case of transmission
spectra, local minima in case of absorption spectra.
3 A baseline is displayed together with the baseline points set.

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 Baseline Correction Chapt. 8

Figure 165: Baseline point set with baseline

4 The result of this baseline correction is immediately shown in

the lower spectrum window (see figure 164).
5 To set further baseline points double click the respective
positions in the original spectrum.
6 To save the settings made click Store.

D e l e t i n g B a s e l i n e P o i n ts

If you want to delete a particular baseline point, just double click

this point.

M o v i n g B a s e l i n e P o i n ts

Click the respective baseline point and move it to the position

desired, pressing the left mouse button.

Z o o m i n g I n / O u t Sp e c t r a

You can also zoom in or out spectra. Right click the original spec-
trum and select the Zoom command from the pop-up menu.

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8.1.3 Baseline Correction Methods

The following baseline correction methods are available in OPUS:

• Scattering correction
• Rubberband correction
• Concave rubberband correction

All methods calculate the baseline as a frequency polygon, consist-

ing of n baseline points. The number of baseline points can be
defined in the corresponding entry field (figure 167). The values
allowed are between 10 and 200.

Note: The greater the number of baseline points the more

exactly the calculated baseline will follow the theoret-
ical baseline, and the more calculation time is
needed. The default values is 64.

Scattering Correction

In case of scattering correction the points are set such that the
baseline shows monotonic decreasing and as small as possible
negative increasing. This, of course, requires the baseline to touch
the corresponding curve minima.

Rubberband Correction

This method uses - figuratively speaking - a rubberband which is

stretched between the spectrum endpoints. The rubberband fol-
lows the spectrum minima (in case of absorption spectra) or the
spectrum maxima (in case of transmission spectra).

Concave Rubberband Correction

This correction method is used in case of spectra whose baseline

curvature has the same sign as the band peak, or whose baseline
shows curvatures with different signs.

This method also uses a rubberband which is stretched from one

spectrum end to the other, and the band is pressed onto the spec-

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 Baseline Correction Chapt. 8

trum from the bottom up (in case of absorption spectra) with vary-
ing intensity.

This method performs iteratively, i.e. depending on the number of

iterations the rubberband is pressed onto the spectrum with varying
intensity. Enter the number of iterations into the corresponding
entry field (figure 167). Values greater than 50 are in most cases
not reasonable. The effect caused by the number of iterations are
shown in figure 166.

Figure 166: Spectrum corrected by concave rubberband correction method

In figure 166 the concave baseline has been calculated, using 40,
15 and 8 iterations (top down). The result spectra are not displayed
to avoid confusion.

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 Chapt. 8 Manipulate

To s e t u p a c o r r e c t i o n m e t h o d . . .

1 ...select the Baseline Correction command and click the

Select Method tab.

Figure 167: Baseline Correction - Select Method

2 Select the baseline correction method, e.g. scattering, rub-

berband or concave rubberband correction.
3 You can exclude spectral ranges which contain CO2 bands
(between 2400 ... 2275 cm-1 and 680 ... 660 cm-1). Activate
the Exclude CO2 bands check box (figure 167).
4 Start baseline correction by clicking the Correct button.

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 Baseline Correction Chapt. 8

8.1.4 Examples of Baseline Correction

Figure 168 shows an original absorption spectrum and a baseline

calculated, using the scattering correction (top) and rubberband
method (bottom).

Figure 168: Original and corrected absorption spectrum

Figure 169 shows the original spectrum together with the result
spectrum after baseline correction has been performed. In this
case the rubberband correction method has been used.

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 Chapt. 8 Manipulate

Figure 169: Original and result spectrum after baseline correction

Note: Baseline corrections can also be performed on trans-

mittance spectra. The procedure is the same as in
case of absorption spectra.

In case of a baseline-corrected spectrum more precise evaluation

results can be achieved when performing a subsequent spectrum
search, spectrum subtraction or peak pick. A baseline-corrected
spectrum is also an essential precondition to be able to correctly
calculate an integral (see chapter 9.2).

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 Spectrum Subtraction Chapt. 8

8.2 Spe c trum Subtraction

Definition This kind of calculation subtracts spectra, with one

multiplication factor each, from a multi-component
spectrum.

Assuming that your sample is not a pure substance

but a mixture which consists of several different com-
ponents, the Spectrum Subtraction command allows
to extract the spectrum of one single component from
within the spectrum of the mixture.

Note: This kind of calculation is only appropriate

for absorbance spectra. Transmittance spectra
are converted to absorbance spectra during cal-
culation. Only if the original spectrum has been of
transmittance mode, will the resulting spectrum
be converted to transmittance when the subtrac-
tion has been finished.

Principle see the following sections

The result of spectrum subtraction is as follows:

S = M – F 1  E 1 – F 2  E 2 ... – F n  E n – C
• S = Subtraction spectrum
• M = Multi-component spectrum
• F1/2/...n = Subtraction factor 1/2...n
• E1/2/...n = Single component 1/2...n
• C = Offset

Note: The optimum result can only be achieved if all single

components are simultaneously subtracted from one
mixture spectrum. This yields to a result of almost 0.

Figure 171 and 170 show the spectrum subtraction dialogs.

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 Chapt. 8 Manipulate

Figure 170: Spectrum Subtraction - Select Files

Figure 171: Spectrum Subtraction - Frequency Range

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 Spectrum Subtraction Chapt. 8

Example of spectrum subtraction

1 Generate an example spectrum, using the spectrum

calculator (see chapter 8.5). The spectrum has to consist of:
- 0.7 components of the ABBOE12.0 spectrum
- 1.3 components of the ABBOE08.0 spectrum
- 2.3 components of the ABBOE05.0 spectrum
Note: The spectra are stored in the *\OPUS_<ver-
sion>\Data directory.
2 Save the spectrum by the CALC.6 name. This spectrum is to
be some kind of generic sample consisting of an unknown
amount of these three components.
3 Select the Spectrum Subtraction command.
4 If required, drag & drop the respective spectrum into the cor-
responding entry fields of figure 170.
5 Click the Subtraction button to start this kind of manipulation.

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 Chapt. 8 Manipulate

I n t e r a c t i v e Spe c t r u m S u b t r a c t i o n

Click the Start Interactive Mode button (see figure 170). The follow-
ing view opens:

H
C

I
F

G Figure 172: Interactive spectrum subtraction

A This entry field shows the name of the multi-component spec-

trum.
B If you click this drop-down list, you can select the spectra to
be subtracted.
C Depending on your spectra selection in (B), the adjusted fac-
tors are displayed. The factor value can be increased or
decreased, using the arrow buttons on the right. The value
can also be entered manually. Click into the entry field and
overwrite the value given.
D If you check this option button, the displayed spectra will be
scaled.
E Clicking this button starts the automatic single-component
spectrum subtraction. Note: The automatic subtraction
mode minimizes the least squares deviation in the differ-
ence spectrum.
F To store the subtraction click this button. The view closes and
the difference spectrum is stored in the file named in (A).
G This slider allows to define the number of decimals, which
causes the factor values of (C) to be adapted.

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 Spectrum Subtraction Chapt. 8

H This window shows both the single-component spectra and

the multi-component spectrum.
I In this window the display is autoscaled and shows the differ-
ence between the multi-component spectrum and the
weighted single-component spectra.
If you right click into the windows (H) and (I), you can zoom in
specific spectral ranges using the pop-up menu. Right click
into the spectrum window and select the appropriate com-
mand from the pop-up menu.

If spectrum subtraction has been fin-

i s he d . . .

...the numerical values used are attached to the spectrum in the

form of a subtraction data block ( ).

T h e s u b t r a c t i o n d a ta b l o c k c o n ta i n s . . .

...the factors used to subtract the spectra, as well as the spectrum

files subtracted. If you right click the subtraction data block, the
Show Report option pops up. Select this option to open the report
view.

Figure 173: Report view of spectrum subtraction

The first column on the right shows the factors used, and the mark
in the Modified column indicates the spectrum which the subtrac-
tion data block has been attached to.

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8.3 AB <-> TR Conversion

Definition This command converts absorbance spectra to trans-

mittance spectra and vice versa. The conversion
direction is set by OPUS depending on the data block
stored in the spectrum file.

Principle • Load the spectrum file.

• Select the AB <-> TR Conversion command.
• If required, drag & drop the spectrum file into the
File(s) to convert selection field.
• Define the conversion direction, if required.
• Click Convert to start this manipulation command.

Figure 174: AB <-> TR Conversion - Select Files

If you definitely determine a conversion direction, only those spec-

tra will be converted which do not have the requested format. The
option buttons allow to create a uniform data block type for several
spectra.

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 AB <-> TR Conversion Chapt. 8

The spectrum displayed in figure 175 by a dotted line has been

generated by an AB TR conversion.

Figure 175: Absorbance spectrum converted into a transmittance

spectrum

The equation required for an TR  AB conversion is:

AB = – log  TR 

Transmittance values less than 10-5 are set to 5 absorbance units.

The equation required for an AB  TR conversion is:

TR = 10 – AB

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 Chapt. 8 Manipulate

8.4 St r ai ght Line Generation

Definition This command allows to correct fringe effects in the

interferogram or artifacts detected in a spectrum.

Principle • Load the spectrum file.

• Select the Straight Line Generation command.
• If required, drag & drop the spectrum file into the
File(s) for straight line generation selection field.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Generate to start this manipulation command.

Figure 176: Straight Line Generation - Select Files

In figure 177 the range between 2,550 and 2,360cm-1 has been
replaced by a straight line. The dotted line shown will not be avail-
able any more in the manipulated spectrum.

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 Spectrum Calculator Chapt. 8

Figure 177: Spectrum before and after generating a straight line

8.5 Spectrum Calculator

Definition The spectrum calculator is used to make calculations,

using spectra and numerical numbers. You can also
enter algebraic terms.

Principle The spectrum calculator cannot be compared with a

normal pocket calculator. If you enter 100 into the
pocket calculator, you expect the result to be 10. The
spectrum calculator, however, operates with alge-
braic formulae. Therefore, you should enter sqrt(100)
in this example.

General

• To enter figures, signs and functions either use the

numerical keypad of your keyboard or click the spectrum
calculator keys. In the latter case inputs will always be
added to the entry field (H in figure ). Delete inputs,
using the button.

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 Chapt. 8 Manipulate

• If the calculation results in a spectrum, the original spec-

trum file will be overwritten by the new result spectrum.
This also applies to data blocks.
• If two spectra are divided, a transmittance spectrum is
generated which may overwrite the original spectrum.

To c a l c u l a t e s p e c t r a . . .

...select the Spectrum Calculator command. The following dialog

opens:

I
F
J

Figure 178: Spectrum calculator

A Use the button to delete your input.

B These buttons provide trigonometric functions. Additional
functions are available if you use the Shift and Hyp button:

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 Spectrum Calculator Chapt. 8

Sine

Inverse of sine (arcus sine)

Hyperbolic sine

Cosine

Inverse of cosine (arcus cosine)

Hyperbolic cosine

Tangent

Inverse of tangent (arcus tangent)

Hyperbolic tangent

Trigonometric number 

C The following mathematical functions are available:

Natural logarithm

Logarithm to the base 10

Square root

Exponent (general)

Exponential function

Takes the following entry to the base of 10, i.e.

10x
Exponent2, e.g. 32=9

Wavenumber value

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 Chapt. 8 Manipulate

D C clears the display in (H) and (I). You can use the brackets
to form mathematical groups that will be calculated first.
E The four basic arithmetic operations can be used.
F Numerical buttons consist of the figures 0 - 9, the decimal
point and exponential function E (e.g. 4.321E3 = 4321).
G This button starts the calculation. The result will be displayed
in the entry field (H).
H The loaded spectrum file to be calculated is available in this
entry field. You can also enter algebraic terms and numerical
values into this entry field.
I Select the result data block from the drop-down list.
J The display field shows the calculation results, or indicates
ERROR in case of an incorrect entry.

Miscellaneous

In some cases it may be necessary to calculate frequency-depen-

dent terms. This can be done using the function, which rep-
resents the frequency values of the spectral data points. The term

sin(x/100) + [4:TR] – [4:TR]

uses the group ([4:TR] – [4:TR]) to generate a spectrum with 0

intensity. The x function causes the frequency limits and data point
(frequency) spacing to be applied. The result will be a sine wave.

If you calculated sin (x/100) + [4:TR], the spectrum intensity values

would be added to the sine wave.

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 Cut Chapt. 8

8.6 C ut

Definition This command minimizes the frequency range of a

data file, which allows to display spectral information
within a certain frequency range more precisely.

Principle • Load the spectrum file.

• Select the Cut command.
• If required, drag & drop the spectrum file into the
File(s) to cut selection field.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click the Cut button to start this manipulation com-
mand.

Figure 179: Cut - Select Files

Figure 180 shows a frequency range (thicker curve line) generated,

using the Cut command.

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 Chapt. 8 Manipulate

Figure 180: Cut - Select Files

You can also use the Cut command to invert the frequency limits of
spectra.

1 Select upper and lower limits which are beyond the spectral
range and define them as new frequency limits in reverse
order.
2 Right click the spectrum and select the Properties command
from the pop-up menu.
3 Invert the axes settings using the Axes tab. This change may
not immediately appear in the spectrum window.

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 Normalization Chapt. 8

8.7 N or malization

Definition This command allows to normalize spectra and per-

form offset corrections on spectra.

Principle • Load the spectrum file.

• Select the Normalization command.
• If required, drag & drop the spectrum file into the
File(s) to normalize selection field.
• Select the appropriate normalization method.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Normalize to start this manipulation command.

Figure 181: Normalization - Select Files

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 Chapt. 8 Manipulate

Normalization methods

• Min/Max normalization
This method is used with spectra which optical layer
thickness substantially varies, to be able to compare
these spectra with each other. For example, the spectra
of a powder sample which have been compacted
unequally during separate measurements.

Figure 182: Non-normalized (top) and normalized (bottom) spectra

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 Normalization Chapt. 8

The shape of the single spectra remains, and the differ-

ences between the spectra can be detected more easily.
Note: The result depends on the frequency range
selected, i.e. specific differences of one section are
distributed to all data points.
• Vector normalization
This method calculates the average y-value of the spec-
trum. The average value is subtracted from the spec-
trum decreasing the mid-spectrum to y = 0. The sum of
the squares of all y-values is calculated and the spec-
trum is divided by the square root of this sum.
The vector norm of the result spectrum is 1:
NPT
  xi 
2
= 1
i=1

• Offset correction
This method shifts spectrum intensities to the effect that
the minimum absorbance unit will be 0.

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 Chapt. 8 Manipulate

8.8 Make Com pat i ble

Definition This command changes the data point grid of the

selected spectrum files to adapt it to the grid of a prin-
cipal file. The files to be processed are manipulated
to make the x-values of the spectra compatible to
those of the principal file.

This causes the frequency base points to be shifted.

If the frequency range of a spectrum selected is
larger than the range of the principal file, the fre-
quency range will be cut.

Principle • Load the spectrum file.

• Select the Make compatible command.
• If required, drag & drop the spectrum file into the
Principal file selection field.
• Select the appropriate method.
• Click Make Comp. to start this manipulation com-
mand.

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 Make Compatible Chapt. 8

Figure 183: Make Compatible - Select Files

Based on the original intensities, the quadratic interpolation is the

method used to calculate the intensities of new frequency base
points. In case of interpolation the curve shape is well preserved.

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 Chapt. 8 Manipulate

Example:

• The frequency limits of the principal file are between

1,000 and 5,000cm-1. The number of data points is
4,001, which corresponds to a resolution of 1cm-1.
• The frequency of the first point is 4,000.5cm-1, of the last
200.5cm-1. The number of data points is 1,901 data
points (resolution: 2cm-1).
• The Make Compatible command creates a new spec-
trum on the basis of the original one. The first frequency
point of this new spectrum is at 1,000cm-1 and the last
one at 4,000cm-1. The number of data points is 3,001
(interpolated resolution: 1cm-1). The x-direction
(high-to-low or low-to-high) of the new spectrum always
depends on the principal file.

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 Convert Spectra Chapt. 8

8.9 C onvert Sp ec t r a

Definition This command performs several data conversions

which mainly involve the y-axis.

When converting spectra certain restrictions may

apply. If you try to select a spectrum file which does
not comply with the conversion method selected, a

warning symbol will be displayed.

Principle • Load the spectrum file.

• Select the Convert spectra command.
• If required, drag & drop the spectrum file into the
File(s) to convert selection field.
• Select the appropriate conversion method on the
Conversion Direction tab.
• Click Convert to start this manipulation command.

Figure 184: Convert Spectra - Select Files

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 Chapt. 8 Manipulate

Conversion Method

The conversion methods available on the Conversion Direction tab

are described in the following.

E
A
F
B
G
C
H
D
I

Figure 185: Convert Spectra - Conversion Direction

A The Kubelka Munk conversion type is appropriate for spectra

which have been measured in diffuse reflectance. Compared
to AB conversion the intensities are more linear to concentra-
tion. The conversion is based on the following formula:
 1 – Refl  2
KM = --------------------------
 2  Refl 
Rfl is the relation between reflected and incidented light.
Absorbance spectra are first converted to transmittance spec-
tra. The smallest value allowed for transmittance or reflec-
tance is 0.001%. This corresponds to a Kubelka Munk value
of about 500.
B The conversion into reflectance spectra is based on the fol-
lowing formula: Refl = 1 + KM –  2  KM + KM 2 

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 Convert Spectra Chapt. 8

C The conversion into ATR spectra is based on the following

X
formula: ATR = AB  ------------
1000
X represents the wavenumber. Transmittance spectra are
first converted to absorbance spectra. As in case of ATR
measurements (Attenuated Total Reflection) the penetration
depth is inversely proportional to the wavenumber (fre-
quency), the spectra are normalized to a constant penetration
depth.
D The conversion from ATR spectra to absorbance spectra is
1000
based on the following formula: AB = ATR  ------------
X
E When logarithmizing reflectance spectra the reflectance val-
ues below 0.00001 will be levelled to a lg(Refl) intensity of 5:
log Refl = – log  Refl 
F To convert logarithmized reflectance spectra the following for-
– lgRefl
mula is used: R = 10
G When converting single-channel spectra the start and end fre-
quencies of a single-channel Raman spectrum will be trans-
formed using the following equations:
FXV  Raman  = RLW – FXV  ScSm 
LXV  Raman  = RLW – LXV  ScSm 
RLW means Raman Laser Wavenumber. This value is regis-
tered within the instrument parameter block of the Raman file
created. OPUS uses the ScSm abbreviation to indicate a sin-
gle-channel sample spectrum. FXV represents the start fre-
quency, LXV the end frequency.
H To convert Raman spectra the following equation applies for
the respective conversion direction selected:
FXV  ScSm  = RLW – FXV  Raman 
LXV  ScSm  = RLW – LXV  Raman 
The RLW parameter belongs to the instrument parameter
block of the Raman spectrum.
I The value of the Raman laser wavenumber is required when
using the ScSM  Raman (G) conversion direction.

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8.10 S m ooth

Definition Based on the Savitzky-Golay algorithm this command

allows to smooth spectra. As experimental spectra
are superimposed more or less by noise interfer-
ences it may be required to smooth single spectra.

Principle The smoothing method is based on the Sav-

itzky-Golay algorithm. The number of smoothing
points are between 5 and 25.

Sm oothi n g.. .

• ...produces more meaningful spectra.

• ...improves S/N ratio.
• ...can produce over-smooth effects when improperly
applied, i.e. single spectra may disappear.
• ...decreases resolution.
• ...reduces spectral noise but also distorts signal intensi-
ties.

To s m o o t h a s p e c t r u m . . .

1 ...load a spectrum file and select the Smooth command.

2 If required, drag & drop the spectrum file into the File(s) to
smooth selection field.

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Figure 186: Smooth - Select Files

3 Define the number of smoothing points and click Smooth to

start the command.

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Interactive smoothing

To start interactive smoothing click the Start Interactive Mode but-

ton (figure 186). The following dialog opens:

A C

B
D

Figure 187: Interactive smoothing

A The slider is used to set the smoothing points interactively.

The currently used number of smoothing points is shown
below the slider.
B If you click Store, the loaded original spectrum file will be
changed. If you click Cancel, the changes made will not be
stored. In both cases the view will close.
C This window shows the original spectrum.
D This window shows the smoothed spectrum.

Figure 188 directly compares the original spectrum with the

smoothed one. The original spectrum band shows more pro-
nounced peaks.

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Figure 188: Smoothing effects on a spectrum

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8.11 Deriv a t i v e

Definition This command allows to manipulate the spectra such

that band positions of spectra can be located more
easily.

Principle The first to fifth derivative of a spectrum is calculated,

using the Savitzky-Golay algorithm. This algorithm
allows a simultaneous smoothing of the spectrum.
The smoothing effect reduces the noise substantially
generated by derivation.

To p e r f o r m a d e r i v a t i v e . . .

1 ......load a spectrum file and select the Derivative command.

2 If required, drag & drop the spectrum file into the File(s) to
derivate selection field.

Figure 189: Derivative - Select Files

3 Define the number of smoothing points and the derivative

order. Note: The minimum number of smoothing points

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 Derivative Chapt. 8

depends on the derivative order. The higher the deriva-

tive order, the more smoothing points need to be set.
You can set a maximum of 25 points.
4 Click Process to start the derivative.

The derivative result is displayed as...

...a data block indicating the actual derivative order of the original
spectrum. If a spectrum of 1st order is subject to a 1st order deriva-
tion again, the result will be a 2nd order spectrum. The kind of deriv-
ative order is displayed in the data block of the resulting spectrum.

3rd and higher order derivations are symbolized as n derivation.

The derivative order is stored in the parameters of the derivation
data block. Right click the spectrum file in the browser and select
the Show Parameters command from the pop-up menu.

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8.12 Freque ncy Calibration

Definition This command allows to re-calibrate the x-axis of a

spectrum. Note: Spectra measured using OPUS
are automatically frequency-calibrated.

Principle • Load the spectrum file.

• Select the Frequency Calibration command.
• If required, drag & drop the spectrum file into the
File(s) to calibrate frequency selection field.
• Define the current frequency values. Enter the
respective values into the Old frequencies entry
fields, i.e. factor M and addend A (see also
chapter 8.12.1).
• Click Calibrate to start this manipulation command.

Figure 190: Frequency Calibration - Select Files

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 Frequency Calibration Chapt. 8

A ft e r c a l i b r a t i o n . . .

...you can have the parameter list displayed. Right click the name
of the spectrum file in the OPUS browser. Select the Show
Para-meters command from the pop-up menu.

Figure 191: Parameter list after frequency calibration

A The frequencies of the first and last data point have been-
changed.
B The two new frequency values, factor M (Mult. for Freq. Calib)
and addend A (Add for Freq. Calib.) have been included in
the parameter list.

Undo frequency calibration

The two current frequencies are stored in the spectrum data block
after calibration. This allows to undo the calibration.

1 Select the Frequency Calibration command once again.

2 Activate the Restore original calibration check box.

3 Click Calibrate.
4 In the parameter list the frequencies of the first and second
data point need to display the original calibration values. The

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two parameters Mult. for Freq. Calib. and Add for Freq.
Calib. need to have the default values 1 and 0.

Figure 192: Parameter list with original calibration values

8.12.1 Frequency Calibration Theory

The two parameters factor M and addend A (see figure 193) have
to be entered as current frequencies.

M A

Figure 193: Current frequencies

These parameters change all of v alt x-values of the data points as

follows:

new = old x M + A (or fnew = fold x M + A)

The x-axis of a spectrum can be modified several times. At first, the

equation reads:

 old ,1 =  old  M 1 + A 1

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 Frequency Calibration Chapt. 8

and later:

 new ,2 =  new ,1  M 2 + A 2

For the first run, select the M1 and A1 parameters, and for the sec-
ond the M2 and A2 parameters. The parameter list will then include
the Mtotal and Atotal parameters, which represent the total change
compared to the original calibration.

 new ,1 =  old  M 1 + A 1

 new ,2 =  new ,1  M 2 + A 2

 new ,2 =  old  M total + A total

   old  M 1 + A 1   M 2 + A 2 =  old  M total + A total

 M total = M 1  M 2

A total = A 1  M 2 + A 2

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8.13 R am a n Correction

Definition This command allows to correct the intensity of single

bands of a Raman spectrum. The special features of
the optics and the frequency-dependant scattering
that occur in Raman spectra can almost be elimi-
nated using this command.

Principle • Load the spectrum file (Raman spectrum only).

• Select the Raman Correction command.
• If required, drag & drop the spectrum file into the
File(s) for Raman Correction selection field.
• Define the appropriate method on the Correction
Method tab and select the reference file (see the
description below).
• Click Correct to start this manipulation command.

Figure 194: Raman Correction - Select Files

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A ft e r c o r r e c t i o n . . .

...you can have the correction parameters displayed. Right click

the name of the spectrum file in the OPUS browser. Select the
Show Parameters command from the pop-up menu.

The correction parameters are stored in the Instrument Parameters

list.

Figure 195: Raman correction parameters

Thus, it is avoided that the same correction is performed several

times. Ensure that the Raman laser wavenumber and the source
temperature have not changed just before performing the correc-
tion.

Undo Raman correction

1 Select the Raman Correction command once again.

2 Activate the Restore original data check box on the Correc-
tion Method tab.

3 Click Correct.
4 The correction parameters need to display the original cor-
rection values.

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C o r r e c t i o n M e t h o d ta b

A C

Figure 196: Raman Correction - Correction Method

A Activating the Scatter correction check box corrects the

dependence between scattered radiation and excitation fre-
quency.
B Activating the Reference Correction check box corrects the
influence which the optics has on the spectrometer. Note:
The spectrum of the diffusely scattered light of a halogen
lamp used to correct the FT-Raman sample spectrum
should be measured as soon as possible after acquiring
data of the FT-Raman sample spectrum. If the instrument
alignment has been changed (e.g. after beamsplitter
exchange or any service action), the instrument back-
ground function changes as well. If no active instrument
realignment has been done, the time distance between
the correction spectrum and the sample spectrum should
be not more than 4 weeks. The used halogen lamp oper-
ates at a temperature of 2.300K and has a life time of
more than 10.000h's. Therefore, no change in its emis-
sion characteristics is expected.

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C To select the correction spectrum, which is almost similar to

the one acquired by the Black Body command, click this but-
ton. The name of the spectrum file selected is displayed
accordingly:

Note: If the sample spectrum and the reference lamp

spectrum do not match in your data point grid, select the
Make Compatible command from the Manipulate menu
(see also chapter 8.8).

8.13.1 Raman Correction Theory

4
Rayleigh's  law relates the scattering as a function of the wave-
number. This effect increases with the spectral distance of the line
of interest to the wavenumber of the Raman laser. In case of scat-
ter correction the Raman spectrum is multiplied point by point
using:   Laser    4

In case of reference correction the point-to-point multiplication for

the Raman spectrum to be corrected will be as follows:

(Black Body spectrum) (Raman spectrum)

(Reference spectrum)

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8.14 B l a c k Body

Definition This command allows to calculate the emission spec-

trum of a black body. The frequency range and data
point grid used to calculate the curve are both based
on a reference spectrum. This also applies to the
units of the x-axis (frequency or wavenumber).

Principle • Load the spectrum file.

• Select the Black Body command.
• If required, drag & drop the spectrum file into the
File(s) to compute black body spectrum for selection
field.
• Define the temperature of the black body.
• Activate the appropriate option button for calculating
energy or photon distribution.
• Click Calculate to start this manipulation command.

Figure 197: Black Body - Select Files

A The black body (light source) temperature will be indicated in

Kelvin. It is stored as TMP parameter together with the calcu-
lated distribution.

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B Optionally, the energy distribution or flux density of the pho-

tons (depending on the frequency or wavenumber) can be
calculated.

In case of Raman spectra...

...the x-axis is displaced such that the Raman laser signal is at 0

wavenumbers and the Stokes spectral range includes positive
wavenumbers. The Raman laser wavelength is determined by the
RLW parameter of the spectrum measured, and can be manually
set to 9394cm-1.

A ft e r c a l c u l a t i n g t h e e m i s s i o n s p e c t r u m . . .

...a datablock for a single-channel sample spectrum ( ) is dis-

played in the OPUS browser. This datablock contains the corre-
sponding parameter values.

8.14.1 Black Body Theory

The radiative properties of a black body are only determined by its

temperature. This enables an approximation of the true light source
spectrum, assuming that a single-channel spectrum of the light
source is available.

Figure 198 shows the radiation spectrum of a black body at a tem-

perature of 1000K.

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 Chapt. 8 Manipulate

Figure 198: Radiation emitted by a black body at 1000K

The energy and photon flux of a black body is determined by:

8
10 hc 2  3
• Energy per wavenumber: y = 2-----------------------------
100hc
------------------
e kT –1
– 15
10 c 2-
• Photon flux per wavenumber: y = 2---------------------------
100hc
------------------
e kT –1

With:
• T = Temperature [K]
• c = 2.99792458 x 108 [ms-1]
• h = 6.626176 x 10-34 [m2kgs-1]
• k = 1.380662 x 10-23 [m2kgs-2K-1]
•  = Wavenumber [cm-1]

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 Interferogram to Spectrum Chapt. 8

8.15 I n t erf erogram to Spectrum

Definition This command allows to convert an interferogram into

a spectrum and performs the same operations which
immediately run after AQP data acquisition:

• Apodization
• Phase computation
• Zerofilling
• Fourier Transformation of the interferogram
• Phase correction

Thus, you can repeat spectra calculation after mea-

surement, using different parameter settings for apo-
dization, zerofilling and phase correction.

Principle • Load the file (interferogram only). The sample or

background interferogram calculated is always a
single-channel spectrum.
• Select the Interferogram to Spectrum command.
• If required, drag & drop the spectrum file into the
File(s) to convert selection field on the Select Files
tab.
• Click Convert to start this manipulation command.

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 Chapt. 8 Manipulate

Figure 199: Interferogram to Spectrum - Select Files

The different tabs are described in the following.

Apodization

On this tab you select the apodization function and zerofilling fac-
tor.

A detailed description of the apodization function would go beyond

the scope of this manual. In case of standard measurements in liq-
uid or solid phases the Blackman-Harris-3-term function is recom-
mended. To obtain the highest resolution, you either select no
(Boxcar) or at best a weak apodization function (Norton-Beer,
Weak).

Zerofilling means adding zeros to both ends of the interferogram

before performing Fourier transformation. This increases the num-
ber of data points in the spectrum, which is equivalent to an inter-
polation. The number of data points can be increased by zerofilling
using the factors selected (e.g. 2, 4, 8,..., 512).

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 Interferogram to Spectrum Chapt. 8

Figure 200: Interferogram to Spectrum - Select Files

A This drop-down list allows to select the appropriate appodiza-

tion function. Due to the finite mirror travel, the interferogram
is only recorded up to a certain point (i.e. a finite resolution).
This leads to artificial side lobes on spectral lines which natu-
ral width is smaller than or comparable with the measured
resolution. These side lobes can be suppressed, however at
the expense of line broadening, by multiplying the interfero-
gram using an apodization function.
B This drop-down list allows to select the zerofilling factor. In
case of a zerofilling factor of 1, zeros are added up to the next
power of 2. If the number of data points has already been a
power of 2, no zeros will be added.
Single-sided interferograms require a minimum zerofilling fac-
tor of 2. In case of double-sided interferograms, the zerofilling
factor can be halved in comparison to single-sided interfero-
grams.
By increasing the number of data points in the spectrum, the
depiction improves by round band shape (a mere cosmetic
effect). However, an n-fold zerofilling requires an n-fold com-
puting time and n-fold storage space (depending on the com-
puting method).

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L i m i t D a ta

On this tab you select the resolution and define which direction of
mirror travel has to be considered during conversion.

Figure 201: Interferogram to Spectrum - Limit Data

A If you activate the check box, you can vary the resolution
entering a value which is greater than or at least equal to the
value used during measurement. In this case only a fraction
of the measured interferogram is used for computation.
B In this group field you specify how precise the phase has to
be determined. Generally, you should enter the same value
as being used for the measurement. The value is limited by
the length of the double-sided part of interferogram.
C In case of interferograms recorded in forward/backward mode
you can specify which direction(s) of mirror travel have to be
evaluated during transformation. If both mirror travels should
be evaluated, the forward and backward scans will be trans-
formed separately, phase corrected and averaged.
D If data have been recorded in multiplex mode, the interfero-
gram contains alternating data from two analog-to-digital con-
verters (ADCs). The Even and Odd option allow the data from

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 Interferogram to Spectrum Chapt. 8

both ADCs to be evaluated separately. There is no such

option in case of backward scans. Therefore, record multiplex
measurements only by using the forward mode.
If you activate the Even option button, the intensity values I0,
I2 ... of the first ADC will be transformed. If you activate the
Odd option button, the intensity values I1, I3 ... of the second
ADC will be transformed.

Phase Correction

On this tab you define the phase correction mode. The phase cor-
rection can be compared with an interferogram symmetrizing,
which is always necessary due to the asymmetry of any measured
interferogram.

Figure 202: Interferogram to Spectrum - Phase Correction

A This drop-down list contains different kinds of phase correc-

tion modes. Select an appropriate mode.
• Mertz: this is the standard procedure for phase cor-
rection, based on the spectrum. Peak search is per-
formed within a limited range.

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• Mertz Signed: modified Mertz function which is used

if the single-channel spectrum is expected to contain
negative contributions.
• Power Spectrum: this can be used instead of Mertz
or Foreman, but only for double-sided interfero-
grams, if the spectrum includes wide ranges of low
light intensity (total absorption, Raman, emission).
Disadvantage: up to 2 more noise compared with
Mertz or Forman.
• Power/No Peak Search: recommended in case of a
temporarily very low signal (e.g. air bubble), or emis-
sion measurements; no peak position is determined
during the current measurement, a stored peak posi-
tion is used instead, which has been determined
during a former measurement, with the signal being
much higher.
• Mertz/Stored Phase: like Mertz, whereas the phase
is not re-calculated but based on previously existing
data which have been calculated, using the regular
Mertz method.
This method can be useful, if the single-channel
spectrum includes less-defined ranges (i.e. an unde-
fined phase), which frequently occurs in case of
emission measurements. Furthermore, it can also
be useful if the spectra are expected to contain neg-
ative contributions. In this case, the phase stored
should derive from a spectrum with absolute positive
values.
• No/Save Complex Data: the data will not be
phase-corrected but Fourier-transformed in complex
form and stored as real and imaginary parts.
• Forman: phase correction based on the interfero-
gram, mathematically equivalent to Mertz, offers a
slightly higher precision which requires, however,
higher a computational period.
• Forman/Preapodized: like Forman, whereas the cor-
rection requires preapodized data, as no internal
apodisation is performed.
• Doubled Phase: the interferogram is self-convolved
and produces a double phase in the spectrum.

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 Interferogram to Spectrum Chapt. 8

• Mertz Full Range Peak Search: like Mertz, whereas

the peak search involves the complete spectral
range.
B You can drag & drop a data block of a stored phase (e.g.
for sample phase or for reference phase) into this
field. Use phase data block types only, other ones will not be
accepted.

Non-Linearity

This tab allows to perform a non-linearity correction. After phase

correction the non-linearity correction coefficients are calculated,
using all the data points of the single-channel spectrum.

Figure 203: Interferogram to Spectrum - Non-Linearity

A To perform a non-linearity correction you have to activate this

check box.
B If you use a preamplifier which reverses the signal polarity,
the value of the detection limit has to be multiplied by -1.
C The modulation efficiency causes an additional multiplicative
correction of the entire spectrum. It can be set either to the
correct value (typically between 0.7 and 1.0), or to 1.0 if the
correct value is unknown.
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What has to be considered in case of non-linearity?

In a single-channel spectrum there should be no signal below the

absorption edge of the detector. The non-linear detector response
causes the signal to be non-zero below this edge.

The non-linearity of the detector can be calculated from the ratio of

the intensity of these artifacts and the total energy flow in the
detector. As soon as this non-linearity is known a corrected spec-
trum can be calculated showing less artifacts.

As a rule, the interferograms stored will not be modified. The

non-linearity correction only effects the spectra.

To ensure a successful non-linearity correction the following condi-

tions have to be fulfilled:
• The measurement must be performed from 0cm-1 up to
the maximum wavenumber at which the detector can
send a signal.
• Electronic filters must not be used. Spectra have to
undergo a broad-band recording to avoid aliasing.
• The phase resolution parameter on the FT tab of the
Advanced Measurement command (see chapter 7.1.5)
should be set to result in at least 500 phase interfero-
gram points. Too low a phase resolution results in an
inaccurate non-linearity correction.

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 Interferogram to Spectrum Chapt. 8

Peak Search

This tab allows to select the position of the zero path difference
(ZPD).

Figure 204: Interferogram to Spectrum - Peak Search

A This drop-down list is used to select the peak search mode for
ZPD. The single modes are described in the following.
• Absolute largest value searches the peak with the
highest absolute intensity.
• Maximum searches the highest peak with the largest
positive value.
• Minimum searches the lowest peak, if known that the
peak has a negative intensity.
• Mid between Min./Max. calculates a value between
the minimum and maximum limit.
• No peak search uses the position saved in the inter-
ferogram. If this value is known, it can be entered
manually.
• Mid between largest two searches the peak between
the two largest values.
• Take from stored phase uses the value calculated for
the phase stored.

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The position of the peak can be influenced, considering addi-

tional data points apart from the range evaluated by one of
the peak search modes mentioned before.
Each position will be tested for its symmetry or asymmetry.
The position with the highest symmetry will be defined as
ZPD.
B To optimize the position define the number of positions to be
tested.
C These option buttons allow to define the symmetry of the
inteferogram.

St o r e

This tab allows to select the frequency range for the spectrum file
and define which kind of spectrum has to be additionally stored.

Figure 205: Interferogram to Spectrum - Store

A The frequency range of the original files has to be between

the upper and lower folding limit parameters used during
measurement.
B In addition to the spectrum calculated, which is always a sin-
gle-channel spectrum, you can also save the phase and

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 Inverse FT Chapt. 8

power spectrum. The latter two spectra are calculated by the

double-sided known part of the interferogram, using the
phase resolution setting made.

8.16 Inver se FT

Definition This command transforms a spectrum into an

inter-ferogram, and can be used for all types of spec-
tra.

Principle • Load the spectrum file.

• Select the Inverse FT command.
• If required, drag & drop the spectrum file into the
File(s) for Inverse FT selection field.
• Define the symmetry assumption.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Inverse FT to start this manipulation com-
mand.

Figure 206: Inverse FT - Select Files

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 Chapt. 8 Manipulate

A You have to specify whether the spectral data are part of a

symmetric or antisymmetric interferogram. Generally, you
activate the Normal symmetry option button, as antisymmetric
interferograms only occur in special cases, e.g. complex
spectra.

Note: Interferograms symetrically generated only contain

values on the positive side of the x axis. Therefore, in
case of Fourier transformation you have to define
how these values have to be completed on the nega-
tive side.

8.17 Pos t Z ero f illin g

Definition This command allows to increase the digital resolu-

tion of a spectrum, i.e. to create more data points per
wavenumber.

This is especially useful for the peak picking in case

of high-resolution spectra, as the result will be
smoother spectra plots. When calculating spectra a
zerofilling is performed, indicating the Zerofilling fac-
tor. This kind of zerofilling increases the digital resolu-
tion of spectra within the entire spectral range.

Note: The advantage of post zerofilling is that

only the spectral range of interest will be interpo-
lated, which allows to save storage space.

Principle • Load the spectrum file.

• Select the Post Zerofilling command.
• If required, drag & drop the spectrum file into the
File(s) to post zerofill selection field.
• Select the additional zerofilling factor.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Zerofill to start this manipulation command.

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 Post Zerofilling Chapt. 8

Figure 207: Post Zerofilling - Select Files

A This drop-down list allows to specify the additional zerofilling

factor. The possible values range from 1 to 512.

Example 1:

• A spectrum with a digital resolution of 8 cm-1 is post

zerofilled by an additional zerofilling factor of 2.
• The digital resolution after the interpolation is 4 cm-1.

Example 2:

• A spectrum with a digital resolution of 8 cm-1 is post

zerofilled by an additional zerofilling factor of 8.
• The digital resolution after the interpolation is 1 cm-1.

In both cases the digital resolution has been 8 cm-1. To avoid arti-
facts allow at least 50 more data points on each side of the desired
interval. This frequency range must also contain meaningful spec-
tral information.

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 Chapt. 8 Manipulate

If you click the Zerofill button (figure 207), the spectra file(s)
selected will be interpolated using the additional zerofilling factor
specified.

Figure 208 exemplifies a post zerofilling factor of 4. The interpo-

lated curve definitely includes more (quadruple) data points as the
original data.

before zerofilling

Figure 208: Digital resolution before and after post zerofilling

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 Fourier Self-Deconvolution Chapt. 8

8.18 F o urier S elf-Deconvolution

Definition This command allows to enhance the apparent reso-

lution of a spectrum, or to decrease the lines width.
Spectral ranges comprising broad and overlapping
lines can thus be separated into sharp single lines.

Note: The Fourier self-deconvolution is only use-

ful in case of lines which are substantially
broader than the spectral resolution.

Principle • Load the spectrum file.

• Select the Fourier Self-Deconvolution command.
• If required, drag & drop the spectrum file into the
File(s) to deconvolute selection field.
• Define the line shape either interactively or by using
the Adjust tab.
• Specify a deconvolution and noise reduction factor,
or alternatively define a factor for the band width
and resolution enhancement. This can be done
either interactively or by using the Adjust tab.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Deconvolute to start this manipulation com-
mand.

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Figure 209: Fourier Self-Deconvolution - Select Files

Interactive Mode

To start the interactive mode click the Interactive button (A in

figure 209). Clicking this button opens the following view:

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 Fourier Self-Deconvolution Chapt. 8

Figure 210: Interactive view of Fourier self-deconvolution

A The slider is used to specify the bandwidth or noise reduction.

The values set are displayed at the lower end of the slider.
B The appropriate line shape type depends on the line-broad-
ening procedure. In case of doubt it is recommended to
assume a Lorentzian shape and activate the respective
option button.
C If you click Store, the interactive view closes. The deconvo-
luted spectrum will be displayed in the spectrum window.

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 Chapt. 8 Manipulate

Adjust Parameter

If you do not work in the interactive mode, you can also make the
settings required by using this tab.

Figure 211: Deconvolution - Adjust Parameter

8.18.1 F o u r i e r S e l f - D e c o n v o l u t i o n T h e-
ory

The Fourier Self-Deconvolution (FSD) assumes that the spectrum

to be measured consists of well-resolved lines which have been
convoluted (broadened) by the same type of line-broadening func-
tion (LBF).

If the shape and width of the LBF are known, its effect can be arith-
metically excluded from the spectrum. It is recommended to per-
form this arithmetic exclusion on the basis of the interferogram as
in this case the deconvolution is equivalent to a simple interfero-
gram division caused by the LBF Fourier transformation.

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 Fourier Self-Deconvolution Chapt. 8

Deconvolution

In general, the deconvolution corresponds to a multiplication of the

interferogram I(x) using the exp(a*x) deconvolution function for
Lorentzian and exp(a*x2) for Gaussian shapes, which intensifies
the interferogram edges. The deconvolution factor is the maximum
value of these functions at the end of the interferogram.

Deconvolution factors of 100, 1000 and 5000 correspond to a max-

imum amplification of 3.4, 12.8, and 40 in case of Lorentzian
shapes, and 1.06, 3.2 and 16 in case of Gaussian shapes. If you
work with Lorentzian shapes it is recommended to increase the
deconvolution factor in the order 50, 100, 1000, 5000, and to stop if
the resultant spectrum shows artificial oscillations.

Signal-to-Noise Ratio

The amplification of the interferogram caused by self-deconvolution

also amplifies both the signal and noise. However, especially on
the interferogram edges the signal-to-noise ratio is worse than at
the centerburst.

To avoid the increase of noise, a Blackman-Harris apodization is

simultaneously performed such that the interferogram is multiplied
by the result of an ascending deconvolution function and a
descending apodization function. The apodization function value is
1.0 at the beginning and 0 at the end of the interferogram. Between
these two limits the value exhibits a maximum.

Noise Reduction

The noise reduction factor should range from 0.0 to 1.0. It is the
fraction of the interferogram, which apodization function has been
decayed to 0 and thus used for evaluation.

A value of 1.0 corresponds to the full interferogram length. It is rec-

ommended to start with a value of 0.5 (half interferogram length). If
the spectrum has been calculated using a zero filling factor >2, a
start value of 1/(zerofilling factor) is recommended to reduce noise.

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 Chapt. 8 Manipulate

Example

Figure 212 shows a spectrum before and after a deconvolution has

been performed, using the parameters shown in figure 211.

The intensity at the maximum of a deconvoluted spectrum line is

usually higher, in relation to its edges, than of an original spectrum.
However, the peak ratios are not changed. The deconvoluted spec-
trum always depicts the higher maxima.

Deconvoluted spectrum

Original spectrum

Figure 212: Spectrum before and after Fourier self-deconvolution

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 Symmetric FT Chapt. 8

8.19 S y mme tric FT

Definition This command is used if a phase correction is not

necessary, e.g. if the interferogram has been gener-
ated by inverse Fourier Transformation, or does only
include one half of a scan, relative to the highest
maximum.

Principle • Load the spectrum file (only spectrum files with

interferogram data blocks).
• Select the Symmetric FT command.
• If required, drag & drop the spectrum file into the
File(s) for symmetric FT selection field.
• Specify the symmetry assumption.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Symmetric FT to start this manipulation com-
mand.

Figure 213: Symmetric FT - Select Files

A Generally, you check the Normal symmetry option button. If,

however, the interferogram has been generated by inverse
Fourier transformation using the antisymmetric function,
check the Antisymmetric option button.
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 Chapt. 8 Manipulate

The result will be...

...a single-channel spectrum. In case of an antisymmetric transfor-

mation only the positive part of the single-channel spectrum will be
saved.

8.20 Kramers-Kronig-Transforma-
tion

Definition This command is used if a phase correction is not

necessary, e.g. if the interferogram has been gener-
ated by inverse Fourier Transformation, or does only
include one half of a scan, relative to the highest
maximum.

Principle • Load the spectrum file.

• Select the Kramers-Kronig-Transformation com-
mand.
• If required, drag & drop the spectrum file intothe
File(s) for Kramers-Kronig transformation selection
field.
• Define the calculation option.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click KKT to start this manipulation command.

C o n d i t i o n s r e q u i re d f o r a s u c c e s s f u l
K r a m e r s - K r o n i g - Tr a n s f o r m a t i o n

• The sample has to consist of a pure, homogeneous

material (neither mixtures, layered systems nor pow-
ders).
• The beam has to be measured in specular (not diffuse)
reflection at nearly normal incidence (e. g. 100 unit).

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 Kramers-Kronig-Transformation Chapt. 8

• The sample must be optically thick (half-space) to

ensure that no light returns from the inner sample to the
sample surface (e.g. after reflection on one back edge).
Especially, multiple reflections and interferences have to
be avoided. If the sample is not thick enough to absorb
all radiation, roughen the backside to prevent possible
reflection.
• The spectral cut-off has to fall in a moderately flat and
unstructured range. It must not be interrupted among
significant structures.

A B

Figure 214: Kramers-Kronig-Transformation - Select Files

A If you activate one of these two option buttons, the result file
includes two data blocks: the real and imaginary part of the
functions indicated by R or I on the data block ( ).
B If an absorbance spectrum is calculated, it only includes pure
absorption contributions, but no reflection losses. To be able
to compare the absorbance spectrum directly with a transmis-
sion spectrum, you have to consider the reflection losses at
both boundaries of the sample layer by means of the correc-
tion -2 lg (1 - [Input - Reflectance spectrum]), using the OPUS
spectrum calculator.

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 Chapt. 8 Manipulate

Note: For a separate description on the theory and applica-

tion of Kramers-Kronig-Transformation as well as
some exemplary spectra refer to Appendix A.

8.21 S p l i t I n t erferograms

Definition This command allows to split interferograms.

Principle • Load the spectrum file. Note: The spectrum file

has to contain an interferogram data block. You
can use single spectra files or 3D files.
• Select the Split Interferograms command.
• If required, drag & drop the spectrum file and the
respective data block into the File(s) to split selec-
tion field.
• Click Split Interferograms to start this manipulation
command.

Figure 215: Split Interferograms - Select Files

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 Split Interferograms Chapt. 8

Basic Features

Due to measurement reasons interferograms are not continuously

but selectively acquired. An efficient acquisition can be achieved
using rapidly scanning interferometers.

Each interferogram can only be acquired up to a maximum limited

path length difference, which is due to experimental restrictions.
Therefore, the spectral resolution is reciprocally proportional to the
maximum path length difference.

Depending on the acquisition mode selected during measurement

you can split interferograms. Splitting interferograms allows to
increase the time resolution, in case of time-resolved measure-
ments (TRS).

If you have selected the Double Sided acquisition mode, two inter-
ferograms will be generated during splitting. In case of a dou-
ble-sided Forward-Backward acquisition mode, four interferograms
will be generated during splitting. This yields to the maximum pos-
sible time resolution of single spectra at a given mirror velocity.

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 Chapt. 8 Manipulate

8.22 S p e c t rum from Interfero -

grams

Definition This command is used to create a spectrum by com-

paring a sample interferogram with a reference inter-
ferogram. This kind of result spectrum can either be
displayed in absorption or transmission.

Principle • Load a sample interferogram and then a back-

ground interferogram.
• Select the Spectrum from Interferograms command.
• If required, drag & drop the respective data block
into the Sample interferogram(s) and Background
interferogram selection field. Note: The interfero-
gram files include the parameters set during
measurement.
• Select the respective result spectrum format.
• Click Calculate to start this manipulation command.

Figure 216: Spectrum from Interferograms - Select Files

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 Extrapolation Chapt. 8

8.23 E x t rapolation

Definition This command allows to extrapolate reflectance

spectra to 0cm-1 or to an upper frequency limit select-
able by the user. The previous wavenumber ranges
are used without being modified. In case of extrapola-
tion to 0cm-1 it is distinguished between insulators
and semiconductors. OPUS interprets the sample as
semiconductor if the input for R (0cm-1) is 1.

Principle • Load the spectrum file.

• Select the Extrapolation command.
• If required, drag & drop the spectrum file into the
File(s) to extrapolate selection field.
• Specify a value to be reached for R.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Extrapolate to start this manipulation com-
mand.

Figure 217: Extrapolation - Select Files

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 Chapt. 8 Manipulate

8.23.1 E x t r a p o l a t i o n t o 0 c m -1

The R0 and i1 parameters are used for the extrapolation to 0cm-1.

R0 can be any value between 0 and 1. i1 represents the inner limit
of the wavenumber interval which the approximate function for the
extrapolation has to fit to.

The beginning of the original spectrum will be selected as the sec-

ond limit i2. If in case of i1 a wavenumber smaller than the lower 
limit of the original spectrum has been specified (i.e. no overlap-
ping range), i1 will be set to include two data points to fit the func-
tion.

Figure 218: Parameters used for extrapolation

Theory of extrapolating n to 0cm-1 in case

of semiconductors

The approximation function is:

a 42
 4 = 1 – a 4  + -----  + a 5  1 5
2
As R  s  =   s  has already been specified (with s being the wav-
enumber of the spectrum beginning), the a5 coefficient can be elim-
inated:
a 42
R  s  = 1 – a4 s + ----- s + a 5  1 5
2
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 Extrapolation Chapt. 8

a2
R  s  – 1 + a 4 s – ----4- s
2-
a 5 = --------------------------------------------------
s 1  5

The remaining function is:

a 42  a 42    1 5
4 = 1 – a4  +  + R  s  – 1 + a 4 s – ----- s ---
----
-
2  2   s
Now, specify a4 in a way that the sum of all error squares within the
overlapping area can be minimized.

Theory of extrapolating n to 0cm-1 in case

of insulators

The approximation function is:

1 = R  0  + a1  2 + a2  4

As R  s  =   s  has already been specified (with s being the wav-

enumber of the spectrum beginning), the a2 coefficient can be elim-
inated:

R  s  = R  0  + a1 s 2 + a2 s 4
R  s  – R  0  – a1 s2
a 2 = ---------------------------------------------
s4
The remaining function is:
 4
 1 = R  0  + a 1  2 +  R  s  – R  0  – a 1 s 2   ---
s
Now, specify a1 in a way that the sum of all error squares within the
overlapping area can be minimized.

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 Chapt. 8 Manipulate

8.23.2 Extrapolation to  (infinity)

The R  , i1 and  end parameters are used for extrapolating to  .

R  and i2 are equivalent to R0 or i1 used in case of extrapolating to
0cm-1.  end represents the wavenumber up to which the extrapola-
tion has to be performed.

Approximation for extrapolating n to 

The approximation function is:

a a
 3 = R    + ----1- + ----2-
2 4
As R  t  =   t  has already been specified (with t being the wave-
number of the spectrum end), the a2 coefficient can be eliminated:
a a
R  t  = R    + ----1- + ----2-
t2 t4
a
a 2 =  R  t  – R    – ----1- t 4
t2
The remaining function is:
a t 4
 3 = R    + a 1  2 +  R  t  – R    – ----1-  ---
t2 

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 Extended ATR Correction Chapt. 8

8.24 Extended ATR Correction

Definition The Extended ATR (Attenuated Total Reflection) Cor-

rection command corrects spectra, which have been
measured by using an ATR unit, in such a way that
the position and intensity of the absorption bands are
similar to those of a spectrum acquired in transmis-
sion mode. The correction method allows to measure
even highly-absorbing samples or dark polymers by
using a ZnSe or diamond ATR unit.

Principle • Load the spectrum filea measured by an ATR unit

(only spectrum files with AB or ATR data blocks;
3D spectra files are also possible if the addi-
tional 3D package is registered in OPUS).
• Select the Extended ATR correction command.
• Select the correction method (see the description
below).
• Click the Calculate button to start this manipulation
command.b
a. Make sure that the spectrum does not contain any ranges with
strong noise. Otherwise, use the Cut or Straight Line Generation
command from the Manipulate menu to modify these ranges. The
extended ATR correction is sensitive to noise, which may lead to
wrong results in case of very noisy spectra.
b.The result spectrum is saved in the ’ATR’ data block, and overwrites
the original spectrum saved in the ’AB’ or ’ATR’ data block.

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 Chapt. 8 Manipulate

Figure 219: Extended ATR correction - Select Files

A The Standard correction method is suited for most sample

types (non carbon-filled, normal refraction index). The ATR
crystal material can be made of ZnSe or diamond. The
method uses the following parameters:
• ATR angle of incidence: 45°
• Mean refraction index of sample: 1.50
• Number of ATR reflections: 1
B The Black Rubber correction method is suited for black car-
bon-filled rubber samples, e.g. O-rings, tyres etc., and uses
the following parameters:
• ATR angle of incidence: 45°
• Mean refraction index of sample: 1.71
• Number of ATR reflections: iteratively changed until an opti-
mum result has been achieved
C The expert mode allows to modify the default parameters. If
the expert mode is activated, the following setting options are
displayed:

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 Extended ATR Correction Chapt. 8

a The value entered defines the number of reflections which

occurred at the boundary between sample and ATR crystal.
Most ATR units have only one reflection, and their resulting
evanescent field may not be completely covered by the
sample. Only liquids can cover the crystal completely.
When measuring powders or other solids the actual value
can be lower than the theoretical one.
Typically, the actual value is between 0.6 and 1.0. It is
advisable to use an initial value of 1.0 for the number of
reflections.
b The value entered defines the angle of incidence with
regard to the surface normal of the ATR crystal.
This value is 45° for all standard fixed-angle ATR units.
c The value entered specifies the mean refraction index of
the sample within the measured frequency range. The typi-
cal refraction index is at around 1.5 for most samples, e.g.
non-blackened polymers. In case of black carbon-filled
samples the index is at around 2, in general.
If the mean refraction index of the sample is not known, it is
advisable to use an initial value of 1.5 and refine this value
iteratively, if required.
d The following material can be selected for the ATR crystal:
- ZnSe (zinc selenide)
- germanium
- diamond

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 Chapt. 8 Manipulate

P h y s i c a l E f f e c ts

The correction is based on the following physical effects:

• In case of total absorption on the ATR crystal, the beam
penetration depth into the sample depends on the wave-
lenght of the beam:

(d: penetration depth,  : wavelength,  : incidence

angle of the measuring light with regard to the surface
normal of the ATR crystal, n 1 : refraction index of the
ATR crystal and n 2 : refraction index of the sample. This
results in modified band intensities, related to the wave-
number in the spectrum. The correction of this effect is a
simple spectra manipulation which is also used with the
OPUS Convert Spectra command.
• The incidence angle of the measuring light with regard
to the surface normal of the ATR crystal (typically: 45°)
has to be greater than the so-called critical angle:
 c = arc sin  n 2  n 1 

With n 2 being the refraction index of the sample, and n 1

being the refraction index of the ATR crystal. If the criti-
cal angle is not reached (e.g. due to a high n 2 ), there is
no total reflection on the ATR crystal, which may theoret-
ically result in infinitely high band intensities. The cor-
rection methods are able to correct even such errors.
• In case of transparent (non-absorbing) materials the
refraction index continuously decreases with the wave-
length of the light, which is called normal dispersion of
light. In case of absorbing materials, however, there is
the so-called anomalous dispersion in areas with high
absorption. This anomalous dispersion results in strong
fluctuations of the refraction index around the absorption
band. On the edge of the band with higher wavenum-
bers, the refraction index is lower than the average one,
and locally higher on the edge of the band with lower
wavenumbers (see figure 220).

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 Extended ATR Correction Chapt. 8

Figure 220: Course of the refraction index (n) around an

absorption band (k)

Since the refraction index has an effect on the penetra-

tion depth and critical angle, asymmetric bands and
artefacts as well as a band shift towards lower wave-
numbers may be detected in the spectrum. The correc-
tion methods1 take all these factors into account, and
corrects even strong spectral artefacts as exemplified in
figure 221:

1. All correction methods are based on the Advanced ATR Transformation by Koi-
chi Nishikida, N & K Spectroscopy, LLC, an Honorary Associate/Fellow, Materi-
als Science and Engineering, University of Wisconsin

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 Chapt. 8 Manipulate

Figure 221: Upper spectrum: uncorrected isocyanat spectrum, measured

by using a diamond ATR unit; lower spectrum: uses the
refraction index: 1.7 and number of reflections: 1.0 parame-
ters

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 1/cm <-> µm, nm Chapt. 8

8.25 1/cm <-> µ m, nm

Definition This command allows to change the x-axis (abscissa)

unit of a spectrum. Wavenumbers can be converted
into micrometer and nanometer, or vice versa.

Principle • Load the spectrum file.

• Select the 1/cm <-> µm, nm command.
• If required, drag & drop the spectrum file into the
File(s) to convert... selection field.
• Specify the conversion direction on the Select Files
tab.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Define the scaling of intensities on the Scaling tab.
• Click Calculate to start this manipulation command.

The different tabs are described in the following.

Select Files

Figure 222: 1/cm <-> µm, nm - Select Files

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 Chapt. 8 Manipulate

A To specify the conversion direction the drop-down list pro-

vides the following options:

Frequency Range, Precision

A
B

Figure 223: 1/cm <-> µm, nm - Frequency Range, Precision

A This check box is activated by default. Thus, the frequency

range from the original spectrum are used. If you want to
select the frequency range interactively (see also
chapter 2.9), you have to deactivate the check box.
B The maximal compression factor (MCF) can be defined using
the slider.
C In case of fixed frequency limits define the number of data
points in the result spectrum. If, however, the frequency limits
of each single input spectrum are used, the interpolation is
determined by the MCF (B).

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 1/cm <-> µm, nm Chapt. 8

Scaling

Figure 224: 1/cm <-> µm, nm - Scaling

A If you check this option button, the intensities will generally

not be changed. Interpolation effects only will play a more or
less important role. The spectrum appearance does not
change, the x-axis, however, will be substantially distorted.
B If you check this option button, the y-values are multiplied by
a frequency or wavelength-dependent factor (proportional to
1/x2). This preserves the integrals, provided the original spec-
trum and the new spectrum both use equivalent integral lim-
its.

8.25.1 Frequency Conversion Theory

The connection between wavenumber [cm-1] and wavelength [µm]

is based on the following formula:

Wavelength [µm] x wavenumber [cm-1] = 10000

Each wavenumber can be converted into a wavelength. Digitally

recorded spectra have no continuous data, but discrete data
points. OPUS saves these equidistant data points, e. g. two data

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 Chapt. 8 Manipulate

points per wavenumber. After the conversion, however, the data

points are no longer equidistant.

Wavenumber [cm-1] Wavelength [µm] Difference [µm]

400 25.00
1.19
420 23.81
1.08
440 22.73
0.99
460 21.74
0.91
480 20.83
0.83
500 20.00

Interpolation

Since OPUS always saves spectra as a set of equidistant data

points only, an interpolation must be performed after abscissa con-
version. The kind of interpolation for frequencies (or wavelenghts)
is determined by the MCF or the number of resulting data points.

The minimum number of data points for the micron spectrum cre-
ated is equivalent to the number of data points found in the cm-1
spectrum. The MCF defines the quality of the conversion properties
within the most inappropriate range, i. e. in the high frequency end
of the spectrum (wavenumbers) which is converted to the low
wavelength end (microns).

Example:

If, e.g., a factor of 5 is selected, 5 frequency intervals are con-

verted to 1 wavelength interval (distance between each data
point), which causes the loss of spectral information. The
ratios get better if lower wavenumbers (higher wavelengths)
are selected.

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 1/cm <-> µm, nm Chapt. 8

The MCF can vary between 0.5 and 50. However, the new spec-
trum has never fewer data points than the original spectrum.
Therefore, it may occur that the number of data points, e.g. starting
from a factor of 20, remain unchanged.

In case of a small MCF the number of data points of the new spec-
trum may become quite large. This depends on the upper and
lower frequency limits as well as on the distance of data points in
the original spectrum. By reconverting the new spectrum and com-
paring it with the original one it can be verified whether the factor
selected has been reasonable.

Example:

The upper left spectrum in figure 225 shows the original spec-
trum scaled in wavenumbers. On the right the spectrum has
been converted to wavelengths, with the intensities remaining
unchanged. In the lower left spectrum the intensities have
been converted without changing the integrals.

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 Chapt. 8 Manipulate

Figure 225: Examples of frequency conversion

The lower right spectrum shows the original spectrum (B)

which has been converted from wavenumbers to wavelengths
and reconverted for comparison. Spectrum (A) uses an MCF
of 1, spectrum (C) an MCF of 15. The number of data points
in (A) is about 10 times higher than in (C), and comes very
close to the original data.

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 Averaging Chapt. 8

8.26 Ave r aging

Definition This command allows to generate a new spectrum

from a set of original spectra of the same type. The
intensities of this new spectrum are calculated by
averaging the intensities of the original spectra.

Principle • Load several spectrum files.

• Select the Averaging command.
• If required, drag & drop the spectrum files into the
respective entry field.
• Define the settings required.
• Click Average to start this manipulation command.

Figure 226: Averaging - Select Files

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 Chapt. 8 Manipulate

A This option button is checked by default. Thus, the names of

the spectrum files are displayed in the selection field on the
right.
B If you check this option button, the dialog looks different (see
figure 227). You can now define the path of the spectrum files
using the Change Path button. The file names of the spec-
trum files can be entered manually into the respective entry
field.
To select the data block type two drop-down lists are avail-
able.

Figure 227: Averaging - Select Files

The average spectrum calculated includes the largest wave-

length range which is common to all original spectra.
C To update an already existing average spectrum activate the
check box.
An additional entry field will be displayed next to this check
box function in which you drag & drop the spectrum file to be
saved from the OPUS browser. If a file with the same file
name already exists, it will be added to the set of spectra to
be averaged, and overwritten by the result file.

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 Averaging Chapt. 8

D If you activate this check box, spectra files are weighted pro-
portionally to their number of scans during measurement.
E Activating this checkbox calculates the standard deviation of
single-spectra intensities from the average spectrum intensi-
ties. An additional entry field will be displayed (only if C has
been activated before) next to this check box function. If you
leave this entry field empty, a new file will be generated which
contains the standard deviation spectrum. If you drag & drop
a spectrum file from the browser into this entry field, this spec-
trum file will be updated.
F If you activate this checkbox, an identity comparison will be
performed between the original set of spectra and the aver-
age spectrum. This will result in an average report which
includes information on the single spectra used to create the
average spectrum.
The report also outlines how much each single spectrum
deviates from the average spectrum, and which frequency
ranges and method have been selected for averaging.
The single-spectra deviation is indicated in multiples of the
standard deviation to make the detection of outliers easier.
The Report Method button is enabled as soon as you have
activated the Compute Av. report check box. Select the
respective kind of method used to calculate the spectral dis-
tance by clicking this button.

8.26.1 Av e r a g i n g T h e o r y

Averaging means to calculate the arithmetic mean of y identity val-

ues included in n original spectra:
n

i=1
yi
y = --------------------
n

The  standard deviation is:

n

2
 yi – y 
i=1
 = ------------------------------------
n–1

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 Chapt. 8 Manipulate

When comparing standard deviation spectra, calculated with and

without weighting the number of scans, the results will slightly differ
even if the number of scans is the same for all original spectra.

The reason is that the sum of 1 to n in the above equation is not

divided by n, but n-1. As n does not represent the number of spec-
tra but the number of scans when weighting, the results will differ
by a constant factor. This factor approaches 1 the more the number
of single spectra increases.

8.27 Merg e Spe c t r a l R a n g e s

Definition This command allows to merge several separate

spectra of the same type to a new spectrum. Any gap
left in the frequency region is filled by a straight line.

Principle • Load the spectrum files. Note: You can only use
one file type, i. e. either only absorption (AB) or
transmission (TR) spectrum files. Each spec-
trum file must contain a reference data block for
the single-channel spectrum ( ).
• Mark the result data block (e.g. or )
of the spectrum files in the browser.
• Select the Merge Spectral Ranges command.
• Click Merge to start this manipulation command.

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 Merge Spectral Ranges Chapt. 8

Figure 228: Merge Spectral Ranges - Select Files

What has to be observed?

If the original spectra overlap within one or more frequency ranges,

the spectra are weighted linearly to avoid the appearance of a step.

If the frequency range of one spectrum is completely overlapped by

a second one (i.e. one spectrum is obsolete), a warning message
pops up and merging is interrupted. The parameter set of the first
spectrum on the list of spectra to be merged is used in the result
spectrum. In case of Raman spectra you have to activate the Adap-
tation for Raman check box.

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 Chapt. 8 Manipulate

Set overlapping ranges interactively

The usable regions on the edges of spectra files, i.e. the overlap-
ping ranges of spectra files can be set interactively. By default, the
signal intensity is predefined by at least 10 % from the maximum of
the reference spectrum. This value should only be changed if nec-
essary.

Note: Once spectra have been merged, the latest range set-
tings made for the overlapping range, either interac-
tively or manually, remain valid. Clicking the Clear list
button (figure 229) allows to delete the range settings.

1 Load the spectrum files as described above.

2 Mark the result data block (AB or TR) of the spectrum file.
3 Select the Merge Spectral Ranges command.
4 Click the Merging multiple spectra tab.

Figure 229: Set overlapping range interactively

5 Click the Start interactive button. The overlapping range is

displayed in a different view and marked in white.

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 Merge Spectral Ranges Chapt. 8

Figure 230: Interactive view of the overlapping range

6 If required, the overlapping range can be changed.

• Zoom in or out the range: position the cursor on
the red line and draw the range to the desired size,
while pressing the left mouse button.
• Move the complete range: position the cursor on
the particular range and move the range, while
pressing the left mouse button.
• Delete the range: right click into the particular range
and select the Remove option.
7 Click the Merge button.

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 Chapt. 8 Manipulate

The merged result spectrum...

...is displayed in the spectrum window. Figure 231 shows result

spectrum merged from two spectrum ranges.

Figure 231: Merged result spectrum

The file name of the merged result spectrum is indicated as

Merge.* by default in the OPUS browser. To view the merge
parameters right click onto the file name and select the Show
Parameters option. On the view displayed, select the Processing
Parameters folder.

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 Atmospheric Compensation Chapt. 8

8.28 Atmo spheric Compensation

Definition This command allows to eliminate disturbing H2O

and/or CO2 bands in ratio spectra. These bands arise
due to different H2O/CO2 vapor concentrations in the
beam path if you measure reference or sample spec-
tra, respectively.

To perform atmospheric compensation a single-chan-

nel reference spectrum and single-channel sample
spectrum are analyzed and transformed into a ratio
spectrum without any (or hardly any) H2O and/or CO2
bands.

The algorithm can be used for MIR and NIR spectra.

Principle • Load the spectrum files (files which contain sin-

gle-channel data blocks only).
• Select the Atmospheric Compensation command.
• If required, drag & drop the data block of the ratio
into the upper selection field of the Atmospheric
Compensation dialog.
• Make further settings, if required.
• Click Calculate to start this manipulation command.

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A
B

Figure 232: Atmospheric Compensation - Select Files

A If you deactivate the H2O or CO2 compensation check box,

you will get an uncompensated transmission spectrum, i.e.
the ratio between a single-channel sample spectrum and a
single-channel reference spectrum.
B Activate the Aqueous solution check box if your measurement
sample is an aqueous solution (e.g. proteins in water). A dif-
ferent compensating algorithm optimized for aqueous solu-
tions will be used for calculation.

A ft e r c o m p e n s a t i o n . . .

...the appropriate ratio block will be calculated for each sin-

gle-channel sample block and added to the original spectrum file.

If a ratio data block already exists, it will be overwritten by the cal-

culated ratio data block and the original data will be replaced.

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 Atmospheric Compensation Chapt. 8

Figure 233 shows the result of atmospheric compensation effects.

Figure 233: Atmospheric compensation effects

The upper curve is the transmission spectrum of a polystyrene film.

H2O and CO2 bands can be clearly seen in several wavenumber
ranges.

The lower curve is the result of atmospheric compensation. Dis-

turbing absorption lines of H2O and CO2 have nearly been elimi-
nated.

General

The Atmospheric Compensation command uses physical models

to estimate the amount of atmospheric gases in the single-channel
spectra and therefore compensates disturbing H2O and/or CO2
bands.

Note: Atmospheric compensation is a kind of data manipu-

lation and has to be used with due care.

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 Chapt. 8 Manipulate

What kind of spectrum is required?

Two single-channel spectra:

• Single-channel sample spectrum
• Single-channel reference spectrum

What kind of spectrum features have to be

considered?

• Wavenumber ranges:
- for H2O compensation (Standard, MIR): from 3600 to
4000 cm-1
- or H2O compensation (Aqueous solution, MIR): from
1900 to 1800 cm-1
- for H2O compensation (NIR): from 5000 to 5600 cm-1
- for CO2 compensation: from 2300 to 2400 cm-1
Sample absorption or a low signal to noise level within
these wavenumber ranges can affect the compensation
quality.
• The sample and reference spectrum have to be
acquired using the same spectrometer resolution. Differ-
ent zero-filling factors are possible.
• The spectrum should not end at a wavenumber which
shows strong absorption of atmospheric gases. In case
of a H2O compensation (see figure 233), the lower wav-
enumber limit must not be around 1700 cm-1.
• For compensation in aqueous solutions the spectrum
has to include wavenumber ranges of 2300 - 2400 cm-1
and 1800 - 1900 cm-1 for both CO2 and H2O. These
wavenumber ranges must be free of sample absorption
bands.

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 Atmospheric Compensation Chapt. 8

A t m o s p h e r i c c o m p e n s a t i o n u s i n g s i n-
gle-channel spectra from one file

In this case the two single-channel spectra data blocks are stored
in one spectrum file.

Example:

Select the spectrum file and drag & drop it into both selection fields
on the Select Files tab.

Note: If the spectrum file additionally contains a ratio spec-

trum, you can drag & drop this ratio spectrum into the
first selection field. Wrong data block types will be
ignored.

If you have selected several spectrum files, a data block will be dis-
played in both selection fields for each spectrum file selected.

A t m o s p h e r i c c o m p e n s a t i o n u s i n g s i n-
gle-channel spectra from different files

In this case two single-channel spectra data blocks are stored in

different spectrum files.

Example:

If the two single-channel spectra data blocks are stored in different

spectrum files, select each data block and drag and drop it into the
respective selection fields.

If you want to compensate several sample spectra simultaneously,

which belong to one single-reference spectrum, drag and drop all
single-channel sample spectra data blocks in the upper selection
field and the single-channel reference spectrum in the lower selec-

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 Chapt. 8 Manipulate

tion field.

8.28.1 Atmospheric compensation as

pa r t o f t h e m e a s u r e m e n t p r o c e s s

If you want to use the Atmospheric Compensation command to

manipulate spectra immediately after the measurement process,
you have to perform the following steps:

1 On the Measure menu, select the Advanced Measurement

command and set the parameters for your experiment.
2 Click the Advanced tab. Activate the Single Channel and
Background check boxes in the Data blocks to be saved
option field.

Note: The group field is only displayed if you do not

work with predefined measurement parameters
(chapter Measurement Parameters).

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 Atmospheric Compensation Chapt. 8

3 Activate the Additional data treatment check box and click

the button. The following message pops up:

4 On the Manipulate menu, select the Atmospheric Compen-

sation command without closing the Measurement dialog.
The Atmospheric Compensation dialog box opens.
5 Select [<FILE>:TR] or [<FILE>:AB] from the Single channel
sample block(s) drop-down list. Activate the different check
boxes, if required.

Figure 234: Atmospheric Compensation - Defining single-channel spectra

6 Click Calculate.

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 Chapt. 8 Manipulate

The Additional Data Treatment option on the Advanced tab of the

Measurement dialog has now to be similar to figure 235. If the sam-
ple measurement has been successful, atmospheric compensation
will be performed immediately after the measurement.

Figure 235: Activated post-measurement manipulation

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 Straylight Correction Chapt. 8

8.29 St r ay light Correction

Definition This command allows to correct two phenomena

which normally occur in case of diffuse reflection
measurements:

• Diffuse reflection of the measurement light at the

window, mainly due to scratches and contamina-
tions.
• Multiple reflections between sample and window,
which lead to increased absorption.

Straylight correction eliminates these errors in the

ratio spectra (i.e. transmission, absorbance,
Kubelka-Munk, reflection) partly by intrinsic correc-
tion spectra and partly by using mathematical algo-
rithms. The result is again a ratio spectrum.

Principle • Load the spectrum file (only data blocks with ratio
spectra, e.g. absorbance, transmittance,
Kubelka-Munk, reflectance or log-reflectance
files).
• Select the Straylight Correction command.
• If required, drag & drop the spectrum file into the
Spectra to apply straylight correction selection field.
• Define the type of window material.
• Click the Record new spectra tab to create new cor-
rection spectra (chapter 8.29.1).
• Click Calculate to start this manipulation command.

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 Chapt. 8 Manipulate

Figure 236: Straylight Correction - Select Files

A If you activate or deactivate this check box check box, you

specify whether your reflection measurement has been per-
formed by an internal or external background.
External in this case means that you have used your own
standard, e.g. a gold stamp or certified Labsphere standard
during background measurement.
Internal in this case means that you have used built-in fea-
tures of the Ulbricht sphere to determine the background
spectra (Sphere Background-Channel in case of an MPA
spectrometer).
B The correction of multiple reflections depends on the refrac-
tion index of the window material. To specify the window
material used, activate either the Quartz or Sapphire check
box.
In most cases quartz has been used as standard window
material. MPA and MATRIX spectrometers, e.g. are always
delivered with quartz windows. Some TENSOR spectrome-
ters are supplied with sapphire windows. If you are not quite

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 Straylight Correction Chapt. 8

sure about the window material used with your spectrometer,

contact Bruker Service.
C The tab allows to create new correction spectra
(chapter 8.29.1).
D Clicking this button generates a ratio spectrum for each ratio
block. The result data calculated will overwrite the original
data in the ratio data block (see also chapter 8.29.2).

8.29.1 Create new correction spectra

Note: Correction spectra reflect the spectrometer status
and have to be acquired before you start straylight
correction for the very first time.

Correction spectra have also to be acquired if e.g. the status of the

measuring window has changed, i.e. if the window is dirty,
scratched or dusty.

Ideally, the signal should be 0, if no sample is positioned on the

measuring window. The signal is, however, >0 if the window is e.g.
dusty. Thus, straylight correction is actually a spectrometer calibra-
tion with regard to absolute reflection.

Best straylight correction results can be achieved if the measuring

window status remains the same when acquiring data and perform-
ing normal measurements. This means, that you should not
acquire correction spectra with the window being dusty, clean the
window afterwards and perform measurement.

Sta n d a r d m a t e r i a l r e q u i r e d

To proceed successfully you need a standard material, e.g. gold

standard or certified Labsphere standard (99%).

It is also possible to create correction spectra even if no standard is

available. This is, however not reasonable, as the measurement
may be falsified when applying straylight correction. The correction
algorithm assumes that the standard used has a diffuse reflection
of about 100% within a wavenumber range of 12,500 to
3,600 cm-1.

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 Chapt. 8 Manipulate

Note: Straylight correction spectra have to be acquired in

regular intervals. We recommend to measure new
stray light correction spectra in the course of the OQ
test (Operational Qualification Test, see chapter 13),
preferably before the validation measurement.

To c r e a t e c o r r e c t i o n s p e c t r a . . .

1 ...click the Record new spectra tab (C in figure 236). A new

dialog opens.

Figure 237: Acquiring correction spectra

2 Enter the reflectivity of the light trap as a number.

Note: Spectrometers equipped with an integrating sphere

are supplied with a light trap. A data sheet includes
the reflectivity value of the respective light trap.

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 Straylight Correction Chapt. 8

If you do not know the exact reflectivity value, you

should not change the default setting of 0. Working
with incorrect values may result in adulterated cor-
rection spectra.
3 Enter the reflectivity of the gold standard as a number
between 0.8 and 1.2.

Note: The latest gold standards have a serial number and

are supplied by an accompanied data sheet. This
data sheet includes the averaged reflectance of the
gold standard.
If you use different types of standard or do not know the
exact reflectance value, you should not change the default
setting of 0.
4 Click the Create button and follow the on-screen instruc-
tions.
5 If you have finished, the new correction spectra will be
stored on hard disk.

When running the new correction spectra

script...

...three different single-channel spectra are measured:

• SCintBG: Single-channel measurement of internal back-
ground
• SCextBG: Single-channel measurement of external
background
• SCStray: Single-channel measurement without sample

Note: If you use an MPA spectrometer, two additional sin-

gle-channel spectra will be measured for the optional
Sphere Microsample channel.

The following ratio spectra are calculated from these three different
single-channel spectra:
• ExtRef: SCextBG/SCintBG
• Stray: SCStray/SCintBG

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 Chapt. 8 Manipulate

These ratio spectra are stored by the ExternalReference_macro.0

and EmptyChannel_macro.0 file name in the *\OPUS\straycorr
directory.

Note: If you use an MPA spectrometer, two additional spec-

tra will be created which have the extension _micro.

The ExtRef and Stray ratio spectra are used to perform straylight
correction on the spectra measured.

The Straylight Correction command always uses the latest correc-

tion spectra measured, i.e. correction spectra which have the big-
gest file name extension in the *\OPUS\straycorr directory.

8.29.2 Correction Algorithm

The correction algorithm considers the following effects:

1 Straylight effects caused by diffuse reflection of the incoming

light at the measurement window. These effects will be
corrected by calculating a corrected ratio spectrum:

TM – Stray
TM corrected = ------------------------------------
Extref – Stray

If TM has been recorded using an internal background.

TM – Stray Extref
TM corrected = -----------------------------------------------
1 – Stray Extref

If TR has been recorded using an external background

(nearly 100%).
TR is the original transmission spectrum, TRcorrected the
resulting spectrum. Stray stands for transmission spectrum
of a measurement performed without sample (open chan-
nel). Extref is the ratio between the single-channel spectra of
the external reference and single-channel spectra of the
internal reference.
2 Multiple reflections between the measurement window and
sample: after the first diffuse reflection of the light at the
sample, a fraction of this light can be reflected again both at

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 Straylight Correction Chapt. 8

the window and the sample. This leads to incorrect measure-

ment results, especially in case of a mid-range sample
absorbance ratio (30 - 70%). This effect is compensated by
multiplying the transmission spectrum by the following factor:

1+c - 2
------------------------ where c = R   1 +  1 – R  
1 + TM  c

TM is the original transmission spectrum and R is the reflec-

tion coefficient of the window material.
3 The ratio spectrum may have different values when using an
internal background instead of an external standard. The dif-
ference between internal and external background is the
portion of light reflected directly at the measurement window.
This part of light leaves the Ulbricht sphere by the input. This
effect is taken into account by a correction spectra which
quantifies this background difference.

Figure 189 shows straylight correction effects.

Figure 238: Straylight correction effects

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 Chapt. 8 Manipulate

8.29.3 St r a y l i g h t c o r r e c t i o n a s pa r t o f
the measurement process

If you want to use the Straylight Correction command to manipulate

spectra immediately after the measurement process, you have to
perform the following steps:

1 On the Measure menu, select the Advanced Measurement

command and set the parameters for your experiment.
2 Click the Advanced tab. Select the result spectrum type from
the Result spectrum drop-down list.

3 Activate the corresponding check box in the Data blocks to

be saved group field.
4 Activate the Additional data treatment check box and click
the button. The following window pops up:

5 On the Manipulate menu, click Straylight Correction without

closing the Measurement dialog. The Straylight Correction
dialog box opens.
6 Select [<FILE>:TR] from the Spectra to apply straylight cor-
rection drop-down list.

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 Straylight Correction Chapt. 8

Figure 239: Straylight Correction - Defining result spectrum

7 Click Calculate.

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 Chapt. 8 Manipulate

The Additional Data Treatment option on the Advanced tab of the

Measurement dialog has now to be similar to figure 240. If the sam-
ple measurement has been completed successfully, atmospheric
compensation will be performed immediately after the measure-
ment.

Figure 240: Activated post-measurement manipulation

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 Noise Generation Chapt. 8

8.30 N o ise Generation

Definition This command adds artificial noise to a spectrum. It

adds random positive or negative numbers to the
spectrum values.

Principle • Load the spectrum file.

• Select the Noise Generation command.
• If required, drag & drop the spectrum file into the
File(s) to generate noise for selection field.
• Enter the respective noise level, i.e. the maximum
value which the spectral values will be changed by.
• Click Generate to start this manipulation command.

Figure 241: Noise Generation - Select Files

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 Chapt. 8 Manipulate

8.31 Mov ing Mean

Definition This command performs a special kind of smoothing

on a spectrum.

Principle • Load the spectrum file.

• Select the Moving Mean command.
• If required, drag & drop the spectrum file into the
File(s) to manipulate selection field.
• Define the kind of manipulation.
• Specify the number of data points.
• Click Calculate to start this manipulation command.

C A

Figure 242: Moving mean - Select Files

A If you activate this option button, spectrum values being next

to each other are averaged and replaced by their mean value.
B If you activate this option button, the first and the last point of
a sequence of data points are used to calculate a straight line
between these two data points. The spectrum values
between these two data points are replaced by values which

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 Make Monotone Chapt. 8

are on the straight line. These steps are repeated by using

the next sequence of data points.

Note: In both types of manipulation the Number of points

parameter always represents the number of subse-
quent spectrum points. These spectrum points are
used for the calculation to be able to create new
spectrum values.
C The number of data points are defined in this entry field.

8.32 Make Monotone

Definition Depending on the options selected and the spectrum

curve shape, this command allows to correct a trace
or spectrum such that the resulting curve increases or
decreases in a monotonic manner.

Principle • Load the spectrum file.

• Select the Make Monotone command.
• If required, drag & drop the spectrum file into the
File(s) to manipulate selection field.
• Define the direction of manipulation.
• Click Calculate to start this manipulation command.

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 Chapt. 8 Manipulate

B

Figure 243: Make monotone - Select Files

A If you activate this option button, the values of each spectrum

will be changed to the effect that the values of the result spec-
trum increase in a monotonic way.
B If you activate this option button, the values of the result spec-
trum will decrease in a monotonic way.
C Based on two data points at the boundary of the wavenumber
interval activating this option button, determines whether the
result curve increases or decreases.

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 Radiometric calibration Chapt. 8

8.33 Radiometric calibration

8.33.1 In t r o d u c t i o n

To perform absolute emission measurement OPUS provides the

Build Radiometric Calibration File and Radiometric Calibration
commands.

Absolute emission

The absolute emission of a sample in terms of spectral radiance

[W / (m2 sr cm-1)] can only be determined if the spectrometer uses
a calibrated reference source, and measurement is performed
under almost constant conditions.

The temperature and the emission coefficient of the reference

source have to be known. Typically, a black body source is used.
The absolute emission spectrum can be calculated from the mea-
sured spectrum of the sample and the calibration file. When calcu-
lating the absolute emission, the self-radiation of the
interferometer is considered and subtracted.

Measurement conditions

It is vital that all measurements of the hot and cold reference

source, as well as the emission sample are made under the same
conditions, using the same optical components and the same mea-
surement parameters.

The measurements should be performed in close temporal order to

avoid any drift in the temperature of the spectrometer or the ambi-
ent. Temperature drifts may result in offset errors. To be able to get
a good phase correction you should use and store the interfero-
grams.

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 Chapt. 8 Manipulate

In case of a non-linear detector, e.g. MCT, it is essential to perform

a proper non-linearity correction during the calculation of the radio-
metric calibration file. Details on non-linearity are described in
chapter 8.33.5.1.

B e a m pa t h

The beam path for the sample and the reference source must be
identical. The emitting surfaces (of both sources) have to be larger
than the spot size received by the spectrometer at the emission
input, and have to be positioned in or imaged to the focal plane of
the spectrometer input.

In addition, the angular range received by the spectrometer at the

emission input must be completely filled by the source radiation.
Typically, that requires an external mirror arrangement (2 parabolic
mirrors of sufficient size) to image the emitting surface into the
focal plane of the spectrometer input. An additional flipping mirror
is required to select between the sample and the reference source.

Accessories like an attenuator or integrating sphere can be

installed in the beam path, provided the conditions and the étendue
of the emission radiation received by the spectrometer are identical
during the measurement of both the reference source and sample.

The spot size received by the spectrometer can be changed by

using an optional aperture wheel. The aperture wheel can be
located e.g. at the focal position in front of the spectrometer input
port. Note that for each aperture size a separate calibration has to
be performed.

Reference source

At moderate temperatures (<100 °C) a flat surface (extended area)

source with a high emission coefficient can be used as reference
source. The surface can be coated by a special paint so that an
emission coefficient of 97% might be achieved.

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 Radiometric calibration Chapt. 8

At high temperatures the emission coefficient of a flat surface

source is low. Besides, it becomes difficult to heat the surface
homogeneously and stable. In such a case, a cavity black body ref-
erence source is required.

8.33.2 T h e o r e t i c a l b a c k g r o u n d i n f o r m a-
tion

The purpose of radiometric calibration is to generate emission

spectra in terms of absolute spectral radiance, brightness tempera-
ture and emissivity of the sample.

Radiometric calibration considers and subtracts the self-radiation

caused by the spectrometer. The interpretation of emission spectra
which have been undergone radiometric calibration is far more
easier. Especially if the emission is displayed as brightness tem-
perature, any spectral features will emerge from the constant line
which is equivalent to the sample temperature.

The measured spectrum of an emission source depends on the

source spectral radiance L (,T) as follows:

[1] S   T  = m     L   T  + b    

S  v T  is the measured spectrum, m    the effective spectral

response factor of the spectrometer and b    the effective spectral
self-emission of the spectrometer, referred to its input.

If the emission coefficient of the reference source     is known,

the emitted source radiance L   T  can be calculated as follows:

[2] L (,T) =    B (,T) +  1 –     B   T amb 

Whereas B   T  is a Planck-type source (ideal black body,

chapter 8.14.1). The first term of the equation refers to the part of
the direct emitted radiation, the second is the radiation from the
ambient with temperature T amb . For an ideal black body source
applies:

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 Chapt. 8 Manipulate

[3] L (,T) = B (,T)

Radiometric calibration requires at least two spectra of a reference

source  S c (,T c) and S h (,T h)  at two different temperatures  T c
and T h  . One temperature should be lower than the range of
expected sample temperatures while the other should be higher.
The parameters b    and m    can be calculated from S c (,T c)
and S h (,T h) by solving two equations with two unknowns.
S h   T h  – S c   T c 
[4] m    = ---------------------------------------------------------------
-
     B   T h  – B   T c  

S c   T c 
[5] b    =  ---------------------
- –     B   T c  +  1 –     B   T amb   
m 

The source radiance L   T u  can be calculated from the corre-

sponding spectrum measured, according to [1]:
S u   T u 
L   T u  =  --------------------- 
 m    - – b   
[6]

[6] can also be written as:

[7] L   T u  = Slope     S u  v T u  – S c  v T c   + Offset  v T c 

with
     B   T h  – B   T c  
[8] Slope    = ---------------------------------------------------------------
-
S h   T h  – S c   T c 
Offset   T c  =    B   T c +  1 –     B   T amb 

Slope    and Offset   T c  are stored in the calibration file.

If interferograms are provided,  S u   T u  – S c   T c   in [7] and

 S h   T h  – S c   T c   in [8] are replaced by FFT
 IFG  T u or h  – IFG  T c   . This results in significantly better phase
correction, as any common terms cancel out, e.g. self-emission of
the interferometer.

However, the following limitations apply:

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 Radiometric calibration Chapt. 8

• All interferograms must refer to the same absolute peak

position. Thus, the scanner must not have been stopped
during the full measuring sequence of the cold and hot
reference source, and emission sample.
• In principle, the calculation of FFT  IFG  T u  – IFG  T c  
will generate a spectrum with exclusively positive ordi-
nate values. Positive ordinate values are physically only
correct, if the intensity of the sample spectrum (T u ) is
higher than the intensity of the cold reference source
(T c ) over the full spectral range. Positive ordinate values
are incorrect, if T u < T c , and can be untrue in case of
low-emissivity samples. To reliably avoid this error,
ensure that T c  = T u and T c  = T amb . If, for any rea-
son, these conditions cannot be met, radiometric cali-
bration must be performed by using spectra.

According to Kirchhoff, the emissivity, reflectivity and transmissivity

of a body are related as:

[9]    = 1 – r    –t   

In the following, it is assumed that the sample reflects and trans-

mits radiation from the surroundings at ambient temperature T amb.1

Then:

[10] L   T u  =  u   B   T u  +  1 –  u    B   T amb 

The equation can be rearranged to yield the sample emissivity as:

 L   T u  – B   T amb  
[11]  u    = ------------------------------------------------------------
-
 B   T u  – B   T amb  

1. A completely transparent sample mounted on a heated holder, however, would

rather transmit radiation which corresponds to the temperature of the holder, and
therefore care must be taken when choosing an appropriate value for Tamb
(figure 246 on page 381).

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 Chapt. 8 Manipulate

More details on the calculation are described in:

H. E. Revercomb, H. Buijs, H. B. Howell, D. D. LaPorte,
W. L. Smith, and L. A. Sromovsky, "Radiometric calibra-
tion of IR Fourier transform spectrometers: solution to a
problem with the High-Resolution Interferometer
Sounder," Appl. Opt. 27, 3210-3218 (1988)

8.33.3 Sta n d a r d p r o c e d u r e o f r a d i o m e t-
ric calibration
1 Measuring the cold reference source.
➣The temperature of the cold reference source should be
lower than the range of expected sample temperatures, e.g.
at room temperature.
2 Measuring the hot reference source.
➣The temperature of the hot reference source should be
close to the highest expected sample temperature, but not
higher. Thus, excessive detector non-linearity is avoided.
3 Measuring the emission sample.
➣Emission sample measurements may be repeated under all
desired sample conditions (temperatures).
4 Generating a radiometric calibration file (chapter 8.33.5),
using the files from (1) and (2).
5 Performing radiometric calibration (chapter 8.33.6) of the
files from (3), using the calibration file generated in (4).
➣The calibration file remains valid until the temperature of the
spectrometer or ambient change substantially.

8.33.4 C u s t o m i z i n g M a n i p u l a t e menu
Note: The two commands available for radiometric calibra-
tion in OPUS are integrated in the Manipulate menu.
As the commands may not be seen in the default
menu configuration, you have to customize the
Manipulate menu.

1 On the Setup menu, select the Customize menu command.

2 On the dialog that opens, click the Commands tab.

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 Radiometric calibration Chapt. 8

➣Keep the dialog open during the entire customizing proce-

dure.
3 In the Categories list box, select the Manipulate menu.
4 In the Commands list box, click the Build Radiometric Cali-
bration File command.
5 While pressing the left mouse button, drag and drop the
Build Radiometric Calibration File command to the Manipu-
late menu.
6 In the Commands list box, click the Radiometric Calibration
command.
7 While pressing the left mouse button, drag and drop the
Radiometric Calibration command to the Manipulate menu.
8 Click the Close button to close the Customize dialog.

8.33.5 Generating radiometric calibra-

tion file
Note: It is highly recommended to use black body spectrum
files which do contain both the interferogram and the
single-channel spectrum. The interferogram allows an
optimal phase correction, whereas the FFT parame-
ters, e.g. apodization and non-linearity correction can
be enforced via the spectrum.

The measurement parameters used to generate the

file for the cold and hot black body must not differ
from each other.

1 On the File menu, select the Load command and load the
spectrum file of the cold and hot black body into the browser.
2 On the Manipulate menu, select the Build Radiometric Cali-
bration File command.
3 On the dialog that opens, make sure that the interferogram
(or spectrum) file for the cold and hot black body is loaded
into the particular list box.
➣If the file contains a ’SIFG’ data block, this data block is
preferably loaded by default. Details on the further setting
options are described in chapter 8.33.5.1.
4 Enter the temperature for the cold and hot black body.

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 Chapt. 8 Manipulate

5 Enter the ambient temperature prevailing during the mea-

surement of the cold and hot body.
6 Activate the particular option button for non-linearity.
7 If the black body has a spectral constant emissivity, define
the emissivity value.
8 If available, select the emissivity spectrum of the black body.
9 Enter a file name for the radiometric calibration file.
10 If required, change the path for the calibration file.
➣The default path is *\<OPUS_version>\DATA.
11 Click the Build button to start generating a calibration file.

8.33.5.1 D e ta i l s o n t h e s e t t i n g o p t i o n s

1
3

2 4

10

11

Figure 244: Setting options for generating a radiometric cali-

bration file

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 Radiometric calibration Chapt. 8

Komponente Definition

1 Interfero- The entry field must contain the interferogram (or spec-
gram/spectrum trum) file of the cold black body.
file - cold

2 Interfero- The entry field must contain the interferogram (or spec-
gram/spectrum trum) file of the hot black body.
file - hot

3 Temperature (°C) The temperature of the cold black body has to be entered.
The temperature is defined in C°.

4 Temperature (°C) The temperature of the hot black body has to be entered.
The temperature is defined in C°.

5 Temperature (°C, The ambient temperature prevailing during the measure-

ambient) ment of the cold and hot black body has to be entered. The
temperature is defined in C°.
The term ambient refers to all types of surfaces in front and
on the sides of the black body. In this context, ambient does
not refer to the spectrometer temperature.

6 Use non-linearity The option button is only enabled if the interferograms or

settings from spectrum files do contain non-linearity settings.
cold/hot files

7 Use the following If the option button is activated, the non-linearity settings
non-linearity set- have to be defined as follows:
tings • Detector cutoff: the detector cutoff describes the spectral
limit (in cm-1), below which the detector is not sensitive
anymore. If you use a preamplifier which reverses the sig-
nal polarity, the value of the detection limit has to be multi-
plied by -1.
• Modulation efficiency: the modulation efficiency causes
an additional multiplicative correction of the entire spec-
trum. It can be set either to the correct value (typically
between 0.7 and 1.0), or to 1.0 if the correct value is
unknown.
More details on non-linearity are described in chapter 8.15
et seq.

8 NL correction dis- Activating the option button makes sense if you use a linear
abled detector type, e.g. DTGS.

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Komponente Definition

9 Use constant The option button should only be activated if the reference
emissivity source has a constant spectral emissivity of <1. In case of a
cavity black body source the typical emissivity is 0.99, in
case of an extended-area black body source the emissivity
is mostly <0.99.
• If activated, enter the value into the entry field next to the
option button.

10 Use emissivity Preferred option, if an emissivity spectrum of the reference

spectrum source is available. The emissivity spectrum to be selected
must comprise the spectral range of the detector used. The
emissivity of the spectrum must be between 0 and 1. The
spectrum should be smoothed to separate out noise during
calculation.

11 File name Enter a unique file name, perhaps referring to the measur-
ing setup.

8.33.6 P e r f o r m i n g r a d i o m e t r i c c a l i b r a-
tion
Note: It is highly recommended to use emission sample
spectrum files which contain both the interferogram
and the single-channel spectrum. The interferogram
allows an optimal phase correction, whereas the FFT
parameters, e.g. apodization and non-linearity correc-
tion can be pre-defined by the spectrum used. The
measurement parameters used to generate the emis-
sion sample spectrum file, must not differ from the
measurement parameters used to generate the black
body spectrum file, except for the number of scans.

Even the geometrical orientation of the sample to the

spectrometer, i.e. the étendue of the emission radia-
tion received by the spectrometer, must be identical
during the measurement of both the emission sample
and black body.

1 On the File menu, select the Load command and load the
spectrum file of the emission sample.
2 On the Manipulate menu, select the Radiometric Calibration
command.

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 Radiometric calibration Chapt. 8

3 On the dialog that opens, make sure that the data block for
the interferogram (SIFG) is loaded (figure 245).
➣If the spectrum file does not contain a SIFG data block, use
the data block for the single-channel spectrum (SSC).
➣If the spectrum file does contain a SIFG and SSC block, the
operator determines whether interferograms or spectra are
used to perform radiometric calibration by selecting either
one of them. Performing radiometric calibration based on
interferograms has some advantages but also some limita-
tions, as outlined at the end of chapter 8.33.2. Radiometric
calibration based on spectra is always possible.

Figure 245: Interferogram to be calibrated

4 Enter the name of the radiometric calibration file previously

generated.
➣The radiometric calibration file will only remain valid as long
as the conditions inside the spectrometer, especially the
internal temperature, do not undergo substantial changes.
5 If required, change the path for the calibration file.
➣The default path is *\<OPUS_version>\DATA.
6 Activate the Calculate emissivity of sample option button
(figure 246), if you want to add a data block, which contains
the emissivity of the sample, to the spectrum file.

Figure 246: Emissivity of sample

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 Chapt. 8 Manipulate

➣By default, the ’Temperature (°C, ambient)' entry field con-

tains the ambient temperature value of the calibration file
selected. When selecting a different calibration file by click-
ing the ’Change File’ button (figure 246), the ambient tem-
perature value indicated in this file will be updated
automatically in the entry field. If, however, a different ambi-
ent temperature prevailed during sample measurement, you
have to enter this new ambient temperature manually into
the entry field. The sample temperature must always be
entered manually into the ’Temperature (°C, sample)’ entry
field. More details are described at the end of
chapter 8.33.2.
7 Click the Calibrate button to start calibration.
➣If the radiometric calibration has been finished successfully,
the ’RAD’, ’BT’ and possibly ’EMIS’ data block are added to
the spectrum file of the emission sample (figure 247).

Figure 247: Data blocks added to

the spectrum file

➣The ’RAD’ data block contains the spectral radiance of the

emission, ’W/(m2 sr cm-1)’ unit.
➣The ’BT’ data block contains the brightness temperature of
the emission, ’K’ unit.
➣The ’EMIS’ data block contains the emissivity of the sample.
The emissivity is dimensionless and ranges from 0 to 1. If
the calculated value is beyond this physically permitted
range, probably the temperature and/or non-linearity set-
tings have not been accurate enough.
➣The spectral data are only valid between the lower detector
cutoff of the detector used, and the maximum wavenumber
up to which the ’RAD’ data block shows intensity. Data
beyond these limits are not valid and must not be used.
➣The calculation is based on the same non-linearity settings
which have been used when generating the radiometric cal-
ibration file.

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8.33.7 Radiometric calibration not

pa s s e d

If radiometric calibration has failed, check whether the measure-

ment parameters used to generate the cold and hot black body
and/or the emission sample files have been identical. If the mea-
surement parameters differ, an error message is displayed
(figure 248).

Figure 248: Error message if radimetric calibration

failed

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 Chapt. 8 Manipulate

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9 Evaluate
The commands included in the Evaluate menu are primarily used
to calculate evaluation results on the basis of existing spectra. The
calculation methods may comprise quantitative data analysis, peak
identification or library search. This kind of calculation does not
cause changes on the spectrum itself.

Figure 249: Evaluate Menu

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 Chapt. 9 Evaluate

9.1 C ur ve F i t

Definition This command allows to calculate single peak posi-

tions, widths and intensities in a system of overlap-
ping peaks. Before starting the fitting calculation you
have to set up a model consisting of an estimated
number of peaks and a baseline.

Note: As the result of this calculation highly

depends on the model selected, make sure that
the model is reasonable from the chemical point
of view.

Principle The model can be set up interactively on the screen

and is optimized during calculation. The model can
be used as initial value for the next curve fit.

B e f o r e y o u s ta r t a c u r v e f i t . . .

1 ...load the spectrum file which has to be an absorbance

spectrum.
2 Perform a baseline correction (see chapter 8.1) on this spec-
trum file.
3 Select the Curve Fit command.
4 If required, drag & drop the spectrum file into the File to fit
selection field.
5 Set up a model (see chapter 9.1.1).
6 Start to adapt the model to the spectrum (see chapter 9.1.2).

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 Curve Fit Chapt. 9

Figure 250: Curve Fit - Select Files

A Make sure that the spectrum file loaded is a baseline-correc-

tion absorbance spectrum.
B Use this entry field to drag & drop the data block ( ) of a
spectrum which has already been fitted.
C If you activate this check box, a new fit will be started by using
the last result.
D If you activate this check box, every fitted peak will be stored
as single file.
E To set up a model (see chapter 9.1.1) click this button.

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 Chapt. 9 Evaluate

9.1.1 Setting up model

1 Click the Start Interactive Mode button (E in figure 250). The
following view opens.

Figure 251: Curve Fit - Select Files

In the upper window (A in figure 251) the spectrum to be fit-

ted is displayed, whereas in the bottom window (B) the dif-
ference between the original spectrum and the fitted
spectrum is shown.
2 Position the cursor into the upper window. The cursor

changes to .

3 If you click the left mouse button, a curve is displayed.

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 Curve Fit Chapt. 9

4 Position the cursor on top of the curve newly displayed. The

cursor changes to .

This kind of cursor allows to move the curve. Click the left
mouse button and drag the curve to the position desired
while pressing the mouse button.

5 Position the cursor slightly below the top of the curve. The
cursor changes to .

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 Chapt. 9 Evaluate

This kind of cursor allows to change the width of the curve.

Pressing the left mouse button and dragging to the left
makes the curve become wider.

Pressing the left mouse button and dragging to the right

makes the curve become smaller.

Defining Peak Parameters

The peak parameters can be defined in the lower end of the curve
fit view. Position, intensity and width can be specified more pre-
cisely than by using the cursor.

To edit the peak parameters...

1 ...click into one of the entry fields and enter the value
manually, or use the arrow buttons above the respective
entry field.

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 Curve Fit Chapt. 9

Figure 252: Curve Fit - Defining peak parameters

2 If certain peak parameters are not to be considered during

automatic curve fit, deactivate the checkbox in front of the
respective parameter.

3 Each peak is shown in one line of the peak list including all
peak parameters. The lines with non-selected peaks are
marked green and the currently selected peak is marked vio-
let. The peaks in the list are always sorted by peak position.

Figure 253: Curve Fit - Peak parameters

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 Chapt. 9 Evaluate

Defining Peak Shape

There are several different options to define the peak shape:

• Lorentz
• Gauss
• Lorentz + Gauss
• Baseline

The default peak shape setting is a pure Lorentz curve.

To edit the peak shap e...

1 ...click one of the arrow buttons on the right. Clicking the

upper arrow button, e.g., changes the curve immediately to
pure Gauss.

Clicking the arrow button again changes the curve to Base-

line.
2 Clicking again the lower arrow button, and based on the
Lorentz type, the peak shape changes to 100%Lorentz +
Gauss. In principle, the peak shape simulated is a pure
Lorentzian function but it represents the special case of a
mixture between Lorentz and Gauss functions.
3 Repeatedly clicking the lower arrow button decreases the
Lorentz function percentage.

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What is to be considered in case of Base-

line peak shape?

In some cases it may be necessary to use a baseline in addition to

the peaks. A baseline is always a straight line defined by a refer-
ence point and a slope. The baseline can be defined by the opera-
tor or calculated by OPUS.

The Width parameter is replaced by the Slope parameter, the

Intensity by the Value parameter when x = 0. To edit the baseline
parameters either click the arrow buttons, or directly enter the
parameters into the peak table.

Defining Method

Two different types of algorithms are available to optimize the

model:
• Levenberg-Marquardt
• Local Least Squares

Activate the respective option button.

Figure 254: Curve Fit algorithms

Note: The Levenberg-Marquardt algorithm is selected by

default. Make sure that the algorithm desired is

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 Chapt. 9 Evaluate

selected before you start calculation. It is also possi-

ble to change the algorithm during calculation.

For further details on the two algorithms see chapter 9.1.4.

D e f i n i n g I t e r a t i o n Tim e

1 Activate the option button.

2 Define the maximum iteration time in seconds for the calcu-
lation.

Figure 255: Maximum iteration time

9.1.2 Calculating Model

1 Click the Auto Fit button. As soon as the calculation starts,
the description of the button changes to Stop. During
calculation the model will be modified such that it becomes
an as precise as possible reproduction of the spectrum.
2 The newly calculated peaks are displayed on the screen in
real time.
3 You can interrupt calculation at any time by clicking the Stop
button.

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 Curve Fit Chapt. 9

A ft e r c a l c u l a t i o n . . .

1 ...the outcome is displayed in the view.

Original Sum spectra from 3 peak

spectrum spectra

3 peak
spectra

Figure 256: View after Auto Fit

2 ...a status line is displayed below the peak parameter table.

This status line shows the iteration time and the error of the
fit.
Example:
The smaller the error value the smaller the deviation
between measured and calculated curve.

If the *Bad Fitting Model!* message is displayed in the status line,

the program has not been able to fit one or more peaks. These
peaks are located at the left or right end of the frequency range,
and usually have a very small intensity.

Delete these bands before you continue with the calculation. To

delete a band click the band number (left row of the band parame-
ter table) and press the Del key on your keyboard. Confirm the dia-
log displayed by clicking Yes.

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9.1.3 Saving Model

There are two possibilities to save the model:

9.1.3.1 As temporary work file

1 Click the Save Report button.
2 The applied model is stored as temporary work file as sum
spectrum in the report data block ( ) and displayed in the
OPUS browser.

Note: Once a suitable model has been found (see next para-
graphs), it can be applied to other spectra of the same
type, there is no need to set up a new model for each
spectrum.

9.1.3.2 A s d a ta b l o c k a d d e d t o t h e
original spectrum
1 Click the Save Peaks and Reps button.
2 The applied model is stored as report data block ( ),
added to the original spectrum displayed in the OPUS
browser.

To d i s p l a y t h e pa r a m e t e r s o f p e a k c a l c u l a -
tion...

1 ...right click the report data block ( ).

2 Select the Show Report option from the pop-up menu.
3 A report view is displayed. The parameters are stored in the
Curve fit parameters directory.

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 Curve Fit Chapt. 9

Figure 257: Curve Fit parameters

9.1.4 Curve Fit Theory

The two algorithms Levenberg-Marquardt and Local Least Squares

are based on the Least Squares method. The difference between
the original and the calculated curve are kept as small as possible.
The fitting model is described by: Y G = y  x ;S 
• YG = measured data
• y = model
• x = frequency
• S = Set of curve parameters

L e v e n b e r g - M a r q u a r dt

The quadratic equation for the deviation between the measured

N
i = 1  YG – y  x ;S  
2 2
and calculated curve is:   S  =
2
•  = quadratic deviation
• N = number of points

The function is minimized by iterations. The gradient of the function

2
 is calculated for the current set of peak parameters. The gradi-
ent is then used to determine a new set of parameters S.

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 Chapt. 9 Evaluate

Some additional restrictions have also been implemented to make

the calculation more effective:
• All peaks have to be within the frequency range speci-
fied.
• The width of a peak must not be greater than the fre-
quency range specified.
• Peak intensities have to be positive.
• The contribution of Lorentz and Gauss functions for mix-
tures has to be within the range 0 to 100%.
• The sum of both parts has always to be 100%.

Local Least Squares

The Local Least Squares algorithm performs an independent fit for

each individual peak. The calculation is thereby restricted to the
range around the peak maximum. This substantially reduces the
amount of data required for the calculation.

Compared to the Levenberg Marquardt method the speed

increases, but this is accompanied by some loss of precision.

The Local Least Squares algorithm is attached to some conditions:

• The parameters for the baseline will not be calculated,
but have to be taken from the model.
• The peak parameters are always variable, none of them
can be firmly defined.

The given model can be seen as an area in an n dimensional

space, with n being the total number of peak parameters. In most
cases this area has one absolute minimum and several local min-
ima.

The quality of the calculation depends on the quality of the model

selected, i.e. the calculation either yields to the absolute minimum
or is around the local minima. The latter case can be detected by a
relatively large error and a visually obvious poor fit. In this case,
start the calculation again by using a new optimized model.

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 Curve Fit Chapt. 9

Criteria for the selection of an algorithm

In most cases the Levenberg-Marquardt algorithm results in a bet-

ter fit compared to the Local Least Squares algorithm, but needs
significantly more calculation time. If the number of points in the
selected range and the number of peaks in the model is small, the
Levenberg-Marquardt algorithm can be used immediately.

If the amount of data is large or many peaks need to be fitted, start

with the Local Least Squares algorithm which converges very
quickly. As soon as the variation of the error becomes small, switch
to the Levenberg-Marquardt algorithm for the final fit.

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9.2 Integ ration

Definition This command allows to integrate peaks as well as

calculate peak heights.

Principle • Load the spectrum file.

• Set up an integration method (see chapter 9.2.1 and
9.2.2).
• Start integration (see chapter 9.2.3).

B e f o r e y o u c a n s ta r t i n t e g r a t i o n . . .

...you have to set up an integration method. This method deter-

mines how to integrate spectra and in which frequency ranges.
Integration methods have the extension *.INT and can be stored
separately in the *\OPUS_<version>\Methods directory.

9.2.1 Setting up integration method

An integration method specifies the frequencies for one or more

areas which are to be considered for integration.

1 On the Integration dialog, click Setup Method. A different

dialog opens (see figure 258).
2 Specify the parameters required.
3 Store the method by clicking the Store Method button.
Define a name for the method.

Note: If you close the dialog without saving the settings

made, the settings will be discarded.

The Setup Integration Method dialog is described in the following.

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A
D

Figure 258: Setup Integration Method

A The list box contains the integration modes available in

OPUS, which are described more exactly in the following. To
select a mode click the respective graphics. The mode cur-
rently selected is displayed in the small image next to the list
box.
B Depending on the integration method selected in (A) you
determine the left and right edge used to perform an integra-
tion or search an extremum.
If you click the Interactive button, a different view opens which
allows to set the limits interactively. Press the left mouse but-
ton and drag the frequency ranges to the wavenumber
desired.
C The current integration area is indicated. Use the arrow but-
tons to switch between the single areas.
D If you click this button, you delete limits, baseline points and
the label of the area indicated in (C). Clicking this button
resets the integration mode to type A, by default.
E Use this entry field to define an individual label for each area.
F The number of the integration area currently specified is indi-
cated.

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 Chapt. 9 Evaluate

G If you click this button, all areas including the relevant infor-
mation will be deleted. Note: Before you set up a new
method click this button to delete possible default set-
tings caused by the previously loaded integration
method.
H Click this button to load or edit an existing method.
I To save all the settings made click this button and define an
appropriate name for the currently created method.

Integration Modes

The following types of integration modes are available:

The integration will be performed between the band,

abscissa and the frequency limits defined.

A straight line is drawn between the peaks of the two fre-

quency limits defined. The area above this line will be
integrated.

The baseline is determined by the first and second base-

line point. The area within the band will be integrated.

The baseline is horizontal and determined by the base-

line point defined.

To eliminate noise the average peak values between the

1st and 2nd as well as the 3rd and 4th baseline point are
averaged. These average values form the baseline in
combination with the abscissa of the 2nd and 3rd base-
line point.

The baseline is determined by a least square fit of a

parabola to the data points between the 1st and 2nd,
and between the 3rd and the 4th baseline point.

Looks for the highest peak between the left and right
edge, and for the minima on the left and right of this
highest peak. The baseline connects these minima.

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Integrates from the left minimum to the maximum.

Integrates from the maximum to the right frequency min-

imum.

Highest absolute peak intensity

Peak intensity relative to the local baseline

Peak intensity relative to the baseline (analog to D)

Peak intensity relative to the horizontal baseline

Peak intensity relative to the baseline defined by the

minima

Minimum between the frequency limits

Intensity at the specified frequency

Peak intensity relative to the baseline (analog to E)

Peak intensity at a given frequency

Defines the minimum between the 1st and 2nd as well as

3rd and 4th baseline point. A straight line, which forms
the baseline, is drawn between these two values. Inte-
gration is performed between left and right edge.

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9.2.2 Interactive Method Setup

The interactive method setup allows to define the single parame-

ters even more precisely. In this case the spectrum file loaded is
displayed in a separate view.

1 On the Integration dialog, click Interactive Method Setup

(see figure 263).
2 Make the settings required in the view displayed (see
figure 259).
3 Store the method by clicking the Store As Method button.
Define an appropriate name for the method.

Note: If you close the view without saving the settings

made, they will be discarded.

The interactive method setup view is described in the following.

Figure 259: Integration - View of interactive method setup

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A The integration modes A, B, D, J, K and R (see chapter 9.2.1)

are available for the interactive method setup. Select the
mode desired from the list box.
B Use this entry field to define an individual label for each area.
The number above this entry field indicates the order in which
the integration areas have been defined.
C Use the arrow buttons to switch between the single areas.
D These buttons allow to either delete one particular area or all
areas including the parameters defined. Note: Before you
set up a new method it is advisable to click Delete All to
delete possible default settings caused by the integration
method previously loaded.
E Click this button to load or edit an existing method.
F To store all settings made click this button and define an
appropriate name for the method.

Adding Integration Area

1 Double click the desired position in the spectrum or left click

somewhere below the spectrum, draw a line and release the
mouse button.
2 The frequency limits (A in figure 260) of the integration areas
are indicated by the exact wavenumber. To edit the wave-
numbers displayed, click into the respective entry field and
change the value.

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Figure 260: Activated and non activated integration areas

The activated integration area of integration mode A and B is dis-

played in red (B in figure 260), non-activated areas are displayed in
bright red (C). In case of integration mode J and K the limits and
maximum spectrum value are displayed by black vertical lines.

Moving Integration Area

1 Position the cursor onto the respective integration area. The

cursor changes to .
2 Move the complete integration area to the desired position
while pressing the left mouse button.

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Figure 261: Moving integration area

Reducing or enlarging integration area

1 Click the outer edge of the integration area. The cursor

changes to .
2 Press the left mouse button and reduce or enlarge the area
to the size desired.

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Figure 262: Reduc-

9.2.3 Sta r t i n g I n t e g r a t i o n
1 Load the spectrum file.
2 Select the Integration command. A dialog opens which con-
tains the name of the spectrum file in the File(s) to integrate
selection field.

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Figure 263: Integration - Select Files

3 Load the integration method created by clicking the Load

Integration Method button.
4 Define the storage mode for the integration report on the
Report tab, if required.
5 Click Integrate to start this evaluation command. If integra-
tion has been finished the integration data block ( ) is
displayed in the browser.

The integration result...

...is displayed in the spectrum window together with the spectrum.

The integration area has the same color as the spectrum dis-
played.

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Figure 264: Integration result displayed in spectrum window

To delete the integration result from the spectrum window right

click the integration data block ( ) and select the Remove from
Display command from the pop-up menu.

To restore the integration result again click the integration data

block ( ) and drag & drop it into the spectrum window.

To d i s p l a y t h e i n t e g r a t i o n r e s u l t i n a
report view

1 Right click the integration data block ( ).

2 Select the Show Report command from the pop-up menu.
The report view is displayed and contains the name of the
integration method, the label of the integration area as well
as the frequency limits.

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Figure 265: Integration report

The integration report shown in figure 265 is based on an absorp-

tion spectrum (AB) and includes two bands (peak 1 and peak 2)
which have been integrated by mode A (see chapter 9.2.1).

In case of this mode the result will be an integral which is indicated

by the Result column. Mode A requires 2 frequencies per area,
indicated in the Freq 1 and Freq 2 columns.

St o r i n g R e p o r t

If the same spectrum is integrated once again, e.g. by using a dif-

ferent method, you can select between three different options avail-
able on the Report tab to store the integration report.

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Figure 266: Integration - Report

A This option button is activated by default and allows to

replace an existing integration report.
B If you activate this option button, the integration result is
added to an existing report.
C If you activate this option button, a new single report will be
created and appended to the existing file.

9.2.4 Printing Integration Result

1 On the Print menu, click Print Spectra. A dialog opens.
2 Click the Change Layout button. Select a layout template
from the C:\Users\Public\Public Docu-
ments\Bruker\OPUS_<version> directory. The layout tem-
plate should contain a spectral frame, e.g.
spectrum_Integ.PLE.
3 To get a preview of the spectrum and the integration areas
click Show preview.
4 Click Print.

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A spectrum file evaluated by integration can also be used to create

a new layout template. For further details on how to create a spec-
tral frame layout template refer to chapter 11.5.4.

9.3 Setup QUANT Method

Definition This command allows to set up a QUANT method

which is required to be able to perform a QUANT
analysis.

Principle A wizard will guide you step by step through the setup
of a QUANT method. Follow the on-screen instruc-
tions.

A Q U A N T m e t h o d c o n s i s ts o f :

• Concentration values of sample component

• Spectra
• Integration area

In case of a QUANT method...

...calibration spectra are required. This so-called set of calibration

samples should contain the component to be analyzed in various
concentration values. The concentration value of this component in
each single sample has to be known and can be determined, e.g.,
by weighing when preparing the sample.

Note: Ideally, the calibration sample set should contain at

least 5 samples. Make sure that the concentration val-
ues of the component to be analyzed are different
with the single calibration samples.

A calibration can be performed by using the known component val-

ues and spectra generated from the calibration samples. Each
component is assigned to exactly one isolated peak in the spec-
trum. Finally, a calibration function (linear, quadratic or polynomial)

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is fitted to the data obtained from the calibration samples, and this
function is then used to determine the concentrations of the
unknown sample.

In case of IR spectra it is recommended to depict them in absorp-

tion. Ideally, for weakly absorbing compounds, a linear correlation
between the concentration and the absorption is to be expected
(Lambert-Beer law).

To s e t u p a Q U A N T m e t h o d . . .

...select the Setup QUANT Method command. The following dialog

opens:

Figure 267: Wizard to set up QUANT method

The first dialog gives a short overview of the steps required to set
up a method. You can load and edit an existing method. Click Next
to continue with the next dialog.

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Figure 268: Set up QUANT method - Define components

Specify the component names and the appropriate unit. Click the
Add Component button.

Comp.1 is displayed as default name for the first component and

mg as default unit of the components in the respective entry fields.

Click again the Add Component button until the desired number of
components has been reached.

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Figure 269: Adding components

The terms for the component and unit can be changed. Select the
respective component and enter the definition into the appropriate
entry field. Click the Set button to update the list.

To delete a component from the list, select it and press the Del key
on your keyboard.

Click Next.

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Figure 270: Set up QUANT method - Enter component values

Click Add Spectra to add spectra to the list.

Based on the type of unit specified enter the value of each compo-
nent for each sample of the calibration set.

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To change the path of the spectra directory click the Change Path
button. If you want to remove a spectrum from the calibration set,
select the spectrum and click the Remove Selected Spectra button.

Click Next to continue.

Figure 271: Set up QUANT method - Define integration areas

Now, you have to define one isolated peak for each single compo-
nent. Either the peak height or integral is used for calibration. Click
the Set Integration Area button. The following dialog is displayed:

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Figure 272: Set up QUANT method - Define integration areas

Define the left and right edge of the integration area by either enter-
ing the values in the respective entry field or clicking the Interactive
button. In case of some integration modes you have to make fur-
ther settings. For information on integration modes refer to
chapter 9.2.1.

If you activate the Use reference peak button, make sure that you
also select the Reference Peak option from the drop-down list.

The reference peak will be used to normalize the spectrum.

If all settings have been made, click OK to get back to the wizard.
In the next dialog you have to select the type of calibration curve.

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Figure 273: Set up QUANT method - Select calibration curve

You can choose between a linear, quadratic or cubic calibration

curve. In case of the last two curve types deviations from Lambert-
Beer law can be taken into account, under certain circumstances.

If you click Calibrate, you will be asked to store the method. After-
wards the calibration curve is calculated for each component and
displayed accordingly.

Depending on the number of calibration spectra, this may take a

few seconds.

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Figure 274: Fit vs. True calibration curve

Below the graphics, the method file, correlation coefficient and cali-
bration equation are indicated.

Apart from the Fit vs True (fit vs the known values) depiction type
you can choose between Difference vs. True (difference vs known
values) and True vs. X (known values vs peak intensity).

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Figure 275: Difference vs. True calibration curve

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Figure 276: True vs. X calibration curve

You can print the results, figures as well as data tables by clicking
Print. The calibration results, graphics and tables as well as the cal-
ibration equation are stored together with the method file.

Click Next to have the calibration report displayed for each compo-
nent separately.

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Figure 277: Setup QUANT Method - Calibration report

Use the slider to get to the lower end of the reports.

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Figure 278: Setup QUANT Method - Calibration results in report view

A table shows the known value (true) of the sample and the value
calculated by the fit. It also shows the difference between these
values, the error of the calculated value and the peak size X calcu-
lated from the spectra.

You can have the results displayed in a report view or table. Acti-
vate or deactivate the Calibration report check box.

Figure 279: Setup QUANT Method - Calibration results in table

Clicking Finish closes the wizard.

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9.4 QUANT Builder (via

O P US w i z a r d )

Definition This command allows to set up a method for quantita-

tive analysis of spectra during sample measurement.

Principle • Prepare a set of samples required to set up a

QUANT method.
• Determine the exact concentration value of the sam-
ple component by using a different technique (e.g.
weighing). This kind of samples are called calibra-
tion samples in the following.
• Set up a QUANT method by using the QUANT
Builder command and the calibration samples.
• Start quantitative analysis by using the QUANT
method set up before and the Quantitative Analysis
command.
• Interpret the analysis.

How to work with QUANT Builder?

1 Measure the first sample by clicking the Advanced

Measurement button in the wizard. The Measurement dialog
opens.
2 Start a background measurement before the sample mea-
surement. Click Background Single Channel. Note: In case
of a background measurement there is no sample in the
sample compartment (transmission) or on the ATR crys-
tal. This kind of measurement is also called reference
measurement.

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1 2

Figure 280: QUANT Builder - Perform measurement

3 Start the sample measurement. Click Start Sample Single

Channel.
4 If the sample measurements have been completed, open the
QUANT Builder.

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Click the appropriate button on the wizard Evaluate level or

select QUANT Builder from the drop-down list. In the latter
case click Go to open QUANT Builder.

Figure 281: Wizard - QUANT Builder

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5 The QUANT Builder - New dialog is displayed.

Figure 282: QUANT Builder

6 The selection field (A in figure 282) contains the spectrum

file name of the sample measured before.
7 Enter the name (B) of the component to be analyzed as well
as the unit (e.g. mg, % etc.). The entries made are displayed
above this group field (see broken arrow lines in figure 282).
8 Enter the concentration value (C) of the component. On the
basis of this value and the corresponding spectrum a calibra-
tion straight line is calculated. The concentration value is dis-
played on this calibration straight line. If you have entered a
wrong concentration value, write the correct value into
the entry field.
9 When creating a new method, the New option button (D) is
activated by default.
10 Define one isolated peak for the component, which peak
height or integral is to be used for calibration. Click the Set
Integration Area button to open the following dialog:

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Figure 283: Define integration area

• Select an integration mode. For detailed information on the

single integration modes refer to chapter 9.2.
• Define the integration area. If you position the cursor on the
area edge, the cursor changes to . Now, you can move
the limit to the position desired. Note: Set the integration
area such, that the band of the sample component to be
analyzed is within this integration area.
• Return to QUANT Builder by clicking Go to QUANT.

St o r i n g Q U A N T m e t h o d

1 On the QUANT Builder dialog, click Save (see figure 282).

2 The following dialog opens:

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Figure 284: Store QUANT method

3 Enter the desired method file name and define the path.
QUANT methods have the extension *.q1.
4 If the settings have been made, click Save.

Measuring further samples

Measure all samples required for the set of calibration samples.

Repeat the steps described above for each sample by means of
QUANT Builder.

Note: Measuring the second and all subsequent calibration

samples does not require to create a new method. It is
possible to add the spectrum/spectra to the method
currently used.

The Add Spectrum option button is activated in QUANT Builder.

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Figure 285: QUANT Builder - Add spectrum

Note: Click Save to allow the spectrum to be added to the

current method. If you click Cancel, the current
method will not be modified.

QUANT Builder closes after saving the method. Continue sample

measuring by clicking Measure Next Sample on the Evaluate level
in the wizard.

Figure 286: Wizard - Measure next sample

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Changing QUANT method

Activate the Change option button in QUANT Builder. The dialog is

displayed as follows:

B
Figure 287: QUANT Builder - Change method

A Activate this option button if the current method is to be

changed. The following changes are possible:
- Value of component
- Name of component
- Integration area
B Select a depiction type for the calibration graph. The following
types are available:
- Fit vs True (adaptation against the known component
value)
- Difference vs True (difference against the known compo-
nent value)
- True vs X (applying known component value against inten-
sity of bands
C Use the Load Method button to load an already existing
method.

To delete a particular calibration spectrum from the graph double

click the respective spectrum.

If all changes have been set, click Save.

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9.5 Q u antitative Analysis

Definition This command allows to determine un unknown com-

ponent concentration value. In most cases the con-
centrations are chemical substances of samples.

Calculating the concentration value on the basis of

the spectrum measured requires a calibration to be
performed before (see chapter 9.3).

Principle • Load the spectrum file.

• Select the Quantitative Analysis command.
• If required, drag & drop the spectrum file into the
File(s) for Quantitative Analysis selection field.
• Load a QUANT method set up before (see
chapter 9.3).
• Click Analyze to start this evaluation command.

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Figure 288: QUANT Analysis - Select Files

A The QUANT method previously used is displayed by default.

T h e r e s u l t o f a q u a n t i ta t i v e a n a l y s i s . . .

• ...is stored in the QUANT data block ( ).

• is displayed in a separate view after the analysis has
been performed.

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Figure 289: Result of quantitative analysis

The QUANT result contains the following types of information:

• name of the component which has been analyzed by
QUANT
• concentration value (prediction) of the respective com-
ponent, calculated by OPUS
• standard deviation (sigma1) of the calculated prediction
value
• unit in which the calculated concentration value is given
• the integration result for the spectral band which results
from the component to be analyzed.

To d i s p l a y t h e q u a n t i ta t i v e a n a l y s i s r e s u l t
i n a r e p o r t w i n d o w. . .

1 ...right click the data block in the browser.

2 Select the Show Report option from the pop-up menu.
3 The report window opens and contains the name and date of
the analysis method, as well as the name of the component
which has been analyzed.

1. Sigma is the standard deviation of the concentration value calculated. The sigma
value is determined by the quality of the QUANT method set up. Ideally, the sig-
ma value should be as small as possible.

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Figure 290: Parameters of QUANT analysis in report view

You can apply more than one QUANT method to analyze a spec-
trum. In this case the results are stored in one single QUANT
report.

On the left side of the report view there will be several Quantitative
Analysis 1 Report folders. Clicking the respective folder shows the
corresponding analysis parameters on the right side.

9.5.1 QUANT Analysis Theory

The functions used for calibration are indicated in the calibration

report as Y = f(X), with Y being the value obtained by the fit, and X
being the peak size obtained from the spectra.

The difference between the true component values (True) and the
predicted values can be indicated by . Note that the true values
are also prone to statistical errors, depending on how carefully they
have been determined. The correlation coefficient r is an indicator
for the quality of calibration:
   Zi – Zm   Yi – Ym  
r = --------------------------------------------------------------------
  Zi – Zm  2   Yi – Ym  2

In this case Z represents the true concentration of the components,

while m is the respective average value. The correlation coefficient
should be close to 1.0.

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The error in analyzing samples of unknown concentration can be

estimated by . There is a ~68% probability that the concentration
of the unknown sample falls within an interval of the predicted
value plus or minus :
1 -
M – f i
 = -----------  Z – Yi 2

• M: number of calibration samples

• f: degree of freedom (linear 2, quadratic 3, cubic 4)
• Z: true concentration
• Y: predicted concentration

9.6 S i gnal-to-Noise-Ratio

Definition This command calculates the signal-to-noise ratio

(SN) of a spectrum within a given spectral range.

Note: The calculation is only reasonable in case

of spectra which are constant, except for the
noise, within the frequency range to be analyzed.
Use transmission spectra only.

Principle • Load the spectrum file.

• Select the Signal-to-Noise-Ratio command.
• If required, drag & drop the spectrum file into the
File(s) to compute signal-to-noise selection field.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Calculate to start this evaluation command.

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Figure 291: Signal-to-Noise-Ratio - Select Files

A If you activate this check box, a parabola is fitted to the curve.

Otherwise, a linear function is fitted to the data.
B If you activate this check box, the results of the fit will be dis-
played immediately after the calculation has been finished.

On the Frequency Range tab you can select between different fre-
quency ranges which have been pre-defined.

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Figure 292: Signal-to-Noise-Ratio - Frequency Range

You can also interactively select the frequency range or use the
current file limits (see also chapter 2.9). If you click Calculate, the
signal-to-noise ratio will be determined.

The calculation result...

...is displayed in a separate dialog on the screen as follows:

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Figure 293: Result of SN calculation

Minimum and Maximum gives the extrema of the ordinate values of

the evaluated range.

To s t o r e t h e r e s u l t . . .

...click Yes (A in figure 293). The OPUS spectrum window displays

the spectrum including the calculated SN ratio.

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Figure 294: Spectrum with SN

To s h o w t h e r e s u l t i n a pa r a m e t e r l i s t

1 Right click the name of the spectrum file in the OPUS

browser.
2 Select the Show Parameters option from the pop-up menu.
The report view opens.

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Figure 295: Parameter list with SN

9.6.1 Theory on SN calculation

Two values are calculated for the noise output:

• RMS (Root Mean Square) - this value is the square root
of the sum resulting from the squared deviations for all
data points within the range selected, divided by the
number of data points. The following equation applies:
  y i – y iFit  2
RMS = -----------------------------
N
yiFit represents the value of the curve adapted (constant
or parabola).
• PP (Peak to Peak) - this value is the difference of the
minimal and maximal bands within a spectral range,
after deducting the adapted curve from the spectrum.
The following equation applies:
PP = y Maximum – y Minimum

In both cases a curve is fitted to the spectrum in the spectral range

of interest. This curve is either a constant or (optionally) a quadratic
parabola, and defines the (nominal) signal. The SN can be calcu-
lated for both noise amplitudes (RMS and PP). The following equa-
tions apply:

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Signal
• SN (RMS) = -----------------
RMS

Signal
• SN (PP) = ---------------------------
PP  Noise 

RMS and PP are divided by the average intensity. The (mean)

nominal signal is divided by the calculated noise values and results
in SN. The PP SN value is normally lower (worse) than that for
RMS SN.

9.7 P e a k Picking

Definition This command allows to identify the maxima (absorp-

tion spectrum) or minima (transmission spectrum) of
a spectrum.

Note: The maxima and minima are also called

peaks.

Principle • Load the spectrum file.

• Select the Peak Picking command.
• If required, drag & drop the spectrum file into the
File(s) to peak picking selection field.
• Define the peak heights on the Y-Limits tab, which a
peak has to show to be included in the peak list.
• Select the peak picking method on the Mode tab.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Click Peak Picking to start this evaluation com-
mand.

Note: Interactive peak picking is also possible,

see chapter 9.7.1.

In the following the different tabs are described in more detail.

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Select Files

Figure 296: Peak Picking - Select Files

A By default, the sensitivity is defined by 20%. The higher this

threshold is the less peaks are displayed. To change this
threshold click into the entry field and enter the desired value
manually.
B Clicking this button starts the interactive peak picking mode,
see also chapter 9.7.1.

Frequency Range

To select a frequency range is described in more detail in

chapter 2.9.

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Y- L im its

Figure 297: Peak Picking - Y-Limits

A The relative peak height allows to define a maximum peak

intensity in relation to the surroundings of the peak and the
baseline. If you select this option, you first have to activate the
check box and enter the value (per cent) manually.
B In case of absolute peak height the limits are set in absorption
units, i.e. peak picking is performed between these limits set.
If you select this option, you first have to activate the check
box and enter the value (per cent) manually.

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Mode

This tab allows to define the direction of peaks and the peak pick-
ing method. In case of absorbance spectra usually the maxima are
of interest, whereas for transmittance or reflectance spectra the
minima are the important features.

Figure 298: Peak Picking - Mode

A If you check the Automatic option button, OPUS uses the

spectrum type information stored in the data block to deter-
mine if maxima or minima are picked. In few cases (e.g. when
subtracting photoacoustic spectra) it is necessary to specify
whether the algorithm should pick minima (i. e. transmittance
spectra) or maxima (i. e. absorbance spectra).
B The standard method is generally used for peaks with small
or no overlapping in spectra. This method is especially rec-
ommended in case of low or average spectral resolution
(0.5cm-1 or above).
C To be independent of the baseline, the second derivative
algorithm is typically used, since the first derivative does not

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isolate peaks sufficiently well in case of weak shoulders. The

Savitzky-Golay algorithm is actually used to obtain the deriva-
tive. Recommended in case of high resolution spectra.
To suppress the effect of noise define the number of smooth-
ing points. As a rule of thumb, the number of smoothing
points should not be greater than the full width at half maxi-
mum of the smallest peak of interest. This value is ignored
when using the standard method.
D This algorithm calculates, from a certain fraction of peak
height, the centroid of an area. The position of this centroid
determines the peak position. Specify which portion of band
area (in %) has to be considered to calculate the gravity, in
the Fraction of peak height entry field. You can only enter
integers between 1 and 99.
E If you use the Peak Picking command on a spectrum that
already has a peak table appended, you can either overwrite
the previous table by the new one, or append the new table to
the existing one.

The peak picking result...

... is stored in the data block. This data block is attached to

the spectrum file and displayed in the OPUS browser.

To d i s p l a y t h e p e a k p i c k i n g r e s u l t i n a
peak list

1 Right click the data block.

2 Select the Show Peak List option from the pop-up menu. A
report view opens which contains the limit value set for sen-
sitivity as well as the number of bands.

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 Peak Picking Chapt. 9

Figure 299: Peak picking result displayed in peak list

9.7.1 In t e r a c t i v e P e a k P i c k i n g
1 Load the spectrum file.
2 Select the Peak Picking command. The Peak Picking dialog
(see figure 296) is displayed.
3 Click the Start Interactive Mode button. The following view is
displayed:

Figure 300: Peak Picking - Interactive mode

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Wor k i n g i n i n t e r a c t i v e m o d e

According to the threshold value set by the slider (A in figure 300)

the number of identified peaks changes. The lower the threshold is
the more peaks are displayed.

A line (B in figure 300) is shown by default which can be moved

upwards and downwards to define a certain threshold value for
peak picking.

Note: In some applications very small bands may be

neglected, and in other cases high-intensity peaks
are normal and thus the low-intensity peaks may be
crucial. These different kinds of requirements can be
met by using a suitable combination of the settings
made by the slider and those made by defining a cer-
tain threshold value.

Moving Line

Left click the line point and move the line upwards or down-
wards.

Note: If the threshold has been changed, only those peaks

will be displayed which are above (absorption spec-
trum) or below (transmission spectrum) this line.

To remove the line from the view, just double click the line point.

Setting Line Point

Double click the line. A new line point is displayed.

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Drag the line point to the position desired while pressing the left
mouse button.

St o r i n g I n t e r a c t i v e P e a k P i c k

Click Store (see figure 300). The interactive mode view closes and
the spectrum window is displayed again.

The interactive peak picking result is stored in the data block.

This data block is attached to the spectrum file and displayed in the
OPUS browser.

9.7.2 Theory of Peak Picking

Sta n d a r d M e t h o d

The standard method is used for peaks with small or no overlap-

ping in spectra of low or average spectral resolution (0.5cm-1 or
above).

The x-position is the x-value of the interpolated maximum or mini-

mum, with intensity being the y-value of this point. To determine
the relative intensity an internal local baseline between two lateral
minima (or maxima) is drawn. The relative intensity is then the y-
axis distance between this baseline and the maximum (or mini-
mum).

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Half width

Relative
intensity

Local baseline

Figure 301: Spectrum with line width, relative intensity and baseline indicated

The lateral extremes are searched, starting from the x-position of

the band, until a different band (or the end of the spectrum is
reached), which is at least as strong as the first one, has been
found. The lowest point within this interval is then used as a lateral
minimum (or maximum).

To determine the half width, a line parallel is drawn to the local

baseline which intersects the middle of a vertical line connecting
the maximum (or minimum) of the band and the local baseline. The
distance between these two line parallel intersection points and the
spectrum are the half width.

Peaks will be included into the peak pick table if their relative inten-
sity is within the interval defined on the Y-Limits tab. This interval
has been normalized such that the difference between maxima and
minima corresponds to 100%.

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Figure 302: Calculation with baseline reference

Second Derivative Method

Peak picking by using the second derivative method is only recom-

mended for spectra where peak positions of strongly overlapping
bands are to be determined.

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Figure 303: Absorptions spectrum and second derivative

The x-positions of the bands are the x-values of the minima (or
maxima) second derivative spectrum which has been smoothed.
This is particularly useful for seriously overlapping bands because
in this case an extremity of the spectrum is frequently not shifted
with respect to the true band position. Weak shoulders can also be
recognized using the second derivative method.

In order to calculate the relative intensities and the half width, the
two zero-points and the minima of the second derivative are
searched.
• [  –1 ,0 ] (zero-point)
• [  0 ,I 0 ] (minimum)
• [  –1 ,0 ] (zero-point)

These points are typical for the original peaks, i.e. before being
overlapped by other lines as the following examples show
(figure 304) where two Lorentzian curves are superimposed. The
zero-points and the minima of both signals are almost identical
(both for the derivatives of the isolated signals as well as for their
superposition). The maxima of the overlapped signals, however,
are shifted and therefore misleading.
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 Peak Picking Chapt. 9

Apparent peak positions

True peak positions

Apparent peak positions

True peak positions

Figure 304: Apparent and true peak positions

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Center of Gravity Method

In case of symmetric bands the center of gravity method provides

the same results as the standard method. In case of antisymmetric
bands the band position is moved towards the broader edge. This
interacts with the size of the peak height used for the calculation.

If the fraction of peak height is too small, the band will not be listed
on the band list. Too small a fraction of peak height could decrease
the number of measuring points, used to calculate the band posi-
tion, to less than 3.

The band position is calculated as follows:

Based on the band maximum Y max X max , which is usually not the
maximum of the measuring values, the measuring points are con-
secutively numbered to the left and right.

The numbering starts from 0 for both sides, while the y- value of
each measuring point must be greater than
Y i  Y max –  Y max – Y min   Fraction , with Y i being the measurement values,
and the Fraction term being the percentage value defined for the
peak height. This yields to the following sums:

SumY =   Y right  i  – Y Fraction  +   Y left  i  – Y Fraction 

i=0 i=0

SumYX =   Y right  i  – Y Fraction    i + 0 ,5  –   Y left  i  – Y Fraction    i + 0 ,5 

i=0 i=0

Thus, the band position yields

PeakPos COG =  x max  + 0 5 + SumYX

------------------
SumY

with  x max  being the next smaller integer of the x-value for the
band maximum.

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The band position in wavenumber units is:

PeakPos COG  v  = PeakPos COG  v + v min and v being the wavenumber dis-
tance between two measuring points and vmin being the wavenum-
ber of the first data point.

Figure 305: Band edge

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9.8 Qui c k Id en tity Tes t

Definition This command provides the possibility to compare

the spectrum of a substance with a reference file. The
test determines the Euclidean distance between the
test and reference spectrum.

Principle • Load the reference spectrum file.

• Select the Quick Identity Test command.
• Drag & drop the spectrum file into the Principal file
for Quick Identity Test selection field.
• Drag & drop the file to be tested from the OPUS
browser into the respective entry field.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Specify the type of data preprocessing on the Data
Preprocessing tab.
• Click Quick Identity Test to start this evaluation
command.

Figure 306: Quick Identity Test - Selected Files

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 Quick Identity Test Chapt. 9

On the Frequency Ranges tab you can define several frequency

ranges. The test only refers to the frequency ranges selected.

Figure 307: Quick Identity Test - Frequency Ranges

If you activate the Use file limits check box the complete spectra
are compared with each other. For further details on defining fre-
quency ranges refer to chapter 2.9.

On the Data Preprocessing tab you can perform a spectrum deriva-

tive and vector normalization. The latter has to be selected to be
able to set the scale level of the spectral distances to a value range
between 0 and 2.

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Figure 308: Quick Identity Test - Data Preprocessing

The quick identity test result...

... is stored in the data block. This data block is attached to

each spectrum file which has been compared to the principal file
and displayed in the OPUS browser.

To d i s p l a y t h e q u i c k i d e n t i t y r e s u l t i n a
report view

1 Right click the data block.

2 Select the Show Report option from the pop-up menu. A
report view opens which contains the spectrum number, hit
quality (spectral distance), sample and file name (based on
the spectrum parameter block).

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Figure 309: Quick identity test - Report view

The closer the hit quality is to 0, the better the spectra matches
within the frequency ranges used. In case of the quick identity test
the following report lines are important:
• Method file: shows the name of the method used for
the test
• Expected Reference: shows the name of the principal
file used
• Vector normalizes spectra: indicates whether a vector
normalization has been used
• X-Ranges: number of frequency ranges
• Order of Internal Derivation: defines the order of the
derivative used
• Smoothing Points for Internal Derivation: defines the
number of smoothing points

Q I D N T. 0 F i l e

During evaluation the QIDNT.0 file is generated and stored in the

C:\User\<User name>\My Documents\Bruker\OPUS\WORK. This
file is displayed in the browser and contains a report which summa-
rizes the reports of all spectra tested. The headers of this report is
identical to the report for each single spectrum file.

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9.9 Qu al i t y Te st

Definition This command assesses the quality of spectra mea-

sured with regard to absorbance values, signal-to-
noise ratio and intensity of the water vapor lines.

Note: Do not use spectra which exceed certain

limit values for analysis.

Principle • Load the reference spectrum file (only a spectrum

file which contains an absorption data block).
• Select the Quality Test command.
• If required, drag & drop the spectrum file into the
File(s) for Quality Test selection field.
• Set up a method (see the following description).
• Click Quality Test to start this evaluation command.

B e f o r e y o u c a n s ta r t a q u a l i t y t e s t . . .

1 ...you have to set up an appropriate test method.

2 On the Load/Save Method tab, click Load method and define
a name for the method.

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Figure 310: Quality Test - Load/Save Method

The method is based on the parameter settings made on the

Parameters tab. Quality test methods have the extension *.QT.

If the method has been set up,...

1 ...you start the quality test.

2 Make sure that the spectrum file loaded is displayed in the
File(s) for Quality Test selection field on the Select Files tab.
3 Click Quality Test.

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Figure 311: Quality Test - Select Files

The quality test result...

... is stored in the data block. This data block is attached to

the evaluated spectrum file and displayed in the OPUS browser.

To d i s p l a y t h e q u a l i t y t e s t r e s u l t i n a
report view

1 Right click the data block.

2 Select the Show Report option from the pop-up menu. A
report view opens.

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 Quality Test Chapt. 9

Figure 312: Quality test - Report view

The first line of the report indicates the test result. A value of 1
means test passed, whereas 0 means test failed. For further analy-
sis do not use spectra which have not passed the test. The second
line includes the name and path of the test method used.

The lower end of the report shows all parameters and their limit val-
ues (minimum and maximum) as well as their measured values.
These parameters set can be edited on the Parameters tab of the
Quality Test dialog.

9.9.1 Defining Parameters

The parameters defined on the Parameters tab are set by default.

To c h a n g e t h e pa r a m e t e r s e t t i n g s . . .

...click into the respective entry field and enter the desired value
manually.

To r e s e t t h e pa r a m e t e r s . . .

...click the Reset method button on the Load/Save Method tab.

Each parameter keeps its default value.

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 Chapt. 9 Evaluate

Figure 313: Quality test - Parameter

Range Definition

x-Range 1 The range defined in the first column (2100 - 1600cm-1)

calculates the maximum and minimum absorbance values
of the original spectrum ([AB] data block). The difference
between these two values has to be higher than the one
indicated in the Delta y min entry field and lower than the
limit defined in the Delta y max entry field (0.345 to 1.245
absorbance units).

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Range Definition

x-Range 2 The range defined has to represent a characteristic band

of the sample (Amide I at 1700 - 1600cm-1). The first
derivative is calculated and the maximum and minimum
absorbance values are determined. The difference
between these two values results in S1, a parameter which
approximately corresponds to the intensity of the band
defined.

S1 is used to calculate the signal-to-noise ratio, i.e. S1 is

divided by the noise determined from the first derivative
within a spectral range which shows no absorbance bands
(as defined in the x-Range 4).

The minimum S1/Noise-ratio value is indicated in the Sig-

nal/Noise entry field (value: 200).

S1 is also divided by the water vapor signal determined in

the x-Range 5. The minimum S1/WaterVapor-ratio value is
indicated in the Signal/Water entry field (value: 100).

x-Range 3 The range defined has to represent a second characteris-

tic sample band (sugar-ring vibration at 960 - 1260cm-1).
The first derivative is calculated and the maximum and
minimum values are determined. The difference between
these two values results in S2, a parameter which approxi-
mately corresponds to the intensity of the band defined.

S2 is used to calculate the signal-to-noise ratio, i.e. S2 is

divided by the noise determined within a spectral range
which shows no absorbance bands (as defined in x-Range
4). The minimum S2/Noise-ratio value is indicated in the
Signal/Noise entry field (value: 40).

S2 is also divided by the water vapor signal determined in

the x-Range 5. The minimum S2/WaterVapor-ratio value is
indicated in the Signal/Water entry field (value: 20).

x-Range 4 The spectrum noise is calculated within a spectral range

that shows no absorbance bands of the sample (range:
2000 - 2100cm-1).

In this range the first derivative is calculated and the maxi-

mum and minimum values are determined. The difference
between these two values is termed noise and should not
exceed the maximum value defined in the Noise max entry
field (value: 0.00015, i.e. 1.5 x 10-4).

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Range Definition

x-Range 5 The water vapor intensity is calculated in a spectral range

which indicates strong water vapor absorbance but no
sample absorbance (range: 1847 - 1837cm-1).

The first derivative is calculated and the maximum and

minimum values are determined within the range defined.
The difference between these two values causes this
strong water absorbance. The value should not exceed
the maximum value defined in the Water max entry field
(value: 0.0003).

x-Range 6 The frequency range is determined if the spectrum shows

interferences (fringes). The defined frequency range has
to be free of any sample absorbance (range: 2200 -
2000cm-1).

The maximal difference between the highest and lowest

value of the first derivative is defined in the Fringes table
line (value: 5 x10-5).

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9.10 Multi Evaluation Setup

Definition This command allows to generate a multi evaluation

(ME) method. In case of multi evaluation different
types of evaluation methods are combined and
applied to one individual spectrum.

Principle • Select the Multi Evaluation Setup command.

• Add one or several evaluation methods.
• Store the ME method.

General Features

The advantage of multi evaluation when analyzing an unknown

sample is that first an identity test (IDENT) analysis can be per-
formed.

Based on the results obtained by this IDENT analysis, you can con-
tinue with a quantitative (QUANT)1 analysis using the same sam-
ple.

This procedure can be helpful in many cases to check whether the

product intended to be used for a quantitative analysis has been
measured at all. The combination of an IDENT analysis and confor-
mity test may similarly be appropriate.

1. You can also perform a QUANT evaluation by using PLS models which have
been created by Unscrambler 9.8. The following preconditions must be met:
- Install the OLUP 9.8 version (this is the only version possible) produced by
Camo into the respective program directory (e.g. C:\Program
Files\Bruker\OPUS_<version>).
- Copy the OLUP.SYS file from the OLUP 9.8 installation directory into the OPUS
root directory.
- To be able to use the OLUP prediction engine in OPUS, you MUST have an
OPUS registry which contains the QUANT or QUANTRUNTIME packages.
- Copy ALL files (e.g. *.42m etc.), which belong to an Unscrambler model, into
the *\OPUS_<version>\ME_Base\Quant directory.
You can use this PLS model for the OPUS Multi Evaluation Setup by adding a
QUANT 2 method.

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M E M e t ho d

Possible components: IDENT, QUANT methods, integration

and/or conformity test method

File extension: *.mev

Directory path: C:\Users\Public\Public Docu-

ments\Bruker\OPUS_<ver-
sion>\ME_Base\ME

Note: To change the ME path you require the OPUS user

right to change parameters. For further details, see
chapter 14.10.

Options of product analysis within an ME

method

• IDENT (no further test)

• IDENT  Conformity Test
• IDENT  Conformity Test  QUANT
• IDENT  Integration
• IDENT  QUANT
• Conformity Test (no further test)
• Conformity Test  QUANT
• Integration (no further test)
• QUANT (no further test)
• QUANT  QUANT1

If you use an IDENT method with several substance groups, and

the test result is not clear or false, no further test would be per-
formed.

An ambiguous result, however, will only be generated if the basic

IDENT method had not been validated properly and overlappings
had not been eliminated either.

1. Only possible with QUANT 2 methods (chapter Adding next step QUANT 2)

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If only one substance group applies to the product, you can con-
tinue multi evaluation by performing a conformity test and/or
QUANT evaluation.

It is also possible to perform multi evaluation by the conformity test

only. If one conformity test method turns out to be successful, you
can continue with the QUANT evaluation.

Applying a QUANT method, without performing an IDENT or con-

formity test, can be useful if the original QUANT result has to be
corrected by, e.g. offset correction, or if warning or alarm limits
have to be set.

9.10.1 F i r s t s t e ps
1 Generate evaluation methods for qualitative and quantitative
analysis (IDENT and QUANT methods). Optionally,
generate methods for integration and conformity test as well.
2 Store the evaluation methods generated in the correct
OPUS directory available for multi evaluation:
- *\OPUS\ME_BASE\Ident or
- *\OPUS\ME_BASE\Quant

Note: To be able to perform multi evaluation you first have

to store the appropriate evaluation methods into the
corresponding OPUS directories. Otherwise, multi
evaluation is not possible.

Store conformity test methods into the *\OPUS_<ver-

sion>\ME_BASE\Ident directory, integration methods into the
*\OPUS_<version>\ME_BASE\Quant.

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9.10.2 S e t t i n g u p a n M E me t h o d

The evaluation methods generated before are now used to create

an ME method, i.e. these methods are added to the new ME
method.

Note: In an ME method it is allowed to add an IDENT method

only once.

The procedure on how to add evaluation methods is the same for

all types of methods.

1 On the Evaluate menu, click the Multi Evaluation Setup

command.

Figure 314: Multi Evaluation Setup

2 Add an evaluation method. On the browser view, right click

the New entry. Select an option from the pop-up menu for
the type of method, e.g. Add Identity Test.

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 Multi Evaluation Setup Chapt. 9

Figure 315: Select type of evaluation

method

3 Click the Add Method button.

Figure 316: Add evaluation method

4 Select the appropriate IDENT method from the dialog that is

displayed. Then, click the Add Method button.

Figure 317: Available evaluation methods

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 Chapt. 9 Evaluate

The group names of the evaluation method are displayed on

the browser view. The name of the evaluation method is
shown above the table.

Figure 318: IDENT evaluation method

The single groups can now be edited individually to be further pre-

pared for the ME method.

You can add methods to each group and define the method param-
eters separately.

The following examples show different editing possibilities which

depend on the type of evaluation method selected. Not all editing
possibilities are valid for all types of evaluation methods.

The following editing possibilities are described in this chapter:

• Defining user-specific group names
• Defining expected reference for one single group
• Undo expected reference for one single group
• Adding another evaluation method to a group
• Deleting the method added to a group

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• Replacing the method added to a group

• Adding calculated component
• Deleting calculated component
• Adding next step QUANT 2
• Undo QUANT 2 analysis of a component
• Setting Output
• Undo setting output

Defining user-specific group names

The pre-defined names of the single groups included in an evalua-

tion method can be changed.

Step 1:
Click the appropriate table cell.

Step 2:
Select the existing group name.

Step 3:
Overwrite the existing group name.
Confirm the setting made by the Return
key.

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Defining expected reference for one single

group

By default, all groups included in an identity test method are

defined as expected reference.

In some cases it may be useful to define a single group only as

expected reference within an identity test method.

Step 1:
• Right click the appropriate group
name.
• Select Set Expected Reference option
from the pop-up menu.

What can be seen?

On the browser view, the group name
selected before is displayed in bold.

The expected reference is indicated

below the method name.

Undo expected reference for one single

group

Step 1:
• Right click the appropriate group
name.
• Click the Set Expected Reference
option from the pop-up menu.

What can be seen?

On the browser view, all group names
are displayed in bold again.

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 Multi Evaluation Setup Chapt. 9

A d d i n g a n o t h e r e v a l ua t i o n m e t h o d t o a
group

You can add one or several methods to the single groups belong-
ing to a method. The procedure on how to add evaluation methods
is the same for all types of methods

The following exemplifies adding a QUANT method to a group.

Step 1:
• Right click the appropriate group
name.
• Select the Add Quant 2 Analysis
option form the pop-up menu.

Step 2:
Click the Add Method button.

Step 3:
• Select the method from the dialog that
opens.

• Click the Add button.

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What can be seen?

Now, the method selected has to be

displayed in the Selected Methods
selection field.

The single components of the

method(s) selected are displayed
below this selection field.

Step 4:
Click the Apply button.

What can be seen?

On the browser view, the components

of the method added have to be dis-
played below the group name.

The method parameters are displayed

on the right side. You can add further
values.

The single parameters of the method can individually be adjusted.

In this case you can further optimize the predicted result by using
user-defined formulae.

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Setting formulae

Step 1:
On the Calculation table cell, click the
Set button.

What can be seen?

The new dialog displayed shows a cal-
culator which can be used to set formu-
lae.

Optionally, you can enter a maximum or

minimum value in the Set Limits for
Output group field. This helps to cus-
tomize the predictive range. Example:
in case of lowest value = 0, all values
below 0 are displayed as "0".

Step 2:
Select the type of formula.

Step 3:
Combine e.g. the method component
with a numerical value. Double click the
component.

The name of the component is now dis-

played in the calculator edit field.

Step 4:
Use the numerical pad to enter a
numerical value.

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 Chapt. 9 Evaluate

Step 5:
• Optionally, enter a name for the for-
mula. By default, an asterisk is set as
formula name.
• Confirm the settings by clicking the
OK button.

The name of the formula must now be

displayed on the parameters side, i.e.
in the Formula table cell.

S e t t i n g v a r i a b l es

During analysis variables allow to change predictive values, e.g.

layer thickness correction.

Step 1:
On the Calculation table cell, click the
Set button.

What can be seen?

The new dialog displayed shows a cal-
culator which can be used to set formu-
lae.

Step 2:
Select the type of formula, e.g. General
Formula.

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Step 3:
Combine e.g. a variable with the predic-
tive value. Double click the variable.

The name of the variable is now dis-

played in the calculator edit field.

Step 4:
• Optionally, enter a name for the vari-
able.
• Confirm the settings by clicking the
OK button. The name of the variable
defined in the calculator remains the
same.

The name of the variable must be dis-

played on the Input Variable tab when
performing the ME test. Enter the
numerical value on this dialog (see also
chapter 9.11.1).

Deleting the method added to a group

Step 1:
Click the name of the first method com-
ponent.

The parameters of the method are dis-

played on the right side.

Step 2:
Click the Remove Method button.

Step 3:
On the dialog that opens, click the
method.

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Step 4:
Click the Remove Method button.

The method components below the

browser group name are no longer dis-
played on the browser view.

Replacing the method added to a group

When replacing one method by another make sure that both meth-
ods contain the same components. Otherwise, replacing the
method is not possible.

Step 1:
Click the name of the first method com-
ponent within a group.

The parameters of the method are dis-

played on the right side.

Step 2:
Click the Replace Method button.

Step 3:
On the Available Methods list box, click
the method you want to use to replace
the previous one.

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Step 4:
On the Selected Methods list box, click
the method you want to replace.

• Click the Replace button.

The new method has now to be dis-

played in the Method Name table row
for each component available.

Adding calculated component

Multi evaluation allows to generate a new component which has

not yet been integrated in the original method.

The quantitative predictive value of this new component is calcu-

lated on the basis of at least 2 real components. These real compo-
nents may belong to a QUANT method. Other types of methods
are not necessary.

Step 1:
• Right click the real component of the
appropriate group.
• Click the Add Calculated Component
option from the pop-up menu.

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Step 2:
• Enter an appropriate component
name.
• Enter reasonable values into the entry
fields.
• Click the Calculation table cell and
enter an appropriate formula.

Note: When adding a calculated

component it is possible to use for-
mulae set up by VBscripts. Store the
VBscript into the *\OPUS\ME_Base
first.

On the browser view, the user-specific

name of the calculated component is
displayed.

Deleting calculated component

Step 1:
On the browser view, click the name of
the component added.

The component parameters are dis-

played on the right side.

Step 2:
Click the Remove Component button.

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Step 3:
• On the dialog that opens, select the
component.

• Click the Remove Component button.

On the browser view, the component is

no longer be displayed.

Adding next step QUANT 2

A single component which belongs to a QUANT 2 method can be

further analyzed in a second step by adding a QUANT 2 analysis to
this component.

This may be appropriate if an analyte has first been evaluated by a

QUANT 2 method, which covers a large concentration range. To
improve the accuracy of the prediction value this analyte can be
evaluated by a second QUANT 2 analysis, which covers a more
suitable concentration range.

In the following, two applications exemplifies how to use the Add

Next Step Quant 2 option within multi evaluation.

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Example 1:

When using the Add Next Step Quant 2 option the table of contents
of the data block should contain only the result of the last
QUANT step. This requires all component names in all QUANT
methods (*.q2) used to be identical, upper and lower case must be
observed.
• The QUANT method (A) used in the first step contains
the ethanol component (apart from methanol and propa-
nol) within the concentration range of 0 to 100%.
• The QUANT method (B) used in the next step contains
the ethanol component within the concentration range of
5.9 to 13.5%, which can improve the accuracy of the
prediction value.

The result achieved in example 1 contains the prediction value for

ethanol, methanol and propanol from the last step of the Add Next
Step Quant 2 option.

Example 2:

When using the Add Next Step Quant 2 option the table of contents
of the data block should contain the results of all components
included in the QUANT methods used.
• The QUANT method used (soybean protein) contain the
protein component within a large concentration range.
Calibration samples of many soybean types with differ-
ent composition form the basis for this concentration
range. The fat and ash components, however, cannot be
determined with sufficient reliability by this QUANT
method.
• Depending on the protein content found in the first step,
individual QUANT methods for fat and ash are now com-
bined in the next step.

Based on the Add Next Step Quant 2 option, the result achieved in
example 2 contains the prediction value for protein (from the first
step) and for fat and ash (from the last step).

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Procedure:

Step 1:
• On the browser view, right click the
name of the component which is part
of the first QUANT 2 method.

• Select the Add Next Step Quant 2

option from the pop-up menu.

What can be seen?

On the upper right you see the name
and calibration range of the component
which is part of the first QUANT 2
method.

The table on the upper left is used to

specify the concentration range for the
second QUANT 2 analysis.

Below the table you see the possible

parameters to be used for analysis.

Step 2:
• Depending on the calibration range
specified, enter a concentration range
which the second QUANT 2 analysis
is to apply for.

• Select the table cell by clicking the

table cell numbering.

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Step 3:
• Click the Add Method button.

• On the dialog that opens, select the

appropriate method. Click the Add
button.

What can be seen?

You see the method selected together
with the method components on the
right selection field.

Click the Apply button.

Step 4:
• Check whether the values specified
for the concentration range corre-
spond to the method selected, and do
not overlap. Click the Check button.

Note: If the numerical values entered

are outside the range specified, or if
there are overlappings, the critical
numerical value is marked red in the
table cell. Additionally, an error mes-
sage pops up.

• Change the critical value. Click the

Check button again.

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Step 5:
• As soon as the values are correct you
can make further settings on the sin-
gle analysis parameters.

• Click the Save button.

Undo QUANT 2 analysis of a component

Step 1:
Click the name of the component dedi-
cated for a QUANT 2 analysis.

Step 2:
Click the Remove Method button.

On the browser view, the component is

displayed without any next step
QUANT 2 analysis.

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Setting Output

The Set Output option allows to define which evaluation data are
displayed in the ME report (see also chapter 9.11).

Step 1:
• Right click the name of a method
component. By default, the Set Output
option is checked.
• Click the Set Output option if the eval-
uation data of this component are not
to be displayed in the ME report.

What can be seen:

On the right table, the Output table row
of the prior selected method compo-
nent has to be unchecked.

On the browser view, the method com-

ponent is displayed in regular style.

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Undo setting output

Step 1:
• Right click the name of the method
component whose evaluation data
had been hidden in the ME report.
• Click the Set Output option.

What can be seen:

On the right table, the Output table row
of the prior selected method compo-
nent has to be checked again.

On the browser view, the method com-

ponent is displayed in bold style.

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9.10.3 St o r i n g M E m e t h o d

Store the ME method by clicking the Save button. A new dialog

opens.

1 Enter a name for the ME method into the lower entry field.

Figure 319: Enter name for ME method

2 Click the Save button. Now, the name of the ME method has
to be shown on the browser view.

Figure 320: Name of ME

method on browser view

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9.11 Multi Evaluation

Definition This command allows the multi evaluation of NIR

spectra for qualitative or quantitative analysis. It com-
bines previously generated IDENT, QUANTa, confor-
mity or integration test methods.

The results are displayed in one single report.

Principle • Load a spectrum file.

• Select the Multi Evaluation command.
• If required, drag & drop the spectrum file into the
Files for Multi Evaluation selection field.
• Load the ME method. Click the Load Multi Evalua-
tion Method button.
• If required, define the numerical values on the Input
Variables tab.
• Click the Test button to start this evaluation com-
mand.
a. A quantitative evaluation can also be performed by using PLS mod-
els which have been created by Unscrambler 9.8 (chapter 9.10).

Figure 321: Multi Evaluation Test - Select Files

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9 . 11 . 1 I n p u t Va r i a b l e s

The Input Variables tab contains types of variables which have

been specified before by the formula calculator, and stored in the
ME method.

Note: If no input variables had been used in the method, the

entry fields are not available on the tab.

If the name of a particular variable has been defined by the formula

calculator, this name is displayed on the Input Variables tab.

By default, the value is set to 0 for all variables. Enter an appropri-

ate value.

Figure 322: Multi Evaluation Test - Input Variables

The multi evaluation result...

...is stored in the ME report block ( ). This data block is

attached to the spectrum file evaluated and displayed in the OPUS
browser.

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To d i s p l a y t h e m u l t i e v a l u a t i o n r e s u l t i n a
r e p o r t v i e w. . .

1 ...right click the data block in the browser.

2 Select the Show Report option from the pop-up menu. The
report view opens.

Figure 323: Multi Evaluation Report

The ME test report contains the method name and path as well as
the results of the different method tests, e.g. QUANT, IDENT, con-
formity test or integration.

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The report overview summarizes the evaluation results as follows:

D
Figure 324: Report overview

Component Definition

A Type of evaluation method

B Number of sub-reports in directory tree:

1
2
3

C Row which includes the relevant evaluation result in the

sub-report (example: integration):

D Evaluation method has/has not been changed after ME

method was generated:
1 = yes
0 = no

Note: To open the sub-reports click the evaluation method

in the directory tree (see C in the above table).

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9.12 Quick Compare

Quick compare is an evaluation method for quality control, which is

mainly used to check the correct identity of a substance or material.
The spectrum of the sample material to be verified is compared
with the reference spectra being part of the quick compare method.

A correlation coefficient is calculated between the query spectrum

and the particular reference spectra, and compared with a thresh-
old. If the correlation value is above the threshold, the query spec-
trum is evaluated as being identical to the reference spectrum.

9.12.1 T h e o r e t i c a l b a c k g r o u n d i n f o r m a-
tion

The comparison between query and reference spectrum is per-

formed by calculating the correlation coefficient.

The correlation coefficient r of the two functions y 1  k  and y 2  k  is

calculated as ratio from the covariance and product of the two stan-
dard deviations  y1 and  y2 :
Cov  y 1  k  y 2  k  
r = ---------------------------------------------
-
 y1   y2
With:
• Y1 (1): intensity value of query spectrum at data point 1
(= wavenumber 1)
• Y2 (1): intensity value of reference spectrum at data
point 1 (= wavenumber 1)
• k: index of all data points for each spectrum
•  y1= standard deviation of all intensity values from the
average value of the query spectrum
•  y2= standard deviation of all intensity values from the
average value of the query spectrum

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The value of r ranges between -1 (inverted spectra) and +1 (identi-

cal spectra). This correlation coefficient r will be calculated into a
percentage and reflects the similarity of the two spectra. The
– 1  r  0 range is mapped to 0%, and the 0  r  1 is linearly
mapped to 0% ...100%.

9.12.2 Creating method

To set up a quick compare method, you need to measure at least

one or more reference spectra. Reference spectra are spectra gen-
erated by samples which exactly meet the quality criteria defined.
These samples are also called reference standards. Observe the
following:
• use only pure samples as reference standard, i.e. sam-
ples without any contaminants and with unambiguous
identity
• prepare the reference standards carefully, e.g. homoge-
nizing inhomogeneous samples
• avoid errors during measurement, e.g. make sure that
the ATR crystal has been carefully cleaned before start-
ing background and sample measurement

Procedure

1 On the Evaluate menu, select the Quick Compare Setup

command, or click the icon in the toolbar.

2 On the Reference Spectra tab, click the Add Reference
Spectra button.
3 Select the reference files to be added to the method from the
particular directory.
➣The file and compound name of the reference spectra as
well as sample form information are shown in a table. More
details are described in chapter 9.12.2.1.
4 On the Parameters tab, make further settings.
➣The setting options are described in chapter 9.12.2.2.
5 On the Validate tab, click the Validate button.
➣The reference spectra are validated. Details are described
in chapter 9.12.2.3.

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6 On the Method tab, click the Store Method button.

➣More setting options are described in chapter 9.12.2.4.
7 On the dialog that opens, define a name for the method and
click the Save button.
➣Methods for quick compare have the extension ’*.qc’.

9.12.2.1 Setting options of reference

file

1 2

Figure 325: Quick Compare Setup - Reference Spectra

Component Definition

1 Add Reference Clicking the button allows to add the particular

Spectra reference spectra for the method (maximum
5,000). The reference spectrum displayed in
the first table line is the master spectrum.
The reference spectrum cannot be added in
the following cases:
• file name already exists
• data type not consistent with the one speci-
fied for the master spectrum
• spectral range not consistent
The reference spectra not added are dis-
played in a separate dialog indicating the path,
file name and reason for the rejection.

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Component Definition

2 Delete Reference Clicking the button allows to delete single or

Spectra multiple reference spectra from the table.
☞ Select the reference spectrum in the table.
☞ Click the Delete Reference Spectra button.
☞ Click Yes to confirm the message dis-
played.

3 Table The table contains the reference spectra

selected. The entries written in the Compound
name and Info column are used from the par-
ticular spectrum file. Compound name uses
the file name (without extension), Info uses the
sample form entry. The entries in the Com-
pound name and Info column are editable.
Equal or very similar compounds or material
can be can be put together in one group, by
entering the same compound name. This can
be useful if spectra of the same material, but
of different batches, are intended to be used in
the method.

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9.12.2.2 S e t t i n g o p t i o n s o f pa r a m e t e r s

1
2

Figure 326: Quick Compare Setup - Parameters

Component Definition

1 Use file limits The check box is activated by default. This

means that the wavenumber range is based
on the first - and possibly only - reference
spectrum.
If the check box is deactivated, the spectral
ranges can be defined individually, see (2) in
this table.

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Component Definition

2 Spectral range The largest common spectral range of all refer-

ence spectra is displayed in autoscaled man-
ner. The Use file limits checkbox is activated by
default.
Note: To be able to define the limits manu-
ally or interactively, the Use file limits
checkbox must be deactivated.
• Defining range manually: enter the limits
into the table
• Deleting range: select the limit in the table
and click the Del button on the keyboard
• Defining range interactively: right in the
view, move the frequency limits (red line), or
right click the spectral range (gray area) and
select a setting option from the pop-up menu.
• Deleting range: right click the spectral
range and select the Remove option from
the pop-up menu.

3 Exclude CO2 If the checkbox is activated, CO2 bands are

regions excluded when calculating the correlation
coefficient. This applies to the spectral ranges
between 660 an 680 cm-1, and between 2,275
and 2,400 cm-1.

4 Data preprocessing • None: activated by default

• First/second derivative: selecting some
kind of derivative as data pretreatment elimi-
nates baseline offsets, but focuses more on
small spectral differences in the spectrum.

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9.12.2.3 D e ta i l s o n t h e v a l i d a t i o n o f r e f-
erence spectra
Note: Validating reference spectra checks the similarity
between the spectra to each other. Each reference
spectrum is compared with all other reference spec-
tra. This kind of spectrum comparison is based on
the correlation coefficient, which defines the correla-
tion1 between at least two spectra.

2
1 3

Figure 327: Quick Compare Setup - Validate

1. Correlation: conformity of spectral ranges; the higher the correlation coefficient

is between the spectra compared, the more similar these spectra are.

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Component Definition

1 Threshold The thresholda determines how similar the ref-

erence and query spectrum must be so that
the quick compare result is OK.
• Quick compare result OK: the correlation
coefficient (chapter 9.12.1) is greater than
the threshold
• Quick compare result not OK: the correla-
tion coefficient (chapter 9.12.1) is smaller
than the threshold
Note: In general, the greater the threshold
the higher the similarity between the refer-
ence and query spectrum must be to get a
quick compare result which is OK.

2 Validate Clicking the button displays the reference

spectra in the table, and evaluates them.

3 Print Clicking the button allows to print the table

with the reference spectra and their neighbor-
ing spectra.

4 Table entries Green entry:

• The correlation coefficient of all spectra com-
pared is below the threshold defined. Click-
ing the plus sign in front of the entry shows
the neighboring spectrum.
• The reference spectra have the same sub-
stance name. The correlation value is identi-
cal for the particular references spectra, but
may be above the threshold.
Red entry:
• The correlation coefficient of all spectra com-
pared is above the threshold defined.
• The reference spectrum cannot be distin-
guished from the others, as they are too sim-
ilar. Clicking the plus sign in front of the entry
shows the names of the reference spectra
being too similar.
a. The threshold can be between 90 and 100%. For quality control,
enter a threshold between 96 and 99%.

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9.12.2.4 Setting options of method

Figure 328: Quick Compare Setup - Method

Component Definition

1 Load Method Clicking the button allows to load an existing

method from the dialog that opens.

2 Store Method When saving the method you have to define

a name for the method in the dialog that
opens. Method files for quick compare have
the file extension *.qc.

3 Description Optionally, you can enter details on the

method, e.g. Two spectral ranges, No data
preprocessing etc.

4 Threshold If the threshold is to be changed, the

method will have to be saved again. Details
on the threshold are described in
chapter 9.12.2.3.

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Component Definition

5 Data preprocessing If data preprocessing is to be changed, the

method will have to be saved again. Details
on data preprocessing are described in
chapter 9.12.2.2.

9.12.3 P e r f o r m i n g q u i c k c o m pa r e
1 On the File menu, select the Load File command and load
the spectrum file.
➣The data blocks of the query and reference files must have
the same spectrum type, i.e. AB (absorption) or TR (trans-
mission). The wavenumber range of the sample spectrum
has to be at least as large as the range defined for the ref-
erence files.
2 On the Evaluate menu, select the Quick Compare com-

mand, or click the icon in the toolbar.

3 Define the evaluation method.
➣The setting options are described in chapter 9.12.3.1.
4 Click the Load Method button, and select a method from the
dialog that opens.
➣Methods are saved in the ’*\OPUS\Methods’ directory. If a
method has already been loaded, the name and path of the
method is displayed. Details on how to create a quick com-
pare method are described in chapter 9.12.2.
5 Define the result view.
➣The setting options are described in chapter 9.12.3.1.
6 Click the Compare tab.
➣The quick compare result is saved in the QC data block.
The block is added to the spectrum file and displayed in the
browser.

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9.12.3.1 S e t t i n g o p t i o n s o f q u i c k c o m-
pa r e

Figure 329: Quick Compare

Component Definition

1 Material verification In case of material verification, the conformity

between query spectrum and a particular
user-defined reference substance is tested.
The substance is selected from the drop-
down list, which contains the entries available
in the method.

2 Material identifica- In case of material identification, the query

tion spectrum is compared to all reference spec-
tra available in the method to identify the sub-
stance with the best conformity.

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Component Definition

3 Quick Compare • Number of hits: the number of hits entered

Result is displayed in the result view of quick com-
pare. Between 1 and 10 hits can be dis-
played in the result view.
• Show Quick Compare result: if activated,
the quick compare result is displayed in a
separate view immediately after quick com-
pare has finished.

9.12.4 Q u i c k c o m pa r e r e s u l t

The quick compare result is displayed immediately in a separate

view after quick compare has finished, if the Show Quick Compare
result checkbox (figure 329) is activated. If the checkbox is not acti-
vated, the result view (figure 301) can be opened by double click-
ing the QC data block. The QC data block is added to the spectrum
file and displayed in the browser.

The following table contains the possible result display for the
Material verification and Material identification modes.

Icon Material verification Material identification

Material is identical toa Material is identified asa

Material is not identical tob Material is not identifiedc

No unique identification possi- No unique identification possi-

bled bled

a. Only one reference spectrum is above the threshold.

b. The reference spectrum selected is below the threshold. It is pos-
sible, however, that the query spectrum is conform with a different
reference substance.
c. No reference spectrum is above the threshold.
d. Several reference substances have been found which are above
the threshold.

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9.12.4.1 Result view

The structure of the result view is the same for both evaluation
modes. Figure 301 exemplifies the result view for the Material veri-
fication mode.

Figure 330: Quick compare result view

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Component Definition

1 Spectrum window The query spectrum is displayed in red in the

spectrum window. All the other spectra origi-
nate from the hit list (see 4 in this table).
☞ Hiding crosshair: right click the spectrum
window
☞ Opening pop-up menu: right click the
spectrum window
- Autoscale-mode: spectra are displayed
in their original size ratio
- Maximize-Y-mode: allows to maximize
the spectra on the y-axis

2 Result display Details are described in chapter 9.12.4.

3 Query spectrum During quick compare, the query spectrum is

compared with one or several reference spec-
tra.

4 Hit list The hit list contains the reference spectra

which come close to the query spectrum, or
are identical to it. The number of hits dis-
played is defined in the Quick Compare dialog
(figure 301). By default, one hit is activated
and displayed with the query spectrum in the
spectrum window.

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9.12.4.2 Vi e w i n g r e s u l t i n t h e r e p o r t
view
1 Right click the QC data block added to the spectrum file and
displayed in the browser.
2 From the pop-up menu that opens, select the Show Report
option.

Figure 331: Quick compare - Report view

The report contains the parameter values used and the result cal-
culated as well as the number of hits found.

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9.12.5 Setting up template for analysis

report

OPUS allows to output the results of quick compare in the form of

an analysis report (chapter 9.12.6). A user-editable template
defines which kind of data have to be written into the report.

Note: Templates for the analysis report have the file exten-
sion *.art. By default, the MIR.art template is part of
OPUS and can be used to create analysis reports for
quick compare.

1 On the Print menu, select the Setup Analysis Report

Template command1.
2 From the view that opens, select a report type (single or mul-
tiple sample report)2 from the drop-down list.
3 On the list box, make the settings required.
➣Clicking a particular setting option on the list box, opens
the group field being part of this setting option (figure 332).

1. Detailed information on the Setup Analysis Report Template command are de-
scribed in chapter 11.2.
2. Single sample report: one report for each single spectrum file; Multiple sample
report: one report for all spectrum files

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Figure 332: Setting options for analysis report

4 From the global result options select Quick Compare and

make the settings required (figure 333).

Figure 333: Setting options example: Quick Compare

5 Click the Save button.

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6 On the dialog that opens, enter a file name for the template.
➣By default, the templates for the analysis report are stored
in the *\User\Public\Public Documents\Bruker\OPUS direc-
tory.
7 Click the Save button.

9.12.6 Generating analysis report

1 On the Print menu, select the Generate Analysis Report
command.
2 From the OPUS browser, drag & drop the spectrum file into
the File(s) for report generation selection field.
3 Define the Report layout.
4 Click the Select Template File button and select a template
file from the dialog that opens.
➣By default, the path and file name of the template previ-
ously used is displayed.
5 Click the Output tab and define the output format of the
report.
6 Click the Generate button.
➣Figure 334 exemplifies an analysis report.

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Figure 334: Example of analysis report - Page 1

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9.13 Lay e r Thickness

Definition Based on interferences which have been caused by

multiple reflection this command allows to determine
the layer thickness from the sub-µm range to mm-
range. The actually available thickness range
depends on the spectral resolution, the spectral
range as well as the kind of sample used.

You can determine the layer thickness for both

homogenous samples (films, semi-conductor, glass
plates etc.) as well as coated samples, provided the
reflection or transmission spectrum contains mean-
ingful interferences.

Principle • Load the reference spectrum file (only a spectrum

file which contains a transmission or reflection
data block).
• Select the Layer Thickness command.
• If required, drag & drop the spectrum file into the
File(s) to determine the layer thickness selection
field.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
Note: If possible, the frequency range should
contain meaningful layer thickness interfer-
ences.
• Define the peak sensitivity and the refraction index
on the Parameter tab.
• Click Determine to start this evaluation command.

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Figure 335: Layer Thickness - Select Files

A If you activate this check box, the result of layer thickness

determination is displayed.

Figure 336: Layer Thickness - Parameters

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B This check box should only be activated if the spectral range

to be evaluated contains significant noise.
C Compared to D this option automatically determines peak
sensitivity. If you activate this checkbox, an algorithm deter-
mines the best possible peak sensitivity for the frequency
range selected, to specify fringe maxima and minima.
The peak sensitivity indicates how meaningful the maxima
and minima have at least to be, to be considered by the algo-
rithm.
The Increment step entry field allows to set the value which
the peak intensity is increased by. It is recommended to
always select the automatic peak sensitivity determination
option and set the increment step to 1. If the result is not OK,
you either have to increase the increment step, or determine
peak sensitivity manually (D).
D Use the manual peak sensitivity determination only, if you
always want to work with one single peak sensitivity, or if the
automatic mode does not work properly. Check whether you
have obtained reasonable results due to the peak sensitivity
value set (the default value of 1 is successful in many cases),
after the layer thickness has been determined. Check the
maxima and minima found which are graphically selected in
the spectrum window.
If maxima/minima had been ignored or if noise had mistak-
enly be interpreted as maxima/minima, this would result in an
erroneous layer thickness. In this case undo the determina-
tion, using the Undo changes command from the File menu.
Perform the determination once again, using an appropriate
peak intensity.
E Use this entry field to define the refraction index which
depends on the type of material used and the frequency
selected.

To h a v e t h e r e s u l t d i s p l a y e d

The result of layer thickness determination is immediately dis-

played after the evaluation has been finished, in a separate dialog.
To do so you have to activate the Show check box (A in figure 335)
before.

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 Layer Thickness Chapt. 9

Figure 337: Result of layer thickness determination

If the results are to be saved with the spectrum, click Yes. The
results are displayed in the parameter list.

To open this list right click the file name in the browser window and
select Show Parameters from the pop up menu.

Figure 338: Parameter list of layer thickness determination

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9.13.1 Theory of layer thickness deter-

mination

The algorithm determines the thickness d from the mean distance

 f of the interference maxima within the selected frequency range,
and from the refraction index n of the measured layer:
d = 1   2  n  f  .

This physical context reveals that the distance of the interference

maxima decreases all the more, the thicker the layer and the
greater the refraction index is.

Apart from the presence of meaningful layer thickness interfer-

ences a precise determination especially depends on the value
used for the refraction index which you have to define as parame-
ter. As the refraction index depends on the frequency, in general,
the value defined is to be consistent with the frequency range
selected.

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 H18 Chapt. 9

9.14 H 18

Definition This command allows to determine the concentration

of hydrocarbons in water. H18 is a standardized
method (DIN 38 409-H18).

Note: The H18 method is designed to work with

absorbance spectra only. Do not use transmis-
sion spectra as they may lead to incorrect results.

Principle • Load the reference spectrum file which contains an

data block.
• Select the H18 command.
• If required, drag & drop the spectrum file into the
Selected Files selection field.
• Define the parameters on the Settings tab.
• Click Calculate to start this evaluation command.

Setting options

Figure 339: H18 method - Settings

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 Chapt. 9 Evaluate

If you activate the Also calculate Aromatics checkbox, the evalua-

tion result additionally contains the total concentration value in
hydrocarbons.

The H18 evaluation result...

• ... is stored in the data block. This data block is

attached to the spectrum file and displayed in the OPUS
browser.
• ...is illustrated in the spectrum displayed in the spectrum
window.

To d i s p l a y t h e H 1 8 e v a l u a t i o n r e s u l t i n a
report view

1 Right click the data block.

2 Select the Show Report option from the pop-up menu. A
report view opens which contains the concentration values.

Figure 340: H18 method - Report view

Note: The data block, which is also attached to the

spectrum file, contains the number of results and the
single band parameters.

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 H18 Chapt. 9

9.14.1 Theory

The H18 methods1 evaluates the concentration of hydrocarbons in

water as sum parameters by detecting the CH valency vibration
bands using infrared spectroscopy.

One of the preconditions to employ infrared spectroscopy in this

case is to use a type of solvent which does not show vibration
bands within the range relevant for hydrocarbons.

Two concentration values are calculated:

A concentration (conc) of aliphatics (mineral oil)
B concentration (conc) of aliphatics and aromatics (total)

A:
1 4  ExtractVol a a
conc  ------- = -----------------------------------------------------------   ----1- + ----2-  DilFac
mg
 l  WaterVol  CellThickn c 1 c 2 
B:
1 3  ExtractVol a a a
conc  ------- = -----------------------------------------------------------   -----1- + ----2- + ----3-  DilFac
mg
 l  WaterVol  CellThickn c1 c 2 c 3 

Symbol Description

a1 absorbance at 2959 cm-1

a2 absorbance at 2924 cm-1

a3 absorbance at 3030 cm-1

c1 extinction coefficient for the CH3 band (8.3 ml/mg x cm)

c2 extinction coefficient for the CH2 band (5.4 ml/mg x cm)

c3 extinction coefficient for the CH band (0.9 ml/mg x cm)

ExtracVol extraction volume (in ml)

1. Based on the DIN 38 409-H18 formula.

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Symbol Description

WaterVol volume of water (in liters)

CellThickn cell thickness in cm

DilFac dilution factor

In case of a1, a2 and a3 the absorbance at peak maxima are used

(not the absorbance values at the described DIN 38 409-H18), as
usually the bands are slightly different from DIN values.

In the H18 report the peak heights used and the associated wave-
numbers are listed according to the spectral data.

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 Spectrum Search Chapt. 9

9.15 Spectrum Search

Definition In case of spectrum search, an unknown spectrum is

compared with spectra stored in a library. Those
spectra from the library which show distinct similari-
ties to the unknown spectrum are detected and dis-
played in a search report.
The degree of consistency between query spectrum
and library spectra is indicated as hit quality.

Principle OPUS provides several demo libraries. The libraries

are stored in the C:\Users\Public\Public Docu-
ments\Bruker\OPUS_<version>\Data\Library direc-
tory.

To p e r f o r m s p e c t r u m s e a r c h . . .

1 ......load the spectrum file.

2 Select the Spectrum Search command.
3 If required, drag & drop the spectrum file into the Spectra to
search selection field.
4 Specify the spectral range and search parameters.
5 Select the libraries you want to work with.
6 Start spectrum search by clicking the Search Library button.

The different tabs of the Spectrum Search dialog are described in

the following.

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Sp e c t r u m S e a r c h

Figure 341: Spectrum search - Query spectrum selected

Component Definition

The Use file limits check box is activated by default. In

this case, spectrum search uses the complete spectral
range of the unknown spectrum and compares this range
with the spectra from the library.
If the Use file limits check box is deactivated, the spectral
range can be selected interactively (chapter Defining
spectral range: interactive selection).

Show search report imme- The search report is shown immediately after the spec-
diately trum search has been completed.

Use search report for When activated, a list box is displayed below the check
search box. You can select an already existing search report
from this list box. In this case, searching is not performed
by means of the settings made on the Select Libraries
tab, but only by those spectra which are included in the
search report. This enables to refine a search query pre-
viously performed.

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 Spectrum Search Chapt. 9

Defining spectral range: interactive

selection

To define particular spectral ranges for spectrum search you can

interactively select these ranges. The interactive spectral range
selection option is only enabled if you deactivate the Use file limits
check box.

If the check box is deactivated, the latest spectral range selected is

displayed on the query spectrum. If no spectral range has been
selected so far, OPUS adds one spectral range which is around the
central wavenumber of the first spectrum in the library list.

The spectral limits interactively defined are displayed in a table

(figure 342).

Figure 342: Spectrum search - Defining spectral range interactively

Defining spectral range limits

1 On the query spectrum, position the cursor onto the red line
(figure 342).
➣The cursor changes to .
2 While pressing the left mouse button, move the cursor to the
spectral range limit desired on the x-axis.
➣Alternatively, you can manually enter the limits into the
table.

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 Chapt. 9 Evaluate

Adding spectral range

1 Right click onto the query spectrum.

2 From the pop-up menu, select the Add Regions option.
➣The white section (figure 342) added to the query spec-
trum is the spectral range which is to be excluded from
searching.

Alternatively, you can also add a new range by entering the limits
into the table. Figure 343 exemplifies two spectral ranges added to
the query spectrum.

Figure 343: Spectrum search - Spectral ranges added

Moving spectral range

1 On the query spectrum, position the cursor onto the spectral

range (white section) to be moved.

➣The cursor changes to .

2 While pressing the left mouse button, move the complete
spectral range to the desired position on the x-axis.

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 Spectrum Search Chapt. 9

Deleting spectral range

1 On the query spectrum, position the cursor onto the spectral

range (white section) to be deleted.

➣The cursor changes to .

2 Right click onto the spectral range.
3 From the pop-up menu, click the Remove command.

Alternatively, you can also remove a particular spectral range by

using the table. Click the respective line number to select the spec-
tral range, and press the DEL button on the PC keyboard.

Search Parameters

Figure 344: Standard search algorithm

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 Chapt. 9 Evaluate

Component Definition

Search algorithm:

Standard In case of the Standard search algorithm, all pieces of

band information, which are available from the query and
library spectrum, are reflected in the hit quality. The infor-
mation contains the position, relative intensity and half-
width of each band.
A library spectrum band is considered to be identified in
the query spectrum if this spectrum contains a band
which position does deviate from the position in the
library spectrum by less than the half-width, which differ-
ence between the half-widths or relative intensities is less
than factor 2.
The Standard search algorithm provides further setting
options with regard to the spectrum to be searched for to
refine the result of the search query.
• One main component: select this option if a pure sub-
stance has been measured in the query spectrum
• Several components: select this option if a compound
has been measured in the query spectrum

Mixture analysis The mixture analysis search algorithm is used to analyze

spectra which have been acquired from mixtures. These
types of mixture spectra contain bands of different sub-
stances and may therefore not be interpreted by one sin-
gle library spectrum. The mixture analysis combines
various library spectra such that all bands being part of the
query spectrum are explained to the extent possible. Each
library spectrum has a spectral portion of the query spec-
trum, this portion is indicated in percentage.

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 Spectrum Search Chapt. 9

Component Definition

Spectrum correlation The Spectrum correlation search algorithm calculates the

sum of the squared deviations between the query spec-
trum and the result spectrum for the data points of the
range defined. The summation can be limited to a spectral
range selected by the user. In case of this search algo-
rithm, the Normalization method and Derivative drop-down
list are available.
More details on these methods are described in
chapter Normalization method.
As spectrum search aims to search for a qualitative con-
formity between spectra, it is recommended to select
vector normalization. Vector normalization eliminates
intensity differences between query and library spectra.
Selecting some kind of derivative as data pretreatment
eliminates baseline offsets, but focuses more on small
spectral differences in the spectrum. This means that the
hit quality of library spectra, which have slightly shifted
bands compared to the query spectrum, is decreased
even more substantially than would have been the case if
derivative was not selected.

Using existing peak table The Use existing peak table search algorithm uses an
already existing peak table.
A peak table is generated by the Peak Picking or Single
Peak Pick command. This command allows to limit spec-
trum search to selected bands only, and to ignore other
types of bands being part of the spectrum as well.

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Normalization method

The following normalization methods are available:

• Vector normalization
This method calculates the average y-value of the spec-
trum. The average value is subtracted from the spec-
trum decreasing the mid-spectrum to y = 0. The sum of
the squares of all y-values is calculated and the spec-
trum is divided by the square root of this sum. The vec-
tor norm of the result spectrum is 1.
• Min-Max normalization
This method is used with spectra which optical layer
thickness substantially varies, to be able to compare
these spectra with each other. For example, the spectra
of a powder sample which have been compacted
unequally during separate measurements. The shape of
the single spectra remains, and the differences between
the spectra can be detected more easily.
Note: The result depends on the spectral range
selected, i.e. specific differences of one section are
distributed to all data points.

Types of derivative

The following types of derivatives are available:

• No derivative
• First derivative
Calculates the first derivative of the spectrum by interpo-
lation. Steep edges of a peak become more important
compared to flat structures.
• Second derivative
The second derivative is similar to the first derivative
and additionally allows to evaluate extremely flat struc-
tures.

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 Spectrum Search Chapt. 9

Setting options for hits

The following setting options are available:

• Minimum hit quality
The Minimum hit quality setting option defines the mini-
mum quality a hit needs to have to be stored in the
search report. A hit quality of 1000 would be a perfect
conformity, whereas a value of 0 is obtained if there is
no correlation at all. In general, the search algorithm
produces a value >0 even if there are no or negligible
similarities between spectra. Therefore, it is reasonable
not to include all hits below a certain limit (default set-
ting: 300) into the search report.
• Maximum number of hits
Specifies the maximum number of hits to be saved in
the search report.

Select Libraries

To start spectrulm search you always have to select one or more

libraries.

A search can involve either one or more libraries, but creates only
one search report in either case.

1 Click the Select Libraries tab.

➣You always have to use the ’Select Libraries’ tab to start a
search run. The libraries displayed are stored in the
*\OPUS_<version>\Data\Library directory.

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 Chapt. 9 Evaluate

Figure 345: Selecting OPUS default libraries

2 Click the Search Library button.

➣Spectrum search is performed in all those libraries which
are activated, i.e. which have a checkmark in the ’Use’ col-
umn.

Selecting other types of libraries

1 On the Select Libraries tab, click the Search Libraries button.

2 From the dialog that opens, select the path/directory of the
other types of libraries (e.g. Sadtler).
3 Click OK to confirm.
➣The libraries are now displayed together with the OPUS
libraries.

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 Spectrum Search Chapt. 9

Generating library list

Libraries which belong together regarding subject matter can be

grouped in separate library lists.

1 On the Select Libraries tab, check the library which is to be

part of the library list.
2 Click the Save Library List button.
3 On the dialog that opens, define a name for the library list
and save this name.
➣Library lists have the file extension *.LLS.

Loading library list

1 On the Select Libraries tab, click the Load Library List

button.
2 From the dialog that opens, select the library list desired.
3 Click the Open button.
➣All the libraries belonging to the list are activated by a
checkmark.

Deleting library from library list

1 On the Select Libraries tab, click the Load Library List

button.
2 From the dialog that opens, select the library list desired.
3 Click the Open button.
➣All the libraries belonging to the list are activated by a
checkmark.
4 Click the table number (first table cell) of the library to be
deleted from the library list.
➣The complete table line is highlighted.
5 Press the Del key on the keyboard.
6 On the message that pops up, click Yes to confirm the
action.
➣The library is now deactivated.
7 Click the Save Library List button.

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 Chapt. 9 Evaluate

8 From the dialog that opens, select the name of the library
list.
➣Library lists have the file extension *.LLS.
9 Click the Save button.
➣The library list is overwritten by the new settings made.

Checking library status

Note: When loading the library from an external data
medium (CD or USB stick) keep the data medium in
the respective drive or port during the search query.

On the Select Libraries tab, check the Status column. Libraries can
have the following status:
• Green checkmark: library is OK
• Red cross: library could not be found (e.g. library
deleted or library directory changed
• Red exclamation mark: library is not accessible (e.g.
registration not valid)

The spectrum search result...

...is added to the query spectrum in the form of the data block
and displayed in a separate result view.

T h e s p e c t r u m s e a r c h r e s u l t v i e w. . .

...is immediately shown after spectrum search has been com-

pleted, provided you have activated the Show search report imme-
diately check box on the Spectrum Search tab.

If you have not activated this check box, double click the data
block in the browser to open the spectrum search result view.

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 Spectrum Search Chapt. 9

Figure 346: Example of a search result view with spectrum and structural formula

Note: The result view consists of four different windows

which can be re-sized by moving the window frames.

Definition

A Structural formula of the hits highlighted in D

Note: The structural formula is only displayed if a formula is stored for the
particular substance in the library.

B Compound information of the hit highlighted in D

C Spectrum window with query and/or hit spectrum:

• the color of the query spectrum is always red (see E)
• to hide the crosshair right click into the window
• right clicking opens a pop-up menu which provides further setting options: the
Autoscale-mode is set by default, which means that the spectra are displayed in
their original size ratio; the Maximize-Y-mode allows to maximize the spectra on
the y- axis

D List of hits found, sorted according to the hit quality:

• by default, the first hit is activated; the hit highlighted determines the data pro-
vided in A and B
• additional list entries are: compound name, entry number, molecular formula,
molecular weight and CASa number
• right clicking on a particular substance name allows to start info or internet
search about the substance, or auto subtraction and a new search runb

E Query spectrum

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 Chapt. 9 Evaluate

a. CAS: Chemical Abstracts Service; international unique numerical identifiers as-

signed by the Chemical Abstracts Service to every chemical described in the
open scientific literature
b. The info search is based on the libraries selected. Auto subtraction means that
the hit is subtracted from the query spectrum, and the new search run is per-
formed by using the differential spectrum.

9 .16 Neu ro Dev e lo p e r C la s s ifi-

cation

For information on the NeuroDeveloper program, refer to the sepa-

rate documentation provided in OPUS as PDF.

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10 D i s p l a y
The commands in this menu allow to modify the display of the cur-
rent spectra in the spectrum window.

The availability of the commands substantially depends on the

steps performed. For example, the Forward and Back commands
are only enabled if you have zoomed in the current display before.

Figure 347: Display menu

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 Chapt. 10 Display

10.1 B ack /Forward

Definition The Back command allows to restore the original dis-

play size of the spectrum in the spectrum window, if
you have first zoomed in a particular spectral range.

If you click the Forward command, the selected spec-

tral range is enlarged again.

Principle • Load a spectrum file.

• Right click into the spectrum and select the Zoom In
command from the pop-up menu.
• Select a particular spectral range. For detailed infor-
mation see chapter 2.8.4.
• The spectral range selected is displayed in enlarged
format.
• Select the Back command to reduce the spectral
range to the original display size.
• The Forward command would enlarge the spectral
range again.

10.2 Stac k e d

Definition If more than one spectrum has been loaded into the
same spectrum window, you can have them dis-
played in stacked mode. In this case the spectra will
not overlap.

The display in the overview window is, however,

not affected by this command.

Principle • Load several spectrum files, one after the other.

• Select the Stacked command. The spectra are dis-
played as follows:

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 Stacked Chapt. 10

Figure 348: Spectra in stacked display mode

Note: The ordinate will be repeatedly shown in case of

spectra in stacked mode.

To d i s p l a y s e pa r a t e a x e s f o r e a c h s p e c-
trum...

1 ...right click into the spectrum window

2 Select the Properties command from the pop-up menu.
3 Activate the corresponding check box on the Axes tab.

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 Chapt. 10 Display

Figure 349 shows two spectra with separate axes for each spec-
trum.

Figure 349: Spectra display with separate axes

Note: If you zoom in a particular spectral range displayed in

stacked mode, all the other spectra displayed in the
spectrum window will be affected.

To undo the stacked display, click the Stacked com-

mand again.

10.3 Scale All /Scale Y

Definition The Scale All command allows to fit a spectrum to the

size of the spectrum window. To scale the ordinate
only, select the Scale Y command.

Principle • Load the spectrum file.

• Select the Scale All or Scale Y command.

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 Page Back /Page Forward Chapt. 10

1 0.4 P ag e Back /Page Forward

Definition If you have enlarged only a particular spectral range

in the spectrum window, this range will be displayed
on a white background in the overview window, while
the rest appears on a gray background.

The spectral range selected can be moved along the

frequency axis using the Page Forward and Page
Backward commands. In this case you can browse a
spectrum while keeping the displayed frequency
range the same.

Principle • Load the spectrum file.

• Right click into the spectrum and select the Zoom In
command from the pop-up menu.
• Select a particular spectral range. For detailed infor-
mation see chapter 2.8.4.
• The spectral range selected is displayed in the over-
view window on a white background.
• Select the Page Back or Page Forward command.

The display in the overview window will be as follows:

Figure 350: Particular spectral range displayed in overview window

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 Chapt. 10 Display

10.5 Zoom In /Zoom Out

Definition The Zoom command allows to enlarge or reduce par-

ticular spectral ranges.
See also the Zoom in command from the pop-up
menu in chapter 2.8.4.

Principle • Load the spectrum file.

• Select the respective Zoom command. A crosshair
is displayed.
• Left click to draw a frame around the range you
would like to enlarge.
• Press the mouse button again. The crosshair disap-
pears and you can reposition the frame.
• Left click again. The area marked by the frame will
be resized to the spectrum window.
• The crosshair can be removed by a right click into
the spectrum window.

10.6 Single Peak Pick

Definition The Single Peak Pick command allows to label single

spectrum peaks.

Principle • Load the spectrum file.

• Select the Single Peak Pick command. The cursor

changes to .
• Left click on the desired peak. The wavenumber of
the generated peak is displayed. In case of equally
large peaks only the peak close to the cursor will
be displayed.
• After a single peak pick the PEAK data block is gen-
erated and displayed in the browser.
• To delete single peak labels right click the wave-
number displayed for the particular peak and select
the Delete peak label command from the pop-up
menu.

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 Maximize All /Reset Maximize All Chapt. 10

Figure 351: Spectrum with peak labels

10.7 M aximize All /Reset Max -

i m i ze A l l

Definition The Maximize All command allows to maximize all

spectra displayed in the spectrum window.

Principle • Load the spectra.

• Select the Maximize All command. All spectra are
maximized on the y-axis.
• To undo the action select the Reset Maximize All
command. Note that the spectra are not dis-
played in their original size ratio when resetting
the maximization, as only the y-axis has been
considered when maximizing the spectra.

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 Chapt. 10 Display

Figure 352: Maximized spectra

10.8 Shift Curve (whole)

Definition The Shift Curve (whole) command allows to shift the

whole curve vertically.

Principle • Load the spectrum file.

• Select the Shift Curve (whole) command. The cursor
changes to .
• Shift the curve vertically, by pressing the left mouse
button.

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Shift Curve (top) /Shift Curve (bottom) /Re- Chapt. 10

10.9 Shift Curve (top) /S h ift

Curve (bottom) /Reset
S h i ft Cu rv e

Definition The Shift Curve (top/bottom) command allows to

stretch the curve in y direction, either up or down-
wards.

Principle • Load the spectrum file.

• Select the Shift Curve (top/bottom) command. The

cursor changes to .
• Stretch the curve up or down, by pressing the left
mouse button.
• To undo the action select the Reset Shift Curve
command. The spectrum is displayed in its original
size ratio again.

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 Chapt. 10 Display

10.10 Cursor (Crosshair) /

( F o l l o w D a ta)

Definition The Cursor (Crosshair/Follow Data) commands allow

to turn the cursor into a crosshair and read out the
crosshair position data.

If you select the Cursor (Crosshair) command, the

current crosshair position (e.g. wavelength or absorp-
tion unit) is displayed in the upper right edge of the
spectrum window.

If you select the Cursor (Follow Data) command, the

cursor is coupled to the spectrum. You can read out
the x/y data points directly from the spectrum, which
are displayed in the upper right edge of the spectrum
window.

Principle • Load the spectrum file.

• Select the Cursor (Crosshair/Follow Data) com-
mand.
• Move the cursor to the desired position and read out
the position data.
• To deactivate the crosshair, right click into the spec-
trum window.

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11 P r i n t
The printing functions in the Print menu allow to print spectra, cre-
ate new printing templates or layouts, and load existing layouts.

Figure 353: Print menu

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 Chapt. 11 Print

11 .1 Print Spectra

Definition The Print Spectra command allows to print spectra

from OPUS.

Principle • Load the spectrum file and select the Print Spectra
command.
• If required, drag & drop the spectrum file into the
File(s) to print for selected frame selection field.
• Select a plot layout.
• If necessary, click the Frequency Range tab and
define the range desired (see also chapter 2.9).
• Define the output format on the Options tab.
• Click Print.

Note: Before printing spectra, make sure that you

have installed a default printer in Windows.

The different tabs of the Print Spectra dialog are described in the
following.

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 Print Spectra Chapt. 11

Select Files

A B

Figure 354: Print Spectra - Select Files

Selecting Plot Layout

1 Click Change Layout (A in figure 354).

2 The Select Print Layout dialog opens.
3 Select a plot layout. Plot layouts are stored in the
C:\Users\Public\Public Documents\Bruker\OPUS_<ver-
sion> directory and have the extension .*PLE. If you have
selected a plot layout, the name and path of this layout will
be displayed. By default, the plot layout last selected for
printing is displayed.

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 Chapt. 11 Print

4 You can select the frames included in a particular plot layout

from the Frame drop-down list. Each data block of a spec-
trum file can have a special frame.
Example: If you select frame1 and the AB data block is dis-
played in the File(s) to print for selected frame selection field,
the AB data block will be printed in frame1. This will also be
indicated in the selection field header.

To learn the meaning of the different frame descriptions

included in a plot layout click the Edit Layout button in the
Select Print Layout dialog.

The plot layout interface opens. The frame definition is indi-

cated in the Item column. For further details on this subject
refer to chapter 11.5.1.

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 Print Spectra Chapt. 11

Show Preview

To display a preview of the plot click the Show Preview (C in

figure 354) button. If the plot consists of several pages, you can
select between a single and two-page display and scroll through
the single pages. Additionally, you can zoom in or out the spectrum
previewed.

Figure 355: Print Preview

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 Chapt. 11 Print

Frequency Range

Figure 356: Print Spectra - Frequency Range

A If you activate this option button, the axis of all spectra in all
frames will be set to their maximum size.
B If you activate this option button, the frequency limits of the
plot layout selected before will be used.
C If you activate this option button, the Select frequencies for...
group field will be enabled. Either type the limit values manu-
ally or define them interactively (see chapter 2.9).
If you click the Get Display Limits button, the current limits
displayed in the spectrum window are set in the appropriate
entry field.

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Options

Figure 357: Print Spectra - Options

A If you activate this check box, the compressed wavenumbers

are plotted, i.e. the wavenumbers above 2000 cm-1 will be
compressed by a factor of 2.
B Define the maximum number of peaks which are to be
labelled.
C Define the output format. The printout can both be sent to the
printer or the clipboard. It is also possible to create a bitmap
or a PDF file.
If you activate the Bitmap or PDF option button, the File name
and Path entry fields are enabled. To save the printing define
the file name and path or edit the path, using the Change
Path button.

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11 .2 Setup Analysis Report Tem -

p l at e

Definition The Setup Analysis Report Template command

allows to setup an individual report template to be
used to depict evaluation results of single or multiple
spectrum files. To do so, the Default.art analysis
report template is edited and stored by a different file
name.

Different setup options are available to define which

kind of data have to be written into the report.

Principle See chapter 11.2.5.

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11 .2 .1 D ia lo g

Figure 358: Setup Report Template dialog

A To open an already existing template file click this button. The

name of the template file is displayed in the entry field below
this button. Template files for reports have the file extension
*.art.
B Different result types (single and multi sample report) are
available, see chapter 11.2.2.
C This list box contains the setting options for the data to be dis-
played in the report. For details see chapter 11.2.3.
D The preview window exemplifies the expected report,
depending on the setting options selected.
E To save the template click this button.

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11 . 2 . 2 R e p o r t Ty p e s

You can select between different report types:

• Single Sample Report: one report for each single spec-
trum file
• Multi Sample Report: one report for all spectrum files

Note: The Default.art template contains all report types.

11 . 2 . 3 S e t t i n g o p t i o n s f o r r e p o r t d a ta

The setting options (C in figure 358) for report data depend on the
report type selected. Not every setting option is available for each
report type.

Report Data Definition

General report settings General data regarding report title, footer

comments for the PDF report, date and time
of printout

Hardware and software Data regarding instrument type, instrument

serial number or OPUS version

Company and user Customized data regarding company and

user, e.g. department, location, operator or
signatures, company logo

Sample info • General sample information, e.g. file and

sample name, measuring time, sample form
• Measurement parameters, e.g. name of
measurement experiment, measurement
channel, resolution
• Product information, e.g. product group,
product name

Global result options Data on evaluation or manipulation results

Spectrum in report Data which specify if and when the spectrum

has to be displayed in the report

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11 . 2 . 4 R e p o r t St r u c t u r e

The structure of an analysis report is similar with all report types

available (chapter 11.2.2). The report can contain:
• general report data
• sample-specific data
• spectrum frame of each sample

Sp e c t r u m F r a m e

The spectrum frame is displayed below the general report data and
product-specific data. This kind of report data is optional and dis-
played either always, never or only if the evaluation result is not ok.

Figure 359: Example of a spectrum frame

11 . 2 . 5 How to set up a template?

Basically, the procedure on how to set up a template is the same

for all report types available (chapter 11.2.2). The procedure
described in the following exemplifies a single report.

In case of sample information and global result options there are

differences on the setup between the single sample and multi sam-
ple report, see chapter 11.2.7.

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Step 1:
Click the Setup Report Template com-
mand and select a report type from the
drop-down list.

Step 2:
Click on one of the setting options from
the list box. A second group field may
be displayed below the setting options.

Step 3:
Activate the respective checkboxes. Fill
in the entry fields or select an option,
where required.

What can be seen?

The report data set are marked by black bullets.

The preview window shows the report settings defined.

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Repeat the steps 2 and 3 for further setting options.

Note: It is not necessary to activate all setting options. It makes

sense to activate only those options which you need to see in the
report.
In case of the global result options you have to observe that even if
many different options are activated, the analysis report only shows
those types of results or evaluations for which data blocks are avail-
able in the spectrum file. As the evaluation results are reported in a
table the number of evaluation parameters, which can be displayed,
is limited. Therefore, it makes sense to activate only the most impor-
tant result options when setting up the analysis report.

Step 4:
Click the Save button to save the tem-
plate.

Note: The reports have the extension

*.art and are stored in the
C:\Users\Public\Public Docu-
ments\Bruker\OPUS_<version>
directory.

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11 . 2 . 6 Examples of a single sample

report template

Figure 360 shows an example of a single sample report template

as displayed in the preview.

Figure 360: Example of a single sample

report template displayed as preview

A Report header
B Analysis data in table format
C Spectrum view

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11 . 2 . 7 Sp e c i a l f e a t u r e s i n c a s e o f a m u l t i
sample report

Compared to the single report, the multi sample report is generated

in landscape format. Some setting options can either be written in
the header or displayed in tabular form as product-specific data.

It is recommended to write data into the header which are identical

for all samples, and are therefore of overriding importance. You
have to activate the Header checkbox (figure 361) of the respective
setting option.

Note: If, however, one or more samples do not match the

header data and a contradiction occurs while generat-
ing the multi sample report, a further multi sample
report will be generated separately for these samples.

Figure 361: Example of setting options:

Measurement parameters

The setting options activated by the Table checkbox in figure 361

indicate that these data are different for each sample.

Report data which exclusively refer to the sample cannot be written

into the header. In these cases there is no Header checkbox in
front of the respective setting option (figure 362).

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Figure 362: Example of setting options with-

out Header checkbox

Sample-specific data are written in tabular form with the multi sam-
ple report. The setting options (chapter 11.2.3) to be selected are
the headers of the table columns, the samples form the name of
the respective table row. There is one table row for each sample.

Figure 363 shows an example of a multi sample report as dis-

played in the preview.

Page 1 C Page 2

Figure 363: Example of a multi sample report template displayed as preview

A Report header
B Analysis data in table format
C Spectrum view

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11 . 2 . 7 . 1 Global result options

In case of the multi sample report, the evaluation results of the

samples can be summarized and depicted accordingly.

Figure 364: Global result options

A An additional table column shows the overall result of all eval-

uations rated for one sample (figure 365), e.g. in case of
IDENT: identified as; in case of QUANT: within the limit.
- OK: green check mark
- Not OK: red cross
Example:

Figure 365: Example: overall sample rating

B The report header summarizes all sample ratings with their

evaluation results being ok or not ok (figure 366). Example:

Figure 366: Example: sample ratings summarized in report header

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C The evaluation result of a sample is only displayed in the

table, if the result is not ok (figure 367). Example:

Figure 367: Example: rating results not ok

11 . 2 . 7 . 2 S i n g l e e v a l u a t i o n r e s u l ts

In case of some evaluation types, e.g. integration, QUANT or

QUANT 2 you can depict the single components of one method in
different ways.

Figure 368: Result option for method com-

ponents

A This type of setting option is reasonable if all components

have been used for the same method.
B This type of setting option is reasonable if no or only a few
pieces of information, behalf of the result, is to be depicted for
each component.

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11 . 2 . 8 Multi Evaluation

The result of a multi evaluation can be depicted both in a single and

multi sample report. The following analysis methods are taken into
account: conformity test, integration, QUANT 1/2. There are sepa-
rate setting options for this kind of analysis methods.

Figure 369: Setting options for multi evalution,

example: QUANT 1

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11 .3 Generate Analysis Report

Definition The Generate Analysis Report command allows to

generate a report for single or multiple spectrum files
to depict evaluation (analysis) results.

Note: The evaluation results can only be depicted

if the spectrum file contains the data block of the
respective evaluation. Evaluation data blocks are
e.g. PEAK, INTEG, QUANT, IDENT, SEARCH, CT.

Principle • Load the spectrum file(s).

• Select the Generate Analysis Report command.
• If required, drag & drop the spectrum file(s) into the
File(s) for report generation selection field.
• Select the report layout (chapter 11.3.1). The report
templatea file previously used is always defined.
• Click the Output to tab to define how the report is to
be printed (chapter 11.3.3).
• Click the Generate button.
a. The Default.art standard template (chapter 11.3.2) is stored in the
C:\Users\Public\Public Documents\Bruker\OPUS_<version> di-
rectory.

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Figure 370: Generate Report - Select Files

11 . 3 . 1 Report Layout

The report layout provides different types of layout options:

• Single sample report: one report for each spectrum file
• Multi sample report: one report for all spectrum files

To generate a single sample report you can use several spectra

files at once. In this case, a separate report is generated for each
spectrum file separately.

A multi sample report lists all spectrum files with the respective
data in one report.

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Figure 371: Generate Report - Select Files

11 . 3 . 2 Sta n d a r d Te m p l a t e

When generating an analysis report for the very first time OPUS
uses the Default.art standard template. The data provided in this
template considers the typical setting options available for the three
different report layouts (chapter 11.3.1), with regard to e.g. sample
parameters and evaluation results.

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11 . 3 . 3 Report Output

There are different possibilities for the report output:

• printer
• file (either as PDF or csv file)
• clipboard (to integrate the report into other types of doc-
uments)

If you activate the PDF option button, the File name and path entry
fields are enabled. To save the report define the file name and path
or edit the path, using the Select Path button.

Figure 372: Generate Report - Output to

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11 .4 Quick Print

Definition The Quick Print command allows to plot the contents

of an OPUS view displayed on the screen. An appro-
priate default template for the currently displayed
view is used.

Note: OPUS views are always indicated by a tab.

Example:

Principle In case of quick print the OPUS view is printed as it is

actually displayed on the screen. That means, if e.g.
only a single part of a spectrum is displayed, only this
part will be printed including possible labels and
annotations.

11 .5 New Layout

Definition The New Layout command allows to create new lay-

out templates using the plot layout editor (PLE).
These templates may include spectra and additional
information, e.g. measurement parameters. You can
add descriptions as well as simple graphic elements
(e.g. logos or bitmaps) to the templates.

The plot layout editor consists of a separate view

which opens when clicking the New Layout com-
mand.

Principle How to create new layout templates is described in

the following.

To c r e a t e a n e w l a y o u t t e m p l a t e . . .

1 ...select the New Layout command. The PLE view opens.

2 Create the template by means of the icons and pop-up
menus.

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3 Store the template. On the PLE view, select the File menu
and click Save as. Template layouts have the file exten-
sion *.PLE.

11 . 5 . 1 P L E Vie w

The PLE view is described in the following.

C
D
B

Figure 373: PLE view

A The PLE drawing area consists of a black grid and a red bro-
ken-line frame. This frame represents the available print area
of the printer.
The PLE drawing area visually represents the plot view of the
current template, containing all the frames. Each frame can
be scaled and positioned individually.
To resize the drawing area right click somewhere on the
drawing area outside any frame. The Ple Page dialog opens.

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Use the different tabs of this dialog to define general settings

for the drawing area (see chapter 11.5.3).
B The OPUS browser window shows an overview of all win-
dows currently open, including spectrum windows and PLE
views. You can change between the spectrum windows and
PLE views by clicking the appropriate icon (see figure 374) in
the browser window.

Figure 374: Icons in the browser to change views

C The Items column shows all items displayed on the drawing

area. Frames will be referred to by the type of data included
(table, spectrum etc.). The active frame is indicated by a red
arrow in the item window and marked by a thick line on the
PLE drawing area.

Figure 375: Item column

Each new frame created is named frame_x, with x being auto-

matically incremented. To activate a particular frame you
have to select it. Left click either the frame displayed on the
drawing area, or the name of the frame indicated in the Item
column. Note: If you assign a peak list or report view to
the PLE layout by means of the pop-up menu (see
chapter ), the Item column contains the Opus View: fra-
mex definition.
D To change between PLE view and the OPUS spectrum win-
dow use the Display or PLE tab.

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PLE Icons

The PLE icons required to create layout templates are provided on

a separate toolbar, and are listed in the following table.

Icon Definition

Drawing a circle or ellipse

Drawing a line or an arrow

Drawing a frame

Drawing a table frame

Drawing an integration report frame; the report frame will be

linked to the spectrum frame (frame1)

Drawing a QUANT report frame; the report frame will be

linked to the spectrum frame (frame1)

Drawing a quick compare report frame; the report frame will

be linked to the spectrum frame (frame1)

Drawing a peak report frame; the report frame will be linked

to the spectrum frame (frame1)

Drawing a standard parameter table; the table frame will be

linked to the spectrum frame (frame1)

Selecting and moving items

Scaling spectrum

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Icon Definition

Adding page (in case of multi-page templates)

Removing page (in case of multi-page templates)

Selecting next page (in case of multi-page templates)

Selecting previous page (in case of multi-page templates)

Selecting active page (in case of multi-page templates)

Deleting items

Deleting item contents

Opening PLE Page dialog (see chapter 11.5.3)

Opening Spectral Frame Properties dialog (see

chapter 11.5.4)

Anchoring object frame or undo anchoring

The most-frequently used commands can be added to the toolbar.

Proceed as follows:

1 Click the arrowhead at the end of the toolbar.

2 Position the cursor on the arrow of the editing field dis-
played.

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3 Position the cursor on the Print Layout Editor command.

4 All icons are displayed which can be added to the standard

toolbar. To add an icon to the toolbar click the respective
icon of the menu opened. A check mark is set in front of the
icon selected. All icons preceded by a check mark are acti-
vated and displayed on the toolbar.

For further details on how to customize toolbars refer to

chapter 14.7.

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11 . 5 . 2 Pop-up menu

If you right click a frame, the PLE pop-up menu opens. This menu
allows to individually configure the frame.

Figure 376: PLE pop-up menu

To change the contents of a frame use the Assign command. You

can assign spectra, peak lists, standard parameters and other
OPUS views as well as reports to a frame.

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The Copy command duplicates the content of a frame as mono-

chrome bitmap, color bitmap or meta file. The content of a page
can be copied as metafile.

By means of the Paste command you can insert text, a bitmap,

meta file or text from the clipboard into the active frame.

The Remove command deletes the frame from the drawing area,
while the Snap to Grid command aligns this frame exactly on the
closest grid lines.

The Edit command allows to manipulate the frame contents. This

command is only available for text and table frames.

If you select the Properties command, the Properties dialog of the

selected frame opens.

11 .5 .3 Resizing Dr a w i ng Ar e a
1 ...right click somewhere on the drawing area.
2 The Ple Page dialog opens.
3 Use the different tabs of this dialog to define the general set-
tings for the drawing area.
4 To confirm the settings click OK.

The different tabs of the Ple Page dialog are described in the fol-
lowing.

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Page

A
E

F
B
G

D H

Figure 377: Ple Page - Page

A To specify the unit that you want to work with (inches or centi-
meters) activate one of the option buttons.
B You can print either in landscape or portrait.
C The maximum print area of the printer can be defined. Each
printer has a particular margin used for paper feed, and which
will not be printed on. These default settings are suitable for
all common printers and have to be rarely adjusted. The max-
imum print area is represented by a dotted red line on the
PLE document.
D The option buttons allow to define the paper size. The equiva-
lent unit has been defined by (A).
E Check this option button if the drawing area is to be enlarged
up to the size of the whole page.
F Check this option button if the drawing area is to be enlarged
up to the page width.
G If you check this option button, the entry field will be enabled.
Enter the scale factor manually. The scale factor required to
view the PLE pages is indicated in per cent. Most monitors
are not large enough to allow viewing the entire page at 100%
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 New Layout Chapt. 11

scale. In case of landscape orientation it is advisable to

use a scale factor of 75%, in case of portrait orientation a
scale factor of 50%.
H Specify the default font to be used when creating a frame
within a document. If a frame includes data, the font can be
changed no matter what kind of default setting you use.
I If you click this button, a color palette is displayed which can
be used to define the background color of the view.
J If you activate this check box, you can assign any type of
OPUS view to a frame.
Draw a frame on the PLE drawing area and right click the
frame. Select the Assign  OPUS View command from the
pop-up menu. The drop-down list includes all OPUS views
available. If you have selected a structure view, you can drag
& drop a structure data block ( ) into the frame. To save
the PLE page as template it is advisable to remove the data
block again, and the frame will only include the view type
assigned to.

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Grid

C
E
D

Figure 378: Ple Page - Grid

A If you activate the check box, the grid will be visible. The grid
can be useful to align objects on the drawing area.
B If you activate the check box, new objects created are posi-
tioned and sized to line up with the closest major grid lines.
C Usually, the grid is only displayed on the screen to simplify
object alignment. Activate the check box if you want to have
the grid printed on paper.
D The Major and Minor settings define the grid size in the unit
specified on the Page tab. Figure 378 exemplifies a grid size
of 0.25 x 0.25 inches. The grid can be further divided by filling
in the Minor entry fields.
E If you click this button, a color palette opens. Select or define
the color for the grid.

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Header

The header and footer are printed on every page. The Header and
Footer tabs are identical, therefore only the Header tab will be
described in the following.

Figure 379: Ple Page - Header

A The header (or footer) can consist of up to 6 fields (2 rows on

the left, middle and right). The entries in the fields consist of
meta strings (also see chapter 11.5.5). You can either enter
these meta strings manually or drag & drop them using the list
box (C). It is also possible to manually enter plain text for the
header or footer.
B To define the header font click this button.
C The list box contains special meta strings. The editor converts
these meta strings into readable text in the preview. You can
drag & drop these commands from the list to the particular
entry field which you want to have the information printed in.

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Te m p l a t e

Figure 380: Ple Page - Template

You can save a particular template as default. When creating new

PLE documents the settings of this particular template will be used.

Note: The default template has the extension default.ple

and is located in the same directory as the OPUS pro-
gram.

The Save As command from the File menu allows to save tem-
plates, using any file name and directory. To load these templates
use the File menu and click Load File.

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11 .5 .4 A d d i n g e l e m e n ts , m o d i f y i n g s p e c -
trum frame

Adding spectrum

There are two possibilities to load a spectrum to the drawing area:

1 Drag & drop the spectrum from the browser directly into the
spectrum frame on the drawing area. Load the spectrum file
from within the PLE view. The spectrum window is displayed
again. Drag the spectrum data block (AB or TR) from the
browser to the PLE tab ( ). Wait until the PLE view
opens by pressing the left mouse button. Drop the spectrum
block into the spectrum frame.

2 Draw a frame by using the icon and assign the spec-

trum to this frame. Right click the frame and select the
Assign Spectra command from the pop-up menu. Select
the particular spectrum from the dialog that opens. The
spectrum is shown within the frame.

Figure 381: Frame with spectrum

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Adding image or logo

1 Click the icon.

2 Drag a frame into the spectrum frame.
3 Right click the newly created frame.
4 From the pop-up menu, select the Assign  Bitmap com-
mand. A file selection dialog opens.
5 Select the bitmap from the respective directory.
6 Click the Open button. Now, the bitmap has to be displayed
on the position defined.

Figure 382: Spectrum with bitmap

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A d d i n g g r a p h i c a l e l e m e n ts a n d p e a k l a b e l

Certain peaks of a spectrum can be highlighted by additional

graphic elements. In particular, you can use circles, arrows and
callout boxes.

Graphical elements

1 Click the icon.

2 Drag a frame into the spectrum frame.
3 Right click the newly created frame.
4 From the pop-up menu, select the Assign Spectra com-
mand. A file selection dialog opens.
5 Select the spectrum from the respective directory.
6 Click the Open button. Now, the bitmap has to be displayed
on the position defined.

7 Click the icon.

8 Drag a frame. A circle is displayed.

9 Click the icon and draw a line to the circle. If you want
the line to have no arrow head, right click the line. From the
pop-up menu, select the Properties command and deacti-
vated the Arrow Head checkbox.

Figure 383: Spectrum with graphical element

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Text

1 Click the icon.

2 Drag a frame into the spectrum frame.
3 Right click the newly created frame.
4 From the pop-up menu, select the Edit command. An edit
field opens.
5 Enter text into the edit field.
6 To close the edit field click somewhere outside the frame.

Figure 384: Spectrum with peak label

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To h a v e t h e s ta n d a r d s p e c t r u m pa r a m e t e r s
displayed...

1 ...click the icon on the toolbar.

2 Press the left mouse button and drag a frame on the drawing
area. This frame includes a table which consists of rows and
columns, by default.

Figure 385: Table frame with standard spectrum parameters

3 To change these default name settings, right click the table

and select the Edit command from the pop-up menu. This
allows to directly get into the table cell to change the text.
4 To change the table size, right click the table frame and
select the Properties command from the pop-up menu. The
Table Properties dialog is displayed. For detailed information
refer to chapter 11.5.6.

To m o d i f y t h e s p e c t r u m f r a m e . . .

1 ...right click into the spectrum frame.

2 Select the Properties command from the pop-up menu.
3 The Spectral Frame Properties dialog opens.
4 Use the different tabs of this dialog to define general settings
for the spectrum frame.
5 To confirm the settings click OK.

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The different tabs of the Spectral Frame Properties dialog are

described in the following.

I t em

C
B

D
E

Figure 386: Spectral Frame Properties - Item

A To change the size and position of the frame on the drawing

area use these entry fields. The unit (cm or inch) has been
specified by the PLE Page dialog on the Page tab (see
chapter 11.5.3).
B The line thickness used for the frame is indicated in pixels in
the drop-down list.
C Using this button allows to define the frame contour color. If
you click Color, a color palette opens. Select or define the
color desired.

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D Normally, the frame contour is not printed. If you activate this

check box, the contour will also be printed on hard copy.
E If you activate the check box, the frame will be filled by the
color specified in (C).
F You can assign a name to any item. This is advisable in case
of complex layout templates as a name simplifies the identifi-
cation of the object. You can use this name to link tables and
text frames to spectrum frames.
G This entry field includes the name of a particular link. This
option is only reasonable in case of tables, report frames
and texts.
If you want to add e.g. data from a particular spectrum frame
to a table, enter the name of the spectrum frame into the
Linked To entry field. This entry has to be adjusted as soon
as the name of the respective spectrum name has been
changed by the operator. Otherwise, the link between the dif-
ferent frames will be lost.

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L i m i ts

A
D

B
F

C
G

Figure 387: Spectral Frame Properties - Limits

A The entry fields allow to define the frame limits. The unit of the
values entered has been specified in the PLE Page dialog on
the Page tab (see chapter 11.5.3).
B The style type selected determines the data depiction within
the frame. You can have the spectra displayed in overlaid or
stacked mode.
C Activate the check box if you want to have the logo displayed
within the spectrum frame.
D If you activate the check box, the spectra x axis will be auto-
scaled within the frame.
E If you activate the check box, the y axis of the spectra will be
autoscaled within the frame.

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F The frame displayed on the drawing area can either include

the entire spectrum (with axes and annotations), or can be
used as outer line of the spectrum itself. If you activate the
Frame is Data Area check box, the axes and annotations will
be drawn outside the frame.
G If you do not activate the check box, only one spectrum can
be displayed within the frame.

Axes

The X Axis and Y Axis tabs are identical except for the Rotate
Numbers check box on the Y Axis tab. This option allows to rotate
the y axis annotations by 90°.

The Show axis for stacked spectra and Compressed Wavenum-

bers check boxes are only available for the x axis.

A
I

B
J

C
K
D

E
L
F

Figure 388: Spectral Frame Properties - x Axis

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A Activate the check box if the axes, tick marks and labels have
to be displayed.
B The drop-down list allows to determine the thickness of the
axis lines. You can also enter the thickness manually.
C This check box is activated by default, i.e. each spectrum is
displayed with a separate x axis. Otherwise, one common
x axis is used for all spectra loaded.
D If you activate the check box, wavenumbers above 2000cm-1
are displayed using a smaller linear scale.
E If you activate the check box, the tick marks of the x axis are
displayed on top of the spectral frame.
F The check box is activated by default, i.e. the tick marks of the
x axis are displayed at the bottom of the spectral frame.
G Activate this check box if you want to have the grid lines dis-
played on the spectral frame.
H The axes are labelled according to the spectrum file loaded
by the editor. To change the axis label enter text into the entry
field.
I Using this button allows to define the axes color. If you click
the button, a color palette opens. Select or define the color
desired.
J If you click the button, a list box is displayed. Use this list box
to determine the font and size of the axis label.
K If you click the button, a list box is displayed. Use this list box
to determine the font and size of the tick marks.
L The check box is activated by default. In this case, the editor
calculates the optimum settings for the tick marks.
If you deactivate the checkbox, you determine the position
and interval of the tick marks manually. In this case, interval
means the wavenumber range between two tick marks. You
can manually enter the number of digits (maximum: 20) used
for the numeric tick mark labels into the Digits check box.

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D a ta

A C

B
E

Figure 389: Spectral Frame Properties - Data

A Spectra added to a frame, are put into a slot. This slot deter-
mines the position of spectra. To change a spectrum view,
you first have to select the corresponding slot of the spec-
trum. Then, you have to define the properties for that slot
using the control elements for color, line style and line width.
B If you click the button, the spectra data selected in (A) is
deleted from the slot.
C The color palette allows to determine the color of the spec-
trum displayed.
D Use the list box to determine the line style of the spectrum
displayed.
E Define the line width of the spectrum displayed. Separate line
widths can be specified for the screen view and printout.

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F These options are only enabled if the spectrum file con-

tains a or data block. The data block for annota-
tions or integration fields can be displayed in the PLE
template by activating the Visible check box.
G Use the Font button to determine the font for the annotations.

Peaks

A E

F
B

G
C
H
D

Figure 390: Spectral Frame Properties - Peaks

A Spectra added to a frame, are put into a slot. This slot deter-
mines the position of spectra. To change a spectrum view,
you first have to select the corresponding slot of the spec-
trum.
B Define the stroke width of the spectrum displayed. Separate
line widths can be specified for the screen view and printout.
Click Color to determine the color for the strokes.

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C Activate this check box if the stroke color has to be the same
as the one for the spectrum labels. This helps to get a clear
display, which is especially useful if the PLE view consists of
more than one spectrum. By means of the Color button (B)
you can define an individual stroke color for each spectrum,
which will be the same for the spectrum label if you activate
the check box (C).
D The check box is activated by default. Therefore, extra space
is provided between the highest peak and the spectrum frame
for the peak labels.
E Use the list box to select the type and position of the labels
you want to assign to the peaks.
F This option is only enabled if the spectrum file contains a
data block. Starting with the highest peak you specify
the number of peaks to be labelled, using the All and None
buttons.
G This option is only enabled if the spectrum file contains a
data block. Enter the number of digits and decimals for
the peak labels.
H Click the button to determine the font type used for the labels.

11 . 5 . 5 Adding text and modifying text

frame

Text can be included using text frames, i.e. either enter text manu-
ally into or import an existing text file to a frame.

For manual text input...

1 ...draw a frame, using the icon.

2 Right click the frame.
3 Select the Edit command from the pop-up menu. This will
transform the frame into a text frame.
4 Now, enter text into the entry field displayed.
5 Close this entry field by left-clicking anywhere outside the
field.

Note: In case of manual text input you can also use meta
strings. The meta strings used for text parameters
can be directly typed into a text frame, and will be

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interpreted by the editor using the data from the spec-

trum frame linked to the text frame.

To r e s i z e t h e t e x t f r a m e . . .

1 ...left click into the frame and scale it up or down using the
marker positions.
2 To edit text use the Edit command from the pop-up menu.
Right click into the text frame to select this command.

To i m p o r t a t e x t f i l e . . .

1 ...draw a frame, using the icon.

2 Right click the frame.
3 Select the Assign  Text File command from the pop-up
menu.
4 Specify the particular text file from the dialog displayed. Note
that only files with the extension *.txt can be imported.

To m o d i f y t h e t e x t f r a m e . . .

1 ...right click into the text frame.

2 Select the Properties command from the pop-up menu.
3 The Spectral Frame Properties dialog opens.
4 Use the different tabs of this dialog to define general settings
for the spectrum frame.
5 To confirm the settings click OK.

The Text and Parameters tabs of the Text Properties dialog are
described in the following. For details on the Item tab refer to
chapter 11.5.4.

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Te x t

B
A

Figure 391: Text Properties - Text

A Defines the position of tab stops for the text in the frame. The
value entered represents the distance to the next tab. Multiple
positions can be used, separated by spaces, e.g. 8 12 20 40.
The last tab spacing is used for subsequent tab stops, if more
tabs are required.
B This button allows to determine the font and font size of the
text.
C To better align text within a frame activate the check box, as
the text lines will be horizontally centered.

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Parameter

Figure 392: Text Properties - Parameters

A Different types of parameters are available. Select one of

them.
B The entries of the list box depend on the type of parameter
selected (A). To add information to a text, select an item from
this list box and drag & drop it to the particular table cell.
The entries in the list box are meta strings, i.e. three-letter
codes preceded by a ^ character. When the editor encounters
such a code, it interprets this code as an instruction to extract
information from the data slot of the linked spectral frame, and
to substitute the information by the code.
If you edit the text using the Edit command from the pop-up
menu, you will see the actual codes which the meta string
consists of.

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11 .5 .6 A d d i n g ta b l e a n d m o d i f y i n g ta b l e
frame

A table can be created by using table frames. By default, tables

consist of 2 columns and 2 rows. The default number of columns
and rows can be changed.

To a d d a ta b l e . . .

1 ...click the icon on the toolbar.

2 Draw a frame on the drawing area by using the left mouse
button. The table consists of two columns and two rows.

To a d d t e x t t o a ta b l e . . .

1 ...right click the position desired in the table.

2 Select the Edit command from the pop-up menu.
3 Now, you are directly in the table cell to enter text. When
editing table cells you can change between the different
cells by using the tab key.

To m o d i f y t h e ta b l e f r a m e . . .

1 ...right click into the table frame.

2 Select the Properties command from the pop-up menu.
3 The Table Properties dialog opens.
4 Use the different tabs of this dialog to define general settings
for the table frame.
5 To confirm the settings click OK.

The Parameters and Formats tabs of the Table Properties dialog

are described in the following. For details on the Item tab refer to
chapter 11.5.4.

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Figure 393: Table Properties - Parameters

A Different types of parameters are available. Select one of

them.
B The entries of the list box depend on the type of parameter
selected (A). To add information to a table, select an item
from this drop-down list and drag & drop it to the particular
table cell.
The entries in the list box are meta strings, i.e. three-letter
codes preceded by a ^ character. When the editor encounters
such a code, it interprets this code as an instruction to extract
information from the data slot of the linked spectral frame, and
to substitute the information by the code.
If you edit the table using the Edit command from the pop-up
menu, you will see the actual codes which the meta string
consists of.
C Normally, the information extracted by the editor to expand
the meta strings is taken from the corresponding spectral
frame in slot 1. If you activate the Treat Parameters as Multi-
ple check box, the parameters will be repeated for each spec-
trum within a particular frame until the maximum number of
rows defined on the Format tab has been reached. A sepa-

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rate table cell is available for each spectrum within the table
frame.
D The more spectra you add to a frame, the more additional
table cells can be created to be able to display the parame-
ters for each spectrum. If you activate the If Multiple, automat-
ically add rows for new spectra check box, the number of
rows set on the Format tab will become meaningless.

Format

A G

B H

I
C
J
D

Figure 394: Table Properties - Format

A Define the number of columns included in the table. The

default setting is 2 columns.
B Define the number of rows included in the table. The default
setting is 2 rows.
C Use the button to determine the font for the title. Make sure
that you first activate the Row 1 has titles check box.
D The check box is activated by default. Therefore, a grid is dis-
played around each table cell for better distinction. The value

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entered into the Thickness entry field determines the thick-

ness of the grid in pixels.
The Color button allows to specify the color of the grid to be
displayed. If you click the button, a color palette opens. Select
or define the color desired. The Color button will be displayed
in this color.
E The check box is activated by default. Therefore, cells will be
adjusted to the size of the table frame.
If you deactivate the check box, define the height and width of
the cells using the two entry fields according to the unit speci-
fied.
F Activate the check box if you want to center text within the
table cell.
G If you activate this check box, the text in column 1 is used as
column header, and displayed in the font specified by the Title
Font button (C).
H If you activate this check box, the text in row 1 is used as row
header, and displayed in the font specified by the Title Font
button (C).
I To better distinguish the rows the check box is activated by
default. The parameters are displayed by the corresponding
spectral color.
J The button allows to specify the body font for the table text.
This font applies to all table cells, provided you have not acti-
vated the Column 1 has titles (G) and Row 1 has titles (H)
check boxes.

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11 .6 Open Layout

Definition The Open Layout command shows a list of existing

templates.

Principle When using this command for the first time after the
OPUS installation you have to navigate to the particu-
lar directory. By default, templates are stored in
C:\Users\Public\Public Documents\Bruker\
OPUS_<version> and have the file extension *.PLE.

Plot layouts have the extension .*PLE and can consist of different
frames, e.g. spectrum or text frames, as well as of tables. For
detailed information on the plot layout elements refer to
chapter 11.5.

Plot layout Layout for...

CHROMPOSTRUN.PLE chromatographic measurements

CLUSTERANALYSIS.PLE cluster analysis results

CORRELCHART.PLE band assignment chart

3D.PLE 3D depictions

DISPLAY.PLE spectrum window

DISPLAY+INFO.PLE spectrum window with information

view

EVALRESULTS.PLE evaluation results

LIBRARY.PLE library

OLDREPORT.PLE report view

PROCESSCONTROL.PLE trend chart of measurement by OPUS

PROCESS

QCOMPRESULT.PLE quick compare results

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Plot layout Layout for...

REPORT.PLE reports

SEARCHRESULTS.PLE search report

STRUCTURE.PLE chemical structures

11 .7 Print /Print Preview

Definition You can view the result of a printout using the Print
Preview command. The Print command starts printing
immediately.

11 .8 Print Setup

Definition Use the Print Setup command to define the printer

and the print parameters, e.g. paper size and print
quality.

Clicking the Properties button opens a different dialog

which can be used to perform further settings,
depending on the printer configuration.

As the available drawing area (A in figure 373) depends on the

printer setup you first have to configure the particular printer set-
tings.

1 On the File menu, click Print Setup.

2 Click the Properties button and set the appropriate paper
size and format.
3 Confirm the settings by clicking OK.

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12 M a c r o
Macros can be created for regularly used OPUS functions. An
OPUS macro is a sequence of OPUS commands that can be exe-
cuted all in one. In addition to the standard OPUS commands there
is a set of macro functions which allow to control the macro execu-
tion, interaction with the user and the evaluation of results.

Basically, an OPUS macro is a text file using the extension *.MTX,

which can be edited by any kind of text editor. For detailed informa-
tion on all macro functions and their syntax, see the OPUS/Pro-
gramming manual.

Figure 395: Macro Menu

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 Chapt. 12 Macro

12.1 Script Recorded History

Definition
This command allows to store data from the
data block in a script.

Principle • Load the spectrum file.

• Select the Script Recorded History command.
• If required, drag & drop the spectrum file into the
File to extract manipulation from selection field.
• Define a file name for the script.
• Click Generate to store the script.

B A

Figure 396: Convert History to Script - Select File

A If you activate the check box, you add the corresponding

measurement parameters as well.
B Once the script has been generated, it can also be applied to
other files. On the File menu, click VisualBasic Script.

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12.2 Insert MyInstrument

Definition MyInstrument is a standardized programming inter-

face for spectrometers running in 32-bit Windows
environments. The design of this interface makes the
spectrometer and the software module, which con-
trols the spectrometer, synonymous. However, the
interface clearly distinguishes between data acquisi-
tion and data processing.

The software allows to set all hardware parameters

and measurement conditions which are typically use-
ful. Special features like the detector temperature or
alignment can be controlled by the MyInstrument
standard.

Principle • Select the Insert MyInstrument command to create

a VisualBasic Script.Load the spectrum file.
• Enter the name of the registered control element
into the Select MyInstrument control entry field.
• Define the file name and path for the resulting Visu-
alBasic Script.
• Click Generate.

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Figure 397: Insert MyInstrument - Select File

12.3 M a cr o Converter

Definition This command allows to convert macros written by

OPUS OS/2 into the OPUS format.

The conversion may require some changes as a

result of the different macro syntax. For any further
details, refer to the OPUS/Programming manual.

Principle • Select the Macro Converter command.

• A wizard opens to help you with the conversion step
by step. Follow the on-screen instructions.

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12.4 R un Macro

Definition This command allows to run a macro.

Principle • Select the Run Macro command. A dialog opens.

• Select the appropriate macro from this dialog.

Note: Any further actions depend on the macro

selected.

12.5 Macro Debuggen

Definition The Debugging term means executing macros step-

by step, or selectively executing single macro lines.
The program is executed until a specified break point
has been reached.

Debugging simplifies the localizing and analyzing of

macro errors.

Principle • Select the Debug Macro command. A dialog opens.

• Select the correct macro from this dialog.

Note: For any further details on this subject, refer

to the OPUS/Programming manual.

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12.6 Edit Macro

Definition This command allows to generate and edit macros.

Principle • Select the Edit Macro command. The macro editor

opens.
• Generate a new macro or load an already existing
one using the Open Macro button.

Note: For very detailed information on this sub-

ject, refer to the OPUS/Programming manual.

12.6.1 Macro editor view

A B C D E

Figure 398: Macro editor view

A Click this button to load an existing macro.

B Click this button to store the macro.
C Click this button to scan all command lines and correct all
macro syntax errors automatically.
D Click this button to search for a special string in the macro
command. Enter the respective string into the entry field
below the two search buttons.
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 Edit Macro Chapt. 12

E Click this button to search for a special variable definition.

Enter the respective variable definition into the entry field
below the two search buttons.
F This list box shows the macro command lines.
G This list box shows the macro variables.

Each list box (F and G) contains a toolbar which allows to insert

( ) or remove ( ) text lines. The macro commands list box con-
tains two additional buttons which allow to move up ( ) or down
( ) selected text lines. Variables cannot be repositioned, but are
listed in the order of their creation.

12.6.2 C o r r e c t i n g m a c r o s y n ta x e r r o r s
1 Click the Open Macro button to load an existing macro.
2 If the macro includes syntax errors, the following error mes-
sage pops up: Suppress Error Messages and load with Auto
Correct Option? Click Yes. The macro is loaded and all syn-
tax errors detected are automatically corrected.
3 A respective message appears. Confirm the message. The
Save File As dialog opens.
4 Store the corrected macro.

12.6.3 Adding special command lines

1 Click the button.
2 A new line is displayed. Enter a macro definition in text for-
mat into this line.
3 Alternatively, click the button. The open Special Macro
Commands dialog opens.
4 Select a command from the drop-down list.
5 Click OK to confirm the settings made.

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 Chapt. 12 Macro

Figure 399: Macro Editor - Special Macro Commands

Depending on the command selected, additional parameter lines

including their meaning will be displayed.

Commands which assign values to variables include two additional

selection fields for the variable name and the array index.

Note: Each parameter field has to include a value to ensure

that the commands work properly.

12.6.4 Adding OPUS commands

1 On the OPUS menu or toolbar, click the respective
command.
2 Click the command execute button. The Assign Macro Vari-
ables to Function Parameters dialog is displayed.
3 Set the parameters. An activated check box means that the
parameter is entered into the macro command list box of the
macro editor interface.
4 Click OK to confirm the settings made.

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 Edit Macro Chapt. 12

Figure 400: Macro Editor - Assign Macro Variables to Function Parameters

12.6.5 Adding variables

1 Click the button.
2 A new line is displayed. Enter a variable definition in text for-
mat into this line.
3 Alternatively, click the button. The open New/Edit Vari-
able dialog opens.
4 Select the type of variable. Activate the respective option
button in the Static group field.

Figure 401: Macro Editor - New/Edit Variable

5 In the Name entry field, enter a unique name.

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 Chapt. 12 Macro

6 In the Value entry field, enter a start value (if required). If no

value has been defined, the variable will be initialized by
zero (numerical) or empty string.
7 Optionally, activate the Update automatically check box. This
means that the uptdate of a variable is automatically acti-
vated or deactivated. Variables to be updated can be recog-
nized by a preceding asterisk "*".
8 Click OK to confirm the settings made.

12.6.6 Adding macros to the toolbar

Macros which you use regularly can be added to the toolbar.

1 Select the C:\Users\Public\Public Documents\Bruker\

OPUS_<version> directory from the Explorer.
2 Click the Usermac.lst file. If this file is not available in the
directory, create the file using the text editor.
3 For each macro you want to add to the toolbar you have to
enter the following information to the Usermac.lst file. Use
the text editor:
• Name and path of the macro file
• Number of the menu (see table below)
• Text to be included in the menu
• Text for tooltips in the toolbar
• Text for the status bar
The entries made in one line have to be separated by the
“@” sign, e. g.:
*\OPUS\Macro\IT.MTX@8@Instrumenttest@IT-Test@Start IT

Note: If you want to have an icon displayed in the toolbar,

the macro directory has to include a bitmap file with
this icon. Make sure that the bitmap is of 16x15 pixels.

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12.6.7 Adding macros to a menu

To add a macro to a particular menu, use the menu numbers indi-

cated in the following table.

Menu Menu Number

Measure 1

Manipulate 2

Evaluate 3

Display 4

Print 5

Macro 6

Edit 7

Validation 8

Settings 9

File 10

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12.7 C ompile Macro

Definition Macros are written and stored as text files. This com-
mand allows to convert these text files to executable
binary codes. Compiled macros are started faster
than macros in text format.

Note: For any further details on this subject, refer

to the OPUS/Programming manual.

12.8 New P ro ce d u r e

Definition This command allows to create a specific procedure

to automate simple sequences of events.

Principle When creating such a procedure you can either fol-

low the on-screen instructions provided by the macro
wizard, or click single OPUS icons from the OPUS
wizard, toolbar or Macro menu to define the proce-
dure manually.

Note: Procedures are stored as Visual Basic

Scripts and have the file extension *.obs.

When selecting the New Procedure command, a separate view

opens.

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Figure 402: New procedure view

A By default, the macro wizard is displayed in this view.

B If you want to change this default setting, deactivate the
check box. In this case you have to define the procedure
manually.

Defining procedure manually

1 Select the desired OPUS command from the respective

OPUS menu.
2 The OPUS command is added to the new procedure view in
the form of a procedure block.
3 Double clicking a procedure block opens the corresponding
OPUS command dialog. Use this dialog to adjust the param-
eters for the respective procedure block.
4 To delete a certain procedure block, left click the block and
press the Del key on the keyboard.
5 To store a complete procedure created right click into the
view and select the Macro  Save option from the pop-up
menu (see chapter 12.8.8).

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 Chapt. 12 Macro

Wor k i n g w i t h t h e m a c r o w i z a r d

The macro wizard facilitates creating procedures. Select the

commands used for a particular procedure from the macro wizard.

Step 1:

Define whether you want to load a file or perform a measurement

block in case of the first procedure step. If you click Next (A in
figure 403), the corresponding procedure block is added to the
graphical view.

Figure 403: Macro wizard - Load file

Step 2:

Define a manipulation command for the next procedure step. The

Other drop-down list includes additional manipulation commands. If
you click Next, the corresponding procedure block is added to the
graphical view.

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 New Procedure Chapt. 12

Figure 404: Macro Wizard - Manipulation command

After selecting a manipulation command and clicking Next, the No

manipulation option button is activated by default in the next dialog.

Figure 405: Macro wizard - No manipulation

Note: To add further manipulation commands check the

respective option button before clicking Next.

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 Chapt. 12 Macro

Step 3:

Define an evaluation command for the next procedure step. The

Other drop-down list includes additional evaluation commands. If
you click Next, the corresponding procedure block is added to the
graphical view.

Figure 406: Macro Wizard - Evaluation command

After selecting an evaluation command and clicking Next, the No

evaluation option button is activated by default in the next dialog.

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 New Procedure Chapt. 12

Figure 407: Macro wizard - No evaluation

Note: To add further evaluation commands check the

respective option button before clicking Next.

Step 4:

For the last procedure step define whether the file is to be saved or
printed. If you activate the Loop check box the procedure
previously defined will be repeated n times.

If all settings are made, click Finish. The complete macro

procedure created is displayed.

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 Chapt. 12 Macro

Figure 408: Macro Wizard - Save, print; complete structure

Double click the procedure block to define the parameters for the
respective block. The OPUS command dialog opens which allows
to set the parameters for the block selected.

Left click the block and press the Del key on the keyboard to
delete a procedure block.

To store the complete procedure right click onto the procedure

view. Select the Macro  Save command from the pop-up menu
(see chapter 12.8.8).

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12.8.8 Pop-up menu

Right clicking somewhere on the procedure view opens a pop-up

menu which consists of the following commands:

Figure 409: Pop-up menu

The pop-up menu commands can be used to edit, check or save

the procedure created. In the following each of the commands will
be described in more detail.

Macro

F
Figure 410: Pop-up menu - Macro

A Starts the macro wizard.

B Opens a new procedure workspace.
C Loads existing procedure.
D Allows to check the procedure created, i.e. it will be checked
whether the course of actions within the procedure is valid. If
not, a message box pops up indicating how the existing pro-
cedure has to be modified, as the following example shows:

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 Chapt. 12 Macro

E Saves the procedure. Define the file name and directory path
in the dialog displayed. The macro procedure is stored as
OPUS basic script and has the file extension *.obs.
F This is a global setting which specifies how the script should
react in case of an error. If you click Error Management, the
following dialog opens:

Activate the appropriate check box or option button to further

define the error management.

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 New Procedure Chapt. 12

To o l s

Figure 411: Pop-up menu - Tools

A Allows to select a certain procedure block. This option is

checked by default. To select a procedure block, left click the
block, and it will be marked by a broken line:

Now, you can move any procedure block to a different place if

you press and hold down the left mouse button. When posi-
tioning a procedure block on a black connecting arrow
between two different procedure blocks, this arrow becomes
red, visualizing that you are now changing the original proce-
dure structure. As soon as you release the mouse button the
procedure block moved will exactly be positioned between
these two different procedure blocks.
B Explicitly creates an arrow link, e.g. in case of IF procedure
blocks. To delete a link, click the arrow which turns red and
press the Del key on the keyboard.

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 Chapt. 12 Macro

Blocks

F
G
Figure 412: Pop-up menu - Blocks

A Creates an IF procedure block which always requires two out-

put links. If you integrate the IF block into an existing proce-
dure, the following dialog opens:

Specify which condition, i.e. True or False has to be used to

continue. Double clicking an IF procedure block, opens the
following dialog:

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 New Procedure Chapt. 12

If you activate the Dialog answer option button, you have to

enter an appropriate question into the entry field. You can
also define whether the IF block shall be based on a previous
evaluation report.
Depending on the report selected from the drop-down list fur-
ther details can be defined with regard to the condition. If you
have, e.g., selected Peak Picking, you can further determine

whether the number of peaks should be than the

number specified in the entry field. In case of a Search report
the value to compare with will be the hit quality.
B Creates a LOOP procedure block. This kind of procedure
block is used to repeat certain commands. Define the loop
count in the dialog that pops up when double clicking the
LOOP procedure block.

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C Creates a WAIT procedure block. This kind of procedure

block is used to interrupt the current course of action. The
period of time can be exactly defined in the dialog that pops
up when double clicking the WAIT procedure block.

D Creates a Message Box procedure block. To manually enter

the text double click the Message Box procedure block.

E Creates a QUICK MEASURE procedure block. If you inte-

grate such a block into the procedure, specific parameters will
be prompted when running the macro. To explicitly define

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 New Procedure Chapt. 12

these parameters double click the QUICK MEASURE proce-

dure block.

F Creates the Input Variable procedure block. Enter the name

and the default value of the variable by double clicking the
Input Variable procedure block.

G Creates the Calculate procedure block. This block can be

used to perform calculations on the basis of evaluation
results. OPUS provides pre-defined variables. Double click
the Calculate procedure block.

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Enter the name of the variable into the Variable entry field.
The pre-defined names of each variable as well as the
description of the corresponding variable value are included
in the list below. Enter the mathematical term for the variable
defined into the Expression entry field. Example:

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Edit

Figure 413: Pop-up menu - Edit

• Move to back: in case of two procedure blocks on the

same position moves the one selected behind the other
• Invert selection: inverts the procedure selected
• Arrange: arranges the procedure
• Select All: selects all procedure blocks

1 2.9 E d i t P ro ce d u r e

Definition This command allows to edit a procedure created.

Principle • Select the Edit Procedure command. A dialog

opens.
• Select the respective procedure from this dialog.

Note: Procedure files have the extension *.obs.

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12.10 Run Procedure

Definition This command allows to start a procedure created.

Principle • Select the Run Procedure command. A dialog

opens.
• Select the respective procedure from this dialog.

Note: Procedure files have the extension *.obs.

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13 Va l i d a t i o n
The Validation menu allows to set up the instrument test (OPUS
Validation Program1) parameters, and start the instrument test.

The OPUS Validation Program (OVP) is part of the OPUS software

and allows a validation of the spectrometer with OQ test (Opera-
tional Qualification) and the PQ test (Performance Qualification).

The Validation menu contains the following commands, among

others:

Figure 414: Validation menu

General features on OVP

OVP is based on a modular concept and works as follows:

• An instrument test consists of several single tests and
qualifies spectrometer performance in daily routine
work.
• Test channels can be defined in OVP for different types
of measurement configurations. Each test channel, e.g.
sample compartment, integrating sphere, is assigned to
one measurement configuration, and has individual
parameter settings.
• For each test channel a time period is defined which

1. In some cases OPUS also uses OVP (OPUS Validation Program) as reference
with regard to the command used to set and perform the instrument test. The in-
strument test itself is sometimes called PQ test (Performance Qualification).

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 Chapt. 13 Validation

determines when a Performance Qualification (PQ) or

Operational Qualification (OQ) test will be required.
These tests can consist of one or more test protocols.
• If the tests have been completed, a simple pass/fail
interface will be shown with the option to view and/or
print a detailed test report.

• If the tests have passed, the OPUS status light

changes its color to green. The operator can continue
using the spectrometer as the instrument has been
properly tested.
• An unattended mode is also available which allows to
run the test(s) completely automatically and without any
user interaction, e.g. over night or in the early morning.
This, however, assumes that the tests themselves do
not require any interaction.

Note: Measurement and test parameters are stored in a set

of databases which have been installed during the
OPUS installation.

If you have received a separate database CD, you also

have to install this CD.
• OVP system databases and instrument-specific user
settings and UserData databases are stored in the local
*\OPUS_<version>\Validation\Database directory.
• Test spectra measured and test reports are stored in the
Validation base path, which can be defined in user set-
tings (figure 415).

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Figure 415: User Settings - Validation base path

13.1 Setup OVP

Definition This command allows to set the respective OVP

parameters.

Principle • Select this command.

➣The Setup OVP dialog is displayed. The dialog is
only displayed if an instrument is connected.
➣Depending on the instrument connected, the
parameters for the test channel configuration are
pre-defined in the drop-down lists.
• Make changes, if required.
➣The setting options are described in chapter Test
channel configuration.
• Calibrate the laser wavenumber (chapter 13.1.1).
• Select the OVP tests (chapter 13.1.2).
• Click Save and Exit.

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Te s t c h a n n e l c o n f i g u r a t i o n

9
1 10

4 11
5
12
6
7 13

Figure 416: OVP test channel setup

Component Definition

1 Current test channel The drop-down list shows the test channel
used in the current configuration

2 Test channel config- For each spectrometer test channel you have
uration to assign a measurement configuration to be
used during actual validation measurement.
This is a valid combination of source, beam-
splitter, measurement channel and detector
type.
The respective entry is pre-defined in the
appropriate selection field by default. As soon
as you have selected the correct entry the
appropriate instrument configuration (4) and
the bitmap (9) specified for the measurement
channel selected will be proposed.

3 Measure LWN To set up the laser wavenumber, click this but-

ton. See also chapter 13.1.1.

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Component Definition

4 Instrument configu- The instrument configuration is displayed as

ration soon as you have selected all parameters.
☞ Always check whether the correct instru-
ment configuration has been suggested. If
required, select a different instrument con-
figuration.

5 Accessory Depending on the test channel selected, the

drop-down list contains appropriate accesso-
ries.
☞ Select the correct accessory type from the
drop-down list.
Details on registering new accessories are
described in chapter 13.6.2.

6 Crystal Depending on the test channel and ATR

accessory selected, the drop-down list con-
tains appropriate crystal types. This only
applies to accessories with a changeable ATR
crystal.

7 Measurement Depending on the accessory type defined, you

experiment can select an appropriate measurement
experiment file from the drop-down list. The
measurement experiment file saves the
default parameters set by Bruker, which are
used to perform a measurement.

8 Information field In special situations, this field contains infor-

mation on the set-up of test channels.

9 Bitmap Depending on the measurement channel or

accessory selected a configuration-specific
bitmap is displayed.

10 Load image Clicking the button loads additional spectrom-

eter images available in OPUS. The bitmaps
are saved in the C:Users\Public\Public Docu-
ments\Bruker\OPUS_<version>\VALIDA-
TION\Bitmaps path.
User-specific bitmaps must have a size of 90 x
90, and can be saved by the
ITnn_<spectrometer name> file name (with nn
being a consecutive number).

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Component Definition

11 Clear current config- Clicking the button deletes the current configu-
uration ration.
Note: Once deleted the settings cannot be
reloaded. If you have deleted a channel,
you have to repeat the complete setup
again.

12 Reset accessory in An accessory already defined for a particular

test channel test channel can be reset. This is required if
you have selected a wrong type of accessory
and used this type to perform a wavenumber
calibration, or if you want to update a regis-
tered accessory. Resetting the configuration
always requires a new measurement of the
laser wavenumber. Details are described in
chapter 13.6.6.

13 Clear accessory in An accessory which has been defined incor-

bench rectly can be re-defined. Details are described
in chapter 13.6.7.

13.1.1 M e a s u r e L a s e r Wa v e n u m b e r

Before starting the instrument test for the current configuration you
may first have to calibrate the laser wavenumber (LWN). Measur-
ing and assigning the laser wavenumber for the current test chan-
nel ensures the wavenumber accuracy of spectral data.

General features

The laser wavenumber is affected by changes in the optical path

length. This can cause considerable deviations when using optical
fibers of different lengths, or accessories with different types of
crystals.

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Proper assignment of test-channel-specific laser wavenumbers

may require an update of the instrument firmware as well. In case
of doubt contact Bruker service.

Note: In case of some spectrometers (e.g. ALPHA) the cali-

bration is automatically performed when starting the
spectrometer for the very first time.

When is a laser wavenumber calibration

required?

• At the initial instrument operation.

• If the warning symbol is displayed in the Setup OVP

dialog (see figure 416). The symbol generally indicates
that the settings for the current configuration have not
yet been completed.

To c a l i b r a t e t h e l a s e r w a v e n u m b e r.. .

1 ...make sure that the correct test channel has been selected.

2 Click the button in the Setup OVP dialog (see

figure 416).

When calibrating...

...a water vapor spectrum is measured. Then, the optimum laser

wavenumber is determined on the basis of a specific water band.
To verify the validity of this water band adjacent water bands are
checked as well.

In a second step the appropriate wavenumber is verified on the

basis of the bands of the filter material on the internal validation
unit (e.g. polystyrene or BRM 2065).

A ft e r c a l i b r a t i o n . . .

1 ...a result dialog pops up.

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 Chapt. 13 Validation

Figure 417a: LWN calibration okay 378a: New LWN setting required

If the LWN has to be set (see figure 417b), click the YES but-
ton.
2 ...a green check mark is added to the button in
the Setup OVP dialog.

What does the result show?

• The LWN test result shows both the water bands speci-
fied and measured.
• You can also see the water band deviation as well as
the laser wavenumber, i.e. both the specified and newly
calculated one.
If the current LWN for a particular channel is within a
certain tolerance, the test has passed and no further
changes are required.
If the deviation is beyond a certain tolerance, the LWN
value for the current measurement channel is set to the
currently computed optimal value when clicking OK.

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If the laser wavenumber calibration has

not been successful,...

... the water vapor concentration of your instrument may be too low
or too high, and a warning pops up in OPUS.

In this case you have to test the LWN_Water.x water vapor spec-
trum (with x being any number) which is located in the
*\OPUS_<version>\Validation\Data\LWNCalibra-
tion\<Date>\<Time>1 directory.

Water vapor concentration What is to be done?

Too low Remove the desiccant cartridge

for a short period of time, or vent
the sample compartment, to
allow the water vapor concentra-
tion in the instrument to increase

Too high Replace the desiccant cartridge,

or purge by using dry air.

In both cases repeat the measurement until the result is OK.

A d d i t i o n a l i m p o r ta n t i n f o r m a t i o n

• The laser wavenumber has been stored and used based

on the test channel specified in OVP. In case of mea-
surements in the empty sample compartment, and mea-
surements in the sample compartment equipped with an
accessory, both configurations have to be setup as two
different test channels in OVP. In this case the laser
wavenumber can be different for both test channels,
even if both configurations use the sample compartment
as measurement channel. Therefore, it is important to
define different test channels for the empty sample com-
partment and the sample compartment equipped with
an accessory.

1. Date: JJJJMMTT (Year/Month/Day); Time: (HHMMSS) (Hour/Minute/Second)

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 Chapt. 13 Validation

• In case of spectrometers equipped with a Quick Lock

baseplate (TENSOR and VERTEX) the accessory is
also identified when calibrating the laser wavenumber,
and the settings are displayed in the measuring configu-
ration.
• It is not necessary to measure the laser wavenumber
separately in case of transmission sample holders which
have no influence on the beam path. This means that
neither an entry is required in the Accessory drop-down
list nor an additional OVP channel has to be set up.

13.1.2 S e t t i n g u p O V P t e s ts

The OVP Test Setup tab contains the OVP test parameters.

Figure 418: OVP Test Setup

What kind of test categories can be

selected?

Basically, you can select between two test categories, PQ and OQ

test. You have to define a specific test interval for both test catego-
ries to determine when the tests have to be performed.

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Note: It is recommend running PQ tests as a short-term test

on a daily basis (24 hours). OQ tests should normally
run after installation, maintenance, replacing optical
components or major repair, e.g. every 6 or 12
months.

Both test categories verify the spectrometer performance.

H o w t o s e l e c t t h e t e s ts ?

1 Activate the Run PQ Test every or Run OQ Test every check

box. In the following example the PQ test category has been
selected.

Figure 419: Configuring PQ test

2 Type the interval period into the entry field and select the
units from the drop-down list. Available units are: hours,
days, or months.
3 Click Setup to have the available PQ tests displayed:

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 Chapt. 13 Validation

Figure 420: OVP - PQ Test Protocol

All tests available for a particular type of spectrometer have

already been selected. Tests which are not available for a
particular type of spectrometer cannot be selected. In excep-
tional cases (not recommended) you can deactivate certain
tests by deleting the check mark.
In case of the wavenumber accuracy test it is possible to
define a frequency value for the filter band, if you have
received a certificate for the filter mounted. OPUS evaluates
this band. A default frequency value is pre-defined in the Fil-
ter Band entry field, which you can overwrite. The test calcu-
lates the deviation between the measured,
temperature-corrected peak location and the filter frequency
specified.
Most of the PQ tests compare the measured data to a set of
reference data which have been recorded after installation,
major repair or exchange of optical components. If these ref-
erence spectra have not yet been measured, you have to
measure them first (see the following section).

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Measuring reference spectra

For some PQ tests reference measurements are required which

are generally performed after the OQ test has been passed.

Note: You will not be able to perform a PQ test without

these reference spectra.

If the reference spectra have not yet been measured, the following
warning symbol is displayed in the OVP - PQ Test Protocol dialog.

Figure 421: OVP - Reference spectra not yet

measured

1 Click Measure Reference Spectra.

2 If the reference measurement has been successfully fin-
ished, the date of measurement will be displayed and a
green check mark is added to the Measure Reference Spec-
tra button.

Figure 422: Reference spectra measured

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Extracting reference spectra

Reference spectra used for the tests are stored in the user data-
base. Whenever used the reference data are temporarily extracted
and afterwards removed again. This avoids accidental deleting or
overwriting. A copy of the reference spectra is stored in the follow-
ing directory:
*\OPUS_<version>\Validation\Data\PQ_Reference\
<Date>\<Time>

A ft e r m e a s u r i n g r e f e r e n c e s p e c t r a . . .

...confirm the PQ test settings by clicking OK. The dialog closes

and the current test setup status is indicated by a green check
mark on the Setup button of the OVP Test Setup tab.

Figure 423: PQ test setup status

Note: If you close the dialog without measuring any refer-

ence spectra, or with reference spectra from previous
measurements, a warning pops up and the warning
symbol remains on the Setup button.

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13.1.2.1 P Q Te s t D e s c r i p t i o n

The PQ test protocol verifies the spectrometer operability in routine

work. Therefore, the PQ test has to be performed on a regular
basis (e.g. daily). The test protocol consists of different single tests
which are described in the following.

Energy Test Signal to Noise Test This test verifies that the
signal-to-noise ratio is better
than a specified limit.

Deviation from 100% This test verifies that the

Line 100% line does not shift on
long term.

Interferogram Peak This test verifies that the

Amplitude interferogram peak ampli-
tude is not below a certain
limit.

Energy Distribution This test verifies, by means

of different methods, the
total energy of the spec-
trometer and its different
components.

Ice Band Test This test verifies the leak

tightness of MCT detectors.

Sealing Test This test checks the water

vapor signals during mea-
suring time, and the abso-
lute water vapor content in
the optical path (only avail-
able with CONFOCHECK).

X-Axis Frequency This test verifies that the

Calibration Test frequency calibration of the
instrument is correct.

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Y-Axis Reproducibil- This test verifies that the

ity Test photometric accuracy is
within specified limits. The
test is performed by using
one or two filter(s) with dif-
ferent absorbing properties.
• Glass Filter A Test
• Glass Filter B Test (not
available for each spec-
trometer)

Position Test This test checks whether

the HTS-XT x/y stage pre-
cisely approaches each
measurement position of
the microtiter plate.
(only available with the
HTS-XT module)

Signal to Noise (S/N) Ratio

The signal-to-noise ratio test determines the sensitivity of the spec-

trometer by calculating the average signal-to-noise ratio of ten
100% spectra.

The S/N ratio is determined by collecting and analyzing a 100%

spectrum. A 100% spectrum is the ratio of two successively
acquired single-channel spectra with no sample in the sample com-
partment. The ratio of these two single-channel spectra is used to
generate a transmission spectrum.

The S/N ratio is calculated by the OPUS Signal-to-Noise Ratio

command from the Evaluate menu, using peak-to-peak by means
of the quadratic parabola fit option. In order to get a reliable result
10 spectra are measured (reference and sample).

The S/N ratio is calculated separately for each spectrum, using the
mean value of all 10 results.

Figure 424 shows a peak-to-peak noise of 0.1%, referring to 100%

transmittance in MIR region. To calculate the S/N ratio the recipro-
cal value is multiplied by 100 (1 / 0.1 * 100). Figure 425 shows a
100% line in NIR region.
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Figure 424: MIR 100% Line

Figure 425: NIR 100% line

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 Chapt. 13 Validation

Deviation from 100% Line

This test measures the maximum deviation of a 100% line within a

larger frequency range.

The average determined by 10 measurements must not exceed the

predefined limit.

Interferogram Peak Amplitude

The interferogram peak amplitude test is a long-term stability test

which compares the amplitude of a measured interferogram to that
of the reference interferogram stored.

The amplitude of the reference interferogram corresponds to

100%. In the PQ test the same measurement is repeated and the
interferogram amplitude of this test spectrum is compared to the
interferogram amplitude of the reference interferogram.

The amplitude of the test interferogram is indicated in the PQ test

report relative to the reference value and must not fall below a
specified limit.

Figure 426 shows an interferogram, which has been measured by

the Double Sided, Forward-Backward acquisition mode.

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Figure 426: Double-sided interferogram

E n e r g y D i s t r i b u t i o n ( S i n g l e - C h a n n e l Sp e c-
trum)

The energy distribution test is a long-term stability test which com-

pares the amplitude of a measured single-channel spectrum to that
of a stored reference single-channel spectrum.

Figure 427 and 428 show the single-channel spectra of the refer-
ence file in MIR and NIR region. The integral over the total refer-
ence single-channel spectrum is set to 100%.

If the power of the spectrometer source decreases, e.g., the dis-

tance between the two single-channel spectra will increase. There-
fore, this test can be used to detect changes in the source power.
In case of this long-term stability test, test spectra are compared to
the reference spectrum stored.

Note: New reference spectra have to be measured as soon

as the instrument has been realigned, or the source
changed.

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Figure 427: MIR reference spectrum

Figure 428: NIR reference spectrum

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I c e B a n d Te s t

If the vacuum of an MCT detector decreases, you can observe the

ice band caused by condensed water vapor in the single-channel
spectrum.

Figure 429: Spectra showing ice bands of different intensities

The ice band test is part of the energy test and compares the inte-
gral in the ice band region (3485 - 3050cm-1) with the integral of the
reference spectrum measured for the PQ test. The integral should
not exceed a preset limit.

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Figure 430: Integrals of ice bands (of different thickness)

S e a l i n g Te s t

This test is part of the dedicated CONFOCHECK FT-IR system for

the analysis of soluble and insoluble proteins in aqueous medium.
For detailed information on the sealing test refer to the CONFO-
CHECK user manual.

X - A x i s F r e q u e n c y C a l i b r a t i o n Te s t ( Wa v e -
number Accuracy)

The x-axis frequency calibration test ensures that the frequency

calibration of the instrument is within the specified limits.

If possible, water vapor is used to determine the wavenumber

accuracy. Water vapor has the advantage of having an extremely

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 Setup OVP Chapt. 13

narrow band(s) and therefore the wavelength position can be mea-

sured to a very high degree of accuracy.

To ensure that the water vapor band is completely resolved the

instrument uses a high-resolution setting. The NIR region uses the
band at 7306.74cm-1 for calibration, and the MIR region at
1554.353cm-1.

Figure 431 and 432 show typical water vapor spectra in the MIR
and NIR region.

Figure 431: MIR water vapor spectrum

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Figure 432: NIR water vapor spectrum

Depending on the spectrometer type it is possible to measure the

spectrum of the mounted filter, instead of the water vapor. This kind
of measurement is also alternatively performed, if the water vapor
test could not be performed due to e.g. too low a water vapor con-
centration.

It is used either a polystyrene standard sample (MIR and NIR) or a

glass filter with a mixture of rare earth oxides (BRM 2065, only
NIR) which composition is identical to the NIST standard SRM
2065. The standard (either polystyrene or BRM 2065) is on the
internal validation unit. Thus, no further actions are required for this
test.

Note: If your instrument is equipped with a Germanium

diode, you have to use the water vapor band for the
X-Axis Frequency Calibration test as there is no suit-
able polystyrene peak in the frequency range of this
detector type. Spectrometers equipped with a silicon
diode can, however, only use the BRM 2065 standard
as the water bands are beyond the measuring range.

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 Setup OVP Chapt. 13

Y- A x i s R e p r o d u c i b i l i t y Te s t ( P h o t o m e t r i c
Accuracy)

The y-axis reproducibility test is a long-term stability test which

compares the total intensity values of glass filter spectra to those of
the reference spectra.

A glass filter transmission spectrum is used to test the precision of

the y-axis. The test spectra of glass filters are compared to the ref-
erence spectra by calculating the mean difference over a large
spectral range (MIR: 4000 - 2000cm-1, NIR: 1000 - 45000cm-1).

Figure 433 and 434 show the spectra of two glass filters in NIR and
MIR.

Figure 433: Glass filter NIR reference spectra

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Figure 434: Glass filter MIR reference spectrum

P o s i t i o n Te s t

This test is only used with the HTS-XT module. For detailed infor-
mation on the position test refer to the HTS-XT user manual.

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13.1.2.2 O Q Te s t D e s c r i p t i o n

The OQ test protocol is a test which checks the instrument perfor-

mance and compares it to the instrument specification.

1 On the OVP Test Setup tab, activate the OQ Test every

checkbox.

Figure 435:

2 Type the interval period into the entry field and select the
units from the drop-down list. Available units are: hours,
days, or months.
3 Click Setup to have the available PQ tests displayed.

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Figure 436: OVP - OQ Test Protocol

Photometric Accuracy This test verifies the photometric accuracy of

Test the spectrometer.

Sensitivity Test This test verifies whether the instrument

reaches the specified signal-to-noise ratio.

Energy Distribution This test verifies the energy distribution of an

Test empty channel over the spectral range com-
pletely achievable.

Wavenumber Accu- This test verifies the absolute x-axis accu-

racy Test racy of the instrument.

Resolution Test This test verifies the spectral resolution

achieved by the instrument

Scan Time Test This test verifies the mechanical properties

of the interferometer and the control elec-
tronics functioning.

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Water Vapor Test This test verifies that the water vapor con-
centration does not exceed a specified value
(only with older spectrometer types).

Alignment Test This test verifies that the interferogram peak

is within the specified range

Linearity Test This test verifies the detector linearity below

the detector cutoff frequency.

Reproducibility Test In case of instruments with several measure-

ment channels verifies the proper mode of
functioning of all mechanical parts which
change the instrument beam path (e.g. mir-
rors).

Position Test This test checks whether the HTS-XT x/y

stage precisely approaches each measure-
ment position of the microtiter plate.
(only available with the HTS-XT module)

Ratio Test This test determines the ratio of specular

reflection to diffuse reflection (only available
with the HTS-XT module).

Sealing Test This test checks the water vapor signals

during measuring time, and the absolute
water vapor content in the optical path (only
available with CONFOCHECK).

The individual tests depend on the type of instrument. In general,

not all tests will be run for a specific instrument series. For exam-
ple, the linearity test is only relevant for MCT detectors.

Tests which are not available for the selected instrument type are
disabled, all the other tests are activated. If you do not want to per-
form a specific test, deactivate the respective check box.

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P h o t o m e t r i c A c c u r a c y Te s t

This test requires specific standards which are available with

Bruker on request, together with a separate operating instruction
manual. The photometric accuracy test verifies, amongst others,
the detector linearity.

The test uses a polystyrene transmission spectrum in MIR and a

water spectrum in NIR which shows total absorption in several
regions (see figure 437 and 438). At these positions the theoretical
transmission of the spectrum should be 0. It is tested whether the
deviation of the transmission value of 0 is within the limits specified
in these regions.

Figure 437: Polystyrene spectrum for MIR

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Figure 438: Water spectrum for NIR with different layer thickness

S e n s i t i v i t y Te s t

The sensitivity test determines the sensitivity of the spectrometer

by calculating the average S/N ratio of ten 100% spectra. A 100%
spectrum is the ratio of two successively measured single-channel
spectra with no sample in the sample compartment. The ratio of
these two single-channel spectra is used to calculate a transmis-
sion spectrum.

The S/N ratio is determined by measuring the maximum deviation

from 100% transmittance, and calculated by the OPUS Sig-
nal-to-Noise Ratio command from the Evaluate menu using
peak-to-peak by means of the quadratic parabola fit option.

In order to get a reproducible result 10 spectra are measured (each

with separate reference and sample measurements). The S/N ratio
is calculated separately for each of the spectra, and the test result
will be the mean value of all 10 results. The region to measure the

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S/N ratio is different for systems used in the MIR and NIR region,
and is displayed in the corresponding report.

The spectrum shown in figure 439 has a peak-to-peak noise of

0.1% from 100% transmittance in the MIR region. To calculate the
S/N ratio the reciprocal value is multiplied by 100 (1 / 0.1 * 100).
Figure 440 shows a 100% spectrum in the NIR region.

Figure 439: MIR 100% spectrum

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Figure 440: NIR 100% spectrum

E n e r g y D i s t r i b u t i o n Te s t

The energy distribution test verifies the achievable frequency range

and the energy at the maximum position of the single-channel
spectrum.

A single-channel spectrum is measured for this test. The absolute

values of energy measured are measured at different wavenumber
positions, see figure 441. These values are divided by the maxi-
mum value achieved, and compared to acceptance values which
are indicated in per cent.

Optical components (e.g. detector, source and beam splitter) as

well as the sampling accessory have an effect on the limits of the
frequency range.

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Figure 441: Single-channel spectrum

Wa v e n u m b e r A c c u r a c y Te s t

The wavenumber accuracy test verifies that the frequency calibra-

tion of the spectrometer is within the limits defined. To test the wav-
enumber accuracy water vapor is used.

Water vapor has the advantage of having extremely narrow bands,

and the position of these bands can be measured to a very high
degree of accuracy.

To ensure that the water vapor band is completely resolved the test
is performed by a high-resolution setting. The NIR region uses the
band at 7306.74cm-1 for calibration, and the MIR region at
1554.353cm-1.

Figure 442 and 443 show a typical water vapor spectrum in the
MIR and NIR region. Depending on the source the BRM 2065 is
alternatively used in NIR for testing if the water vapor band speci-
fied is beyond the limits defined.

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Figure 442: MIR water vapor spectrum

Figure 443: NIR water vapor

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R e s o l u t i o n Te s t

The resolution test verifies the achievable spectrometer resolution

by measuring a single-channel (single-beam) spectrum of the
water vapor available inside the spectrometer. The spectrum will
be measured using the maximum spectrometer-specific resolution.

This means for most spectrometer types: 1cm-1 for MIR and
2cm-1 for NIR, see figure 444. The spectrum is first logarithmized.
Then, the full width at half maximum (FWHM) of a water band
(7306,74cm-1 for NIR and 1554,353cm-1 for MIR) is determined.
The result is compared to the specified resolution of the spectrom-
eter.

Figure 444: Water vapor band at 1553.353cm-1(MIR)

S c a n Tim e Te s t

The scan time test is used to test the interferometer functioning. A

single-channel spectrum is measured with a defined number of
scans, at the highest scan velocity. The time needed to measure
the spectrum is determined and compared to the limit.

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Wa t e r Va p o r Te s t

The water vapor test determines the concentration of water vapor

inside the instrument.

A single-channel spectrum is measured to determine the peak

height of a water band within a small frequency region, i.e. 1660 -
1643cm-1 for MIR (figure 445) and 7315 - 7297cm-1 for NIR
(figure 446).

Figure 445: MIR water vapor band, 1660 - 1643cm-1

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Figure 446: NIR water vapor band, 7315 - 7297cm-1

The water vapor concentration is calculated from the measured

data as follows:

Water vapor concentration = 100 - ((YMin * 100)/ YMax)

The value calculated is compared to the maximum value allowed.

A l i g n m e n t Te s t

The alignment test verifies that the absolute peak position of the
interferogram is within the range specified.

A single-channel spectrum is measured and the absolute peak

position is determined from the measurement parameters stored.

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L i n e a r i t y Te s t

The linearity test determines the energy contribution of certain

detectors below the detector cutoff frequency.

A single-channel spectrum is measured up to 0cm-1 (figure). The

energy contribution in the region below the detector cutoff fre-
quency is determined and compared to the energy value of the sin-
gle-channel spectrum at the maximum.

Figure 447: Single-channel spectrum around detector cutoff frequency

The following formula is used to calculate the linearity value:

Linearity Value = ((Abs(YMaxCutoff + YMinCutoff) / 2) / YMaxSpectrum) * 100

The linearity value must not exceed a maximum limit.

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R e p r o d u c i b i l i t y Te s t

The reproducibility test confirms that all moving parts (mirrors etc.)
of a multi-channel instrument are positioned correctly and in a
reproducible way.

A single-channel spectrum is measured for a specific channel and

used as background spectrum. After measuring the background
spectrum all moving parts relevant for the specific channel are
moved and a new single-channel spectrum is recorded in the chan-
nel position. From this single-channel spectrum and the back-
ground spectrum a transmission spectrum (100% line) is
calculated. This procedure is repeated 10 times.

The deviation from one another of these ten transmission spectra

is computed. The greatest deviation must not exceed the maximum
limit.

P o s i t i o n Te s t

This test is only used with the HTS-XT module. For detailed infor-
mation on the position test refer to the HTS-XT user manual.

R a t i o Te s t

This test is only used with the HTS-XT module. For detailed infor-
mation on the position test refer to the HTS-XT user manual.

S e a l i n g Te s t

This test is part of the dedicated CONFOCHECK FT-IR system for

the analysis of soluble and insoluble proteins in aqueous medium.
For detailed information on the sealing test refer to the CONFO-
CHECK user manual.

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13.1.2.3 A d d i t i o n a l Te s ts ( o p t i o n a l )

Optionally, additional tests are available:

• PhEur 2.2.40 (European Pharmacopoeia for NIR)
• USP 1119 (US Pharmacopoeia for NIR)
• PhEur 2.2.24 (European Pharmacopoeia for MIR)
• JP 2.25 (Japanese Pharmacopoeia for MIR)
• Raman

Note: For detailed information on these tests refer to the

separate documentation available.

H o w t o s e l e c t t h e t e s ts ?

1 Activate the Run check box and select the respective type of
test.

Figure 448: OVP - Additional tests (optional)

2 Select the correct test category, either PQ or OQ.

3 Click Setup. If you have selected a test which is not available

for a certain kind of instrument configuration, a warning will
be displayed when clicking Setup.

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Note: You have to acquire a separate licence for most of

these tests. Make sure that you have a correct regis-
tration, otherwise you will not be able to run these
tests.

13.2 Run OVP Te s ts

Definition This command allows to start the OVP tests.

Principle • Select this command. The Run OVP Tests dialog is

displayed.
• Select the respective test category.
• Click the Run selected Tests button.

The Run OVP Tests dialog is described in the following.

1
2

Figure 449: Run OVP tests

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Component Definition

1 Test channel The drop-down list contains the active test

channel selected

2 Test category The tests set up for the active test channel
selected, as well as the their status are dis-
played. The following status types are possi-
ble:
• test passed and expires in
• test not yet run
• test failed
• test expired since
Note: Tests which have expired, or which
have not yet been performed are automati-
cally activated for measurement. Tests
which have not yet expired are not acti-
vated, and their remaining time is dis-
played accordingly.
If the validity period of a test has not expired,
but the remaining time is e.g. 2 hours, you can
activate the check box for that test and run the
test earlier.
If the validity periof of a test has already
expired, but you are not prepared to perform
that test (external standards required), you
can deactivate the check box for that test.
Note: If you decide not to perform a test
which has already been expired, you may
not be allowed to use this test channel in
regulated environment.

3 Tree structure of Depending on the test category activated, a

single tests tree structure shows the single tests to be per-
formed.

4 Comment To append a comment to the current test

report, write a comment into the entry field.

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Component Definition

5 Test report The test report can be printed and displayed.

Activate the respective check box. You can
skip the spectrum pages created for each test
when printing the test report.
Note: To have the reports displayed make
sure that the Adobe Acrobat Reader is
installed on your computer. The Adobe
Acrobat Reader is available on the OPUS
installation stick.

W h e n s ta r t i n g t h e t e s ts . . .

...they run in the background, invisibly for the user. The names of
the single tests are shown on the OPUS status bar.

The spectra produced when running the tests are stored in a direc-
tory structure which will be automatically generated. In the
*\OPUS_<version>\Validation\Data directory a sub-directory is cre-
ated for the current date, supporting the following format: YYYYM-
MDD1 (e.g. 20090212).

An additional sub-directory for the time is created in the directory

for the current date, supporting the following format: HHMMSS2
(e.g. 113423).

The spectrum file names always start with either PQ or OQ, the
spectrometer configuration and a test definition:
e.g. PQ_MPA_Sample_Compartment_Energy.0.

The date and time is also used for the report name to allow a clear
correlation between spectra and reports. The spectra contain the
test result together with other important data in the information data
block ( ).

1. Y: year, M: month, D: day

2. H: hour, M: minute, S: second

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A ft e r t h e t e s t r u n . . .

...the result is stored, displayed or printed as test report (PDF for-

mat), provided you have activated the respective check boxes (see
figure 449).

Te s t r e p o r t

The test report contains one summarized test result page and sev-
eral different pages for each test with all the test spectra and mea-
suring parameters included. Reports are stored in the separate
VALIDATION\REPORTS directory. Figure shows the test report of
a PQ test.

Figure 450: OVP - Test report

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13.2.1 Running OVP test using the

I n s t r u m e n t St a t u s d i a l o g

To o p e n t h e d i a l o g . . .

...click the OPUS status light at the lower right end of the OPUS
interface.

W h a t d o e s t h e s ta t u s l i g h t i n d i c a t e ?

The status light always indicates both the hardware status as well
as the current test status of the active test channel. The test status
is displayed in different colors and can be as follows:
• Green: all tests have been configured, or have passed
and are still valid
• Yellow: at least one test has expired
• Red: last test has failed

I n s t r u m e n t St a t u s d i a l o g

The Instrument Status dialog is described in the following.

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Figure 451: Instrument Status

A The first row of icons represents the test status of the instru-
ment hardware components (see also chapter 7.8).
B The second and third row of icons are reserved for OVP tests.
If more than one test channel has been set up in OVP, the
corresponding icons are displayed for all channels.
The test status of the OVP tests is indicated as follows:
- INACTIVE (yellow): the single tests of the particular test
category are disabled
- PASSED (green): test configured or passed and still valid
- EXPIRED (light-blue): test expired
- FAILED (red): last test failed

To s ta r t t h e O V P t e s t . . .

1 ...click the icon of the test channel. The following dialog is

displayed:

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Figure 452: OVP Measurement Dialog

2 Activate the check box for the respective test category. The
single tests of the test category are displayed in a
browser-like view.
3 Define whether the test report is to be printed and/or dis-
played automatically, with or without the spectrum pages
created for each test. Note: To have the reports displayed
make sure that the Adobe Acrobat Reader is installed on
your computer. The Adobe Acrobat Reader is available
on the OPUS installation stick.
4 If desired, add a comment into the respective entry field.
5 To start the test(s) click Run Tests.

W h e n s ta r t i n g t h e t e s ts . . .

...they run in the background, invisibly for the user. The names of
the single tests are shown on the OPUS status bar (see also
chapter 13.2).

A ft e r t h e t e s t r u n . . .

...the result is stored, displayed or printed as test report (PDF for-

mat), provided you have activated the respective check boxes (see
figure 452).

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Te s t r e p o r t

For more information refer to chapter 13.2.

13.2.2 Sta r t i n g O V P t e s ts f o r m u l t i p l e
test channels sequentially
Note: The sequential starting of OVP tests for multiple test
channels makes sense in case of OVP tests which do
not require any user interaction.

1 For all test channels to be started sequentially, define the

test channel configuration (chapter 13.1) and the test
category (chapter 13.1.2).
2 On the Validation menu, select the Run the Instrument Test
command, or click the icon in the toolbar.
3 On the dialog that opens, click the OVP - Run Multiple Test
Channels tab.
➣ In the list box on the right dialog side, all test channels
which have been configured are displayed.
4 Set a checkmark in front of those test channels which you
want to perform OVP tests for (figure 453).

Figure 453: Example for activating multiple

test channels

5 If required, enter a comment for the test sequence.

6 Make the settings for the test report.
➣ Details on the test report setting options are described in
chapter 13.2.
7 Click the Run selected Tests button.

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13.3 M easuring with test chan-

nel-specific laser wave-
number

Generally, you have to measure the laser wavenumber for each

measurement channel or measurement setup separately. This
mainly affects multi-channel spectrometers or measurements
which optionally use special accessories (e.g. ATR unit).

The laser wavenumber may slightly change due to the different

optical paths.

Note: A change of the laser wavenumber directly influences

the frequency calibration of the spectrometer.

M e a s u r i n g St e ps :

1 On the Measure menu, select the Advanced Measurement

command.
2 Click the Optic tab. In case of spectrometers supported by
OVP it is ensured that the correct laser wavenumber is auto-
matically used with each measurement. This requires, how-
ever, that the measuring configuration (combination of
source, beamsplitter, measurement channel and detector)
has first been defined in OVP.
OVP checks during each measurement whether the respec-
tive measuring configuration has already been defined in
OVP. If not, the symbol will be displayed on the Optics
tab, and the respective drop-down lists will be yellow.

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Figure 454: Measurement - Yellow drop-down lists

3 Position the cursor above a yellow drop down list, a tool tip is
displayed.

Figure 455: Measurement - Tool tip displayed

The tool tip indicates what kind of problem has occurred and
how it can be solved.

Note: If you use OPUS in validated mode, measurement is

only possible with configurations which have been
set up in OVP before. Otherwise, an error message
pops up.

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13.4 O VP in unattended mode

The Open Planner command from the Setup menu allows to auto-
matically run the OVP PQ test. For detailed information on the
Open Planner command refer to chapter 14.11.

If single tests are to be repeated within a certain interval, you can

define these tests as recurring items, using the Open Planner com-
mand.

Setting up unattended mode

1 On the Setup menu, select the Open Planner command. The

calendar view is displayed.
2 Right click the respective day and select the New Appoint-
ment command from the pop-up menu. The following dialog
is displayed:

Figure 456: Set up OVP appointment

3 Select the respective OVP test configuration from the Sub-

ject drop-down list.

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4 Click Recurrence. A different dialog is displayed.

5 Select e.g. Weekly as recurrence pattern.

Figure 457: OVP - Set up tests as recurrence

6 Define the start of the test either manually or use the arrow
buttons.
7 Activate the No end date option button for the range of recur-
rence.
8 Confirm the settings made by clicking OK.

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13.5 OVP Trend Chart

Definition This command allows to plot the results of single

OVP tests in a trend chart.

Due to the graphical depiction of test results, changes

in relation to the spectrometer performance (e.g.
worsened signal-to-noise ratio) can quickly be recog-
nized, and preventive measures (spectrometer main-
tenance or service) be taken.

Principle • Select this command. The OVP Trend Chart dialog

is displayed.
• Select the active channel and the test category.
• Select an OVP test according to the test category.
• Click the OVP Trend Chart button.

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Figure 458: Example of the OVP Trend Chart dialog

A The drop-down list contains the names of OVP configura-

tions set up for the active test channel.
B Depending on the active test channel selected, this
drop-down list contains the respective test category (OQ/
PQ).
C The list box shows all OVP tests which have been performed
for the test category selected in B.

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13.5.1 Displaying trend chart

1 Select an OVP test according to the test category chosen.

Figure 459: Selecting OVP test

2 Click the OVP Trend Chart button. The test result is dis-
played.

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E
Figure 460: Trend Chart of a sensitivity test

A Name of test
B Limit: the test-specific limit is displayed without data points as
this line is a constant
C Measured value: the data points represent the values mea-
sured
D Y-axis: is automatically scaled
E X-axis: shows date and time of measurement

Depending on the test selected, the limit can be greater or less

than the values measured. In case of the 100% test exemplified in
figure 460 the value measured must not exceed the limit. In case of
the sensitivity test exemplified in figure 461 the measured value
must be above the limit.

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Figure 461: Trend chart of a 100% test

Depending on which test you have selected, there may be two lim-
its shown in the trend chart. In this case, the measured value has to
be within these two limits (figure 462).

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Figure 462: Trend chart of a PhEur 2.2.40 linearity test

13.5.2 Pop-up menu in trend chart

Right click into the trend chart. The following menu pops up:

Figure 463: Pop-up menu in trend chart

A This option allows to zoom into a particular trend chart sec-

tion. Click the option and draw a frame around the desired
section. If you release the right mouse button, the section is
enlarged.
B This option allows to zoom out the trend chart. Click the
option and then the trend chart. Each click zooms out the
chart by a particular factor.
C This option restores the initial state of trend chart. Click the
option, and all previous zooming actions are undone.

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D This option allows to show and hide the lines displayed in the
trend chart. Click this option to open the following dialog:

Figure 464: Trend chart properties

Hiding trend chart lines

Depending on whether you want to hide the line displayed for the
limit or the measured value, click the respective Visible column to
remove the check mark.

Figure 465: Hiding lines

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Changing color of trend chart line

1 Depending on whether you want to hide the color of the line

displayed for the limit or the measured value, click the
respective Color column. A small arrow is displayed.

Figure 466: Changing color of trend chart line

2 Click the arrow to open the color palette.

Figure 467: Color palette

3 Select a color and click the OK button.

Figure 468: Color changed

The selected line must now be displayed in the trend chart,

with the color being changed.

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13.6 A utomatic Accessory Rec-

ognition

When installing an accessory for the very first time, the accessory
has not been registered yet in OPUS. If an accessory is positioned
into the sample compartment, OPUS reads the data of the acces-
sory and checks whether the accessory has already been used in
one of the OVP test channels defined.

If this is not the case, OPUS prompts you to prepare a new test
channel for the current accessory used.

This step is repeated whenever a new accessory is installed into

the sample compartment for the very first time. Each accessory
has a unique and integrated identification code. Even if you have
two accessories of the same type, the code will be different.

13.6.1 Activating automatic accessory

recognition

To allow OVP to automatically recognize1 the accessory (ATR,

transmission, etc.) mounted into the sample compartment, you first
have to activate the specific parameter for automatic accessory
recognition.

1 On the Measure menu, select the Optic Setup and Service

command.
2 Click the Devices/Options tab.
3 Activate the Automatic Accessory Recognition checkbox.
4 Click the Save and Exit button.

1. This only applies to accessories mounted on a QuickLock baseplate.

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13.6.2 Registering new accessories

Any new type of accessory has to be registered in OPUS first, and

a new OVP test channel has to be set up.

1 Position the accessory into the sample compartment of the

spectrometer.
2 The Setup OVP dialog pops up. You are prompted to set up
a new test channel.
3 Enter a title for the new configuration. Click the Add new
configuration button.
4 Define the test channel configuration, using the drop-down
lists.
5 Select the appropriate type of accessory from the Accessory
drop-down list.

Figure 469: Accessory drop-down list

6 Optionally, select the crystal type from the Crystal drop-down

list when using ATR accessories with changeable crystals
(see chapter 13.6.5).
7 Optionally, select a standard measurement experiment from
the Measurement Experiment drop-down list. This experi-
ment is automatically loaded whenever the accessory is
inserted into the spectrometer.

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Figure 470: Measurement experiment drop-down list

Note: For each accessory a unique set of measurement

parameters is defined in a measurement experiment
file. This file has the extension *.XPM.
Selecting a measurement experiment is not mandatory. It is
possible to select the measurement experiment later.

8 Measure the laser wavenumber by clicking the

button. For more details refer to chapter 13.1.1. The acces-
sory is now listed in the Accessory ID line, indicating its ID
number as well. Example:

Figure 471: Accessory ID

9 Set up the OVP tests on the OVP Test Setup tab. More
details are described in chapter 13.1.2.
10 Click Save and Exit to store all settings made.

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All registered accessories are listed in the Accessory drop-down

list of the Measurement dialog. To display this drop-down list pro-
ceed as follows:

1 On the Measure menu, select the Advanced Measurement

command.
2 Click the Optic tab.
3 Select the type of external accessory from the Accessory
drop-down list.

Figure 472: Measurement experiment drop-down list

4 On the Advanced tab, click the Save button to save the mea-
surement experiment for the accessory.

Note: Whenever you generate a measurement experiment

for a specific type of accessory, first select this
accessory from the Accessory drop-down list before
storing the experiment.

This guarantees that the correct test channel is acti-

vated, and that measurement is performed by the
right laser wavenumber. Furthermore, this experiment
cannot be accidentally used with a different type of
registered accessory.

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13.6.3 P e r f o r m i n g O V P t e s ts

After setting up the test channel for the accessory perform the OVP
tests.

1 Select the Run OVP Tests command.

2 Click the Run selected Tests button in the dialog that pops
up. For more details refer to chapter 13.2.

13.6.4 A u t o m a t i c P e f o r m a n c e Te s t

A performance test starts automatically if you insert the accessory

once again into the spectrometer, or if you start OPUS with the
accessory already inserted into the spectrometer.

In case of the performance test only one reference and one sample
measurement starts. Wait for the test result before you continue
measuring.

If the performance test has finished, the result is indicated in a yel-

low message bubble. A background measurement can be started
immediately from this message bubble, if you have already
selected measurement experiment for this kind of accessory.

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13.6.5 Wo r k i n g w i t h s p e c i a l t y p e s o f
accessories

External accessories (HYPERION or

HTS-XT)

External accessories such as HYPERION or HTS-XT can also be

registered, although they are not QuickLock coded.

1 On the Validation menu, select the Setup OVP command.

2 Enter a title for the new configuration. Click the Add new
configuration button.
3 Define the test channel configuration, using the drop-down
lists.
4 Select the type of external accessory from the Accessory
drop-down list.

Figure 473: Selecting accessory

5 Select the measurement experiment from the Measurement

Experiment drop-down list.
6 Click the Measure LWN button to measure the laser wave-
number. The accessory ID must now be indicated in the
Accessory ID line.
7 Set up the OVP tests on the OVP Test Setup tab. For more
details refer to chapter 13.1.2.
8 Click the Save and Exit button.

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The external accessory is now registered and can be selected from

the Accessory drop-down list of the Measurement dialog. To acti-
vate this drop-down list proceed as follows:

1 On the Measure menu, select the Advanced Measurement

command.
2 Click the Optic tab.
3 Select the type of external accessory from the Accessory
drop-down list.
4 On the Advanced tab, click the Save button to save the mea-
surement experiment for the external accessory.

Note: Make sure that the type of external accessory has

been selected and saved with all measurement exper-
iments to be used in connection with the accessory.

AT R a c c e s s o r i e s w i t h e x c h a n g e a b l e c r y s -
ta l s ( T E N S O R a n d V E R T E X s e r i e s o n l y )

The exchangeable crystals for ATR accessories are not hardware

coded. Thus, an exchange of the crystal cannot be detected auto-
matically. If you use these types of accessories, proceed as fol-
lows:

1 On the Validation menu, select the Setup OVP command.

2 Set up an OVP test channel for each crystal type separately.
3 Enter a title for the new configuration. Click the Add new
configuration button.
4 Define the test channel configuration, using the drop-down
lists.
5 Select the type of accessory from the Accessory drop-down
list.

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 Automatic Accessory Recognition Chapt. 13

Figure 474: Selecting accessory

6 Select the crystal type from the Crystal drop-down list.

Figure 475: Selecting crystal type

7 Select the measurement experiment from the Measurement

Experiment drop-down list. It is possible to select a different
measurement experiment for each crystal type.
8 Click the Measure LWN button to measure the laser wave-
number. The accessory ID must now be indicated in the
Accessory ID line.
9 Set up the OVP tests on the OVP Test Setup tab. More
details are described in chapter 13.1.2.
10 Click the Save and Exit button.
11 Repeat the steps 1 to 7 for all crystal types used.

The ATR accessory is now registered and can be selected from the
Accessory drop-down list of the Measurement dialog. To activate
this drop-down list proceed as follows:

1 On the Measure menu, select the Advanced Measurement

command.
2 Click the Optic tab.
3 Select the type of accessory from the Accessory drop-down
list. You will find separate entries for the same accessory in
the list, distinguishing between each crystal type.

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 Chapt. 13 Validation

4 Generate a separate measurement experiment for each

accessory-crystal combination. Select the correct combina-
tion from the Accessory drop-down list before saving the
experiment.
5 On the Advanced tab, click the Save button to save the mea-
surement experiment.

F i b e r p r o b e s ( F T- N I R s y s t e m s o n l y )

Optical properties of fiber probes are determined by the probe itself

and the length of the fiber which exists between the instrument and
the probe.

Probes and fiber length can be selected separately in the OVP

setup dialog (as of OPUS version 7). Proceed as follows:

1 On the Validation menu, select the Setup OVP command.

2 Enter a title for the new configuration. Click the Add new
configuration button.
3 Define the test channel configuration, using the drop-down
lists.
4 Select the probe type from the Accessory drop down list.

Figure 476: Selecting fiber probe

5 Select the appropriate length from the Fibre Length

drop-down list.

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 Automatic Accessory Recognition Chapt. 13

Figure 477: Selecting fiber length

Since the optical properties do not change linearly with the

fiber length, the distances between the selectable lengths
become larger with increasing fiber length.

Figure 478: Distances between selectable fiber lengths

If the exact length is not listed, always select the next higher
length, e.g. select 100m if the length of the fiber used is 95m.

Note: Configurations set up with previous OPUS versions

(<7) are automatically converted. Due to the new algo-
rithm used to calculate the parameters, the new
parameters can deviate from the previous ones.
6 Select the measurement experiment from the Measurement
Experiment drop-down list.

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 Chapt. 13 Validation

7 Click the Measure LWN button to measure the laser wave-

number. The accessory ID must now be indicated in the
Accessory ID line.
8 Set up the OVP tests on the OVP Test Setup tab. More
details are described in chapter 13.1.2.
9 Click the Save and Exit button.

The fiber probe is now registered and can be selected from the
Accessory drop-down list of the Measurement dialog. To activate
this drop-down list proceed as follows:

1 On the Measure menu, select the Advanced Measurement

command.
2 Click the Optic tab.
3 Select the fiber probe from the Accessory drop-down list.
4 On the Advanced tab, click the Save button to save the mea-
surement experiment for the fiber probe.

13.6.6 Resetting accessory in test chan-

nel
Note: The option is not available with Raman spectrometers
and the LANCIR NIR spectrometer.

1 On the Validation menu, select the Setup OVP command.

2 On the dialog that opens, select the active test channel,
which contains the particular accessory, from the drop-down
list.
3 Click the Reset Accessory in Test Channel button.
➣ The accessory is no longer assigned to the test channel.

4 Click the button to start measuring the laser

wavenumber.
➣ Details on measuring the laser wavenumber are described
in chapter 13.1.1.

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 Automatic Accessory Recognition Chapt. 13

5 If required, on the OVP Test Setup tab select the OVP test
category.
➣ Details on the OVP test categories are described in
chapter 13.1.2.
6 Click the Save and Exit button.

13.6.7 Clearing accessory in bench

Note: The option is not available with ALPHA, LUMOS and
TANGO spectrometers. An accessory which has been
defined incorrectly can be re-defined.

1 On the Validation menu, select the Setup OVP command.

2 On the dialog that opens, select the active test channel from
the drop-down list.
3 Click the Clear Accessory in Bench button.
4 Enter a new name for the configuration.
5 Click the Add new configuration button.
6 Use the drop-down lists to define the test channel configura-
tion.

7 Click the button to start measuring the laser

wavenumber.
➣ Details on measuring the laser wavenumber are described
in chapter 13.1.1. the new accessory definition is saved in
the AAR.INI file.
8 If required, on the OVP Test Setup tab select the OVP test
category.
➣ Details on the OVP test categories are described in
chapter 13.1.2.
9 Click the Save and Exit button.

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 Chapt. 13 Validation

13.6.8 Setting up test channel for

non-validated accessory
Note: If the accessory is inserted into the sample compart-
ment of the spectrometer for the very first time, the
Setup OVP dialog opens automatically. At this time,
the inserted accessory is unknown to OPUS.
☞ On the dialog displayed, click the Non-validated accessory1 button.
➣ Clicking the button indicates that the accessory is not relevant for
OVP. The ’Setup OVP’ dialog is closed.
➣ In case of a non-validated accessory, a new test channel is not
explicitly set up for the new accessory. Instead, the test channel of
the particular basic configuration is used when performing the PQ
and OQ test.
➣ If the PQ test for the test channel of the particular basic configuration
is still valid, you can use the accessory to perform sample measure-
ment. If the PQ test for the test channel of the corresponding basic
configuration has expired, failed or has not yet been performed, the
accessory must be removed from the sample compartment, and a
PQ test for this test channel must be performed (chapter 13.1.2.1). If
the PQ test has passed, sample measurement can be started.

1. In case of a non-validated accessory there is no test configuration in the OVP

database of OPUS available. To find out whether the particular accessory used
is a validated or non-validated one, refer to the documents attached to the ac-
cessory.

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14 S e t u p
The Setup menu includes all functions to be required to configure
menus and toolbars as well as the workspace.

Figure 479: Setup menu

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 Chapt. 14 Setup

1 4.1 Lo g o u t

Definition This command allows to log out the current user and
login a new one.

Principle If you select this command, the Login dialog is dis-

played (see chapter 1).

• Select the correct user ID from the drop-down list.

The user last logged in will be displayed by default.
• Enter the correct user password.
• Select one of the workspaces using the drop-down
list.
• Click Login to log in the new user.

If you click Exit from OPUS, you close the login dialog
and terminate OPUS.

Note: The Logout command does not unload files from the
browser, nor stops processes still running (e.g. mea-
suring).

Figure 480: OPUS Login

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 Setup JCAMP <-> OPUS Conversion Chapt. 14

14.2 Setup JCAMP <-> OPUS

Conversion

Definition This command allows to set the conditions for the

conversion of JCAMP files into OPUS files, i.e. the
conversion tables to be used will be defined.

Note: The settings made apply both to the Con-

vert3dJCAMP command on the Edit menu and to
the Load File command on the File menu.

Principle • Select the Setup JCAMP <-> OPUS Conversion

command. A dialog opens.
• Load the files which contain the conversion tables
desired by using the Change button.
• Click OK to start the conversion.

Figure 481: Setup JCAMP <-> OPUS Conversion

A If you activate the check box, a comma is used as decimal

separator during conversion.

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 Chapt. 14 Setup

Basic Features

To avoid the loss of information when converting JCAMP files

define how the JCAMP labels correlate with OPUS parameters and
information lines. This has to be done by using a conversion table.

A conversion table is a text file with the extension *.PCT, and can
be generated by any kind of text editor. Additionally, you have to
specify the file containing the info text definition.

The general syntax of the file with the *.PCT extension is as fol-
lows:

#Ixx:yyy:LABEL with:
Ixx defining the number of the line in the info block, xx being a
two-digit number starting with 01.

yyy being a three-character OPUS parameter.

LABEL being the name of the JCAMP label.

It is mandatory to indicate the consecutively numbered info line.

Each line needs to have two colons. The parameter name and the
JCAMP label definition are optional.

The following example refers to the DEFAULT.PCT file which is

stored in the OPUS Methods directory.

#I01::SNM:TITLE
#I02::MOLFORM
#I03::MW
#I04::CAS REGISTRY NO
#I05::MP
#I06::BP
#I07:SFM:SAMPLING PROCEDURE
#I08::
#I09:CNM:ORIGIN
#I10::CROSS REFERENCE
#I11::CHARGE NO
#I112:HIS:DATA PROCESSING

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 User Management Chapt. 14

14.3 User Management

Definition The User Management command allows to create,

edit or delete user records in OPUS.

Principle To allow immediate access to OPUS a default user

database is available after the installation. This
default database includes three pre-defined user
records, which allow full access to OPUS and all
workspaces.

The user records are stored in the C:\Users\Pub-

lic\Public Documents\Bruker\OPUS_<version>\User-
DataBase directory in the UserDatabase.dat file. The
file is encrypted and cannot be modified externally.

Make sure that this file is protected against accidental

deletion using Windows security options. Make a
backup copy whenever you modify this file.

Note: Do by no means set this file to read only.

U s e r D a ta b a s e

The pre-defined user records of the OPUS user database are as

follows:

User ID Default Administrator LabManager

Password OPUS OPUS OPUS

User name Default Administrator LabManager

User group Administrator Administrator LabManager

Assigned workspaces Unlimited access to all user workspaces

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 Chapt. 14 Setup

What is to be considered when creating

user records?

The entry fields can have the following colors:

Color Definition

White Correct entry

• If the minimum number of characters is reached, the entry

field color changes to white indicating a valid input.

Red Initial or wrong entry

• All entry fields which must be filled in are initially marked

red. If you start typing into any of the red entry fields, the
color of the entry fields changes to white.
• Double user IDs are not allowed and will be indicated by
red entry fields.

Yellow Incomplete entry

• The color of the entry fields remains yellow as long as the

number of characters typed in is smaller than the number
specified for the current field.

Orange Expired entry (e.g. password)

Note: User records can only be stored, if all obligatory

fields have been filled in properly.

Creating User Record

Note: To be able to create user records make sure that you

have OPUS administrator rights.

1 Select the User Management command.

2 Define the user record by means of the different tabs in the
User Management dialog.
3 Store the settings made.

In the following the different tabs of the User Management dialog

are described.

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 User Management Chapt. 14

Setup Record

F
G
H

Figure 482: User Management - Setup Record

A The total number of user records is displayed in the top line of

the dialog. The number of the current user record is displayed

between the and buttons. Use these buttons to

go to the previous and next user records.
B Enter the user ID for the user. The user ID must have a mini-
mum length which can be specified on the Global Options tab.
It is not possible to log in OPUS without any user ID.
C Enter the password for the user. The password must have a
minimum length which can be specified on the Global Options
tab. The entry in the Password entry field is indicated by a
number of “*”. It is not possible to log in OPUS without any
password.
D Confirm the password for verification. The entry in the Pass-
word Verification entry field is indicated by a number of “*”.
The entry field will only change to white if the text entered is
identical to the text defined as password.
The password can be empty if the appropriate check box is
activated on the Global Options tab. In this case the Pass-
word entry field will be yellow and the Password Verification
entry field white.

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 Chapt. 14 Setup

E Enter the user name. The user name is stored in newly mea-
sured spectra and in the audit trail of spectra and methods,
and shown accordingly.
F The user group specifies the access rights of a user. The
drop-down list includes the Administrator, Labmanager and
Operator user group. The first two user groups have unlimited
access to all OPUS workspaces. The Operator user group
has only access to the workspace assigned. Note: For users
with Operator rights at least one workspace must be
assigned.
If you select the Operator user group, the list of assigned
workspaces is displayed on the right.

Click Add Workspace. Select the appropriate workspace from

the dialog that opens. OPUS workspaces are stored in the
C:\Users\Public\Public Documents\Bruker\OPUS_<ver-
sion> directory. The name and path of the workspace
selected is displayed.

To delete a workspace select it in the list and click Remove

Workspace.
G This button allows to delete the current record.
H If you activate this check box, the user will be locked. The
user cannot access OPUS anymore. Note: This check box

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 User Management Chapt. 14

is activated if a user tries to log in by using a wrong pass-

word several times. The number of login attempts can be
defined on the Global Options tab.
I Activate this check box if you want to force the user to change
his password when logging in the next time.

Global Options

Figure 483: User Management - Global Options

A By default, 4 characters are defined for the minimum length of

the user ID. Note: Any changes made will have an immedi-
ate effect on all user records.
B By default, 3 characters are defined for the minimum length of
the password. Note: Any changes made will have an
immediate effect on all user records.
C If you activate this check box, empty passwords are allowed.
Note: Empty passwords will never expire, regardless of
the password duration set.
D This check box either activates or deactivates the password
duration option. By default, the check box is activated. If you
deactivate the check box, an additional entry field is dis-
played.

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 Chapt. 14 Setup

Figure 484: Password validity period

Define the password duration in days. Note: The duration

period starts with the date when the user record is cre-
ated or modified. If you deactivate the Password never
expires check box, the Password entry field (C in figure 482)
becomes orange for those users whose password has been
expired and has to be changed when logging into OPUS next
time.
E In this entry field you define the maximum number of illegal
login attempts. By default, 10 login attempts are defined. An
illegal login is using a wrong password while trying to log into
OPUS. The user gets a warning indicating how many
attempts are left.
Note: If the last attempt has not been successful either,
the user will be locked and not be able to run OPUS any-
more. The administrator only can undo this lock by deactivat-
ing the Lock user check box (H in figure 482) on the Setup
Record tab.
F In this entry field you define the number of passwords previ-
ously used by the user, and not allowed to be used anymore
when changing the password. Note: The default setting is
3. This option forces the user to use a completely new pass-
word if the duration of his password has expired.
G If you activate the check box, OPUS will be locked after a cer-
tain period of time has passed in which you have not worked
with the PC. As soon as you have activated the check box,
the entry field is enabled. Use this entry field to define the
period of time in minutes.
OPUS will be locked if the defined period of time has passed.
Any OPUS access will be impossible. The OPUS Login dialog
is displayed. Note that only the previous user or any adminis-
trator can log in again. Restart OPUS to have the locking
changes become effective.

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 User Management Chapt. 14

Note: Any changes made on this tab have an immediate

effect on all user records in the data base. Therefore,
check all user records after changing any of these
settings. Improper entries will be marked in red.

A u d i t Tr a i l

The Audit Trail tab indicates the audit trail of the following actions
for each user.
• Successful login
• Login attempt of a locked user
• Login with password expired
• Changing password

For users with Administrator rights the following actions are

additionally recorded:
• Creating, editing or deleting a user record
• Locking or unlocking a user
• Creating, editing or deleting a signature
• Locing or unlocking a user
• Exporting one audit trail or all audit trails
• Deleting one audit trail

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 Chapt. 14 Setup

C
E
D

Figure 485: User Management - Audit Trail

A Use this buttons to go to the previous or next user record.

B This field includes the audit trail of the actions performed by
the respective user.
C Use this button to store the current user data recorded in the
audit trail.
D Use this button to store all user data recorded in the audit
trail. If you click Save all, a dialog opens. Define the file to be
used to store the audit trail data and confirm the entry. Audit
trail data are stored in ASCII format.
E If you click this button, the audit trail data of the current user
will be deleted. Note: This button is only enabled if the
audit trail data have been stored first.

Note: The Save and Clear Audit Trail actions are recorded in
the audit trail of the user currently logged in.

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 Change User Password Chapt. 14

14.4 Change User Password

Definition Each user can change his own password. There are
different reasons for changing a password:

• A new user record has been created. In this case

the administrator defines the initial password which
can later be changed by the user.
• The Password duration option (figure 484 on
page 718) is enabled and the password has been
expired according to the period of time defined. In
this case the user cannot log in OPUS anymore.
• The Administrator has checked the Force user to
change password option button (I in figure 482).
• A user assumes that someone else knows his pass-
word.

Principle • Select the Change User Password command.

• Change the password, using the dialog that opens.
• Store the changes made.

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 Chapt. 14 Setup

Figure 486: Change User Password

A The user name and user group are displayed.

B Enter the old password into the entry field.
C Enter the new password into the entry field. Note: When
defining a new password make sure that it is different
from the last ones previously used. The number of pass-
words recorded in OPUS are defined on the Global Options
tab in the User Management dialog (F in figure 483 on
page 717).
Furthermore, the new password has to have the minimum
length defined on the Global Options tab in the User Manage-
ment dialog (B in figure 483 on page 717).
D Enter the new password into the entry field to verify it.
E To store the changes made click OK.

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 Change User Password Chapt. 14

I f y o u r pa s s w o r d h a s a l r e a d y e x p i r e d . . .

...and you try to start OPUS, a warning pops up.

Figure 487: Warning - password expired

Clicking OK opens the OPUS Login dialog. Enter the new

password and verify it.

Figure 488: Enter new password

Click Change Password. The OPUS Login dialog opens. You can
now log in OPUS by using the new password.

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 Chapt. 14 Setup

14.5 Setup User Macro List

Definition This function allows to integrate macros or VB scripts

into OPUS, and add them to the toolbars. It is possi-
ble to add macros and scripts in different languages.

Note: To integrate macros and scripts use the

Customize menu command (see chapter 14.8).

Principle • Select the Setup User Macro List command.

• Make the settings required in the dialog that opens.
• Store the list.

I
G

J
Figure 489: Setup User Macro List - User Macro Entry

A Select the correct language for the entry from the drop-down
list. The default language is the language in which OPUS has
been started. You can only edit the entries for the selected
language. If the language has been changed, you can access
the entries for the language newly selected.
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 Setup User Macro List Chapt. 14

B Shows the total number of entries and the number of entries

for the current language.
C Use these buttons to go to the previous or next user record to
scroll between the different entries for the current language.
D Select the menu which the macro/script is to be added to from
the drop-down list.
E Use the browse button to select the macro/script for the entry.
To avoid errors the path and file name of the macro/script
cannot be entered manually.
F Fill in the entry fields by the correct text for the menu, tooltip
and status bar.
G If you want to remove the current entry from the list, click this
button.
H You can also copy an entry for a different language into the
list by clicking this button. Before, you have to select a lan-
guage from the drop-down list (I). Make sure that the lan-
guage is not the same as specified in (A). Otherwise, an error
message pops up indicating that you cannot copy an entry
using the same language. Translate or modify the entry
accordingly.
I Use this drop-down list to select the target language for copy-
ing. See also (H).
J Use this button to store all entries for all languages in the
USERMAC.LST file.

Example of USERMAX.LST file

The USERMAC.LST file in the OPUS directory is stored as plain

text file, e.g.:

[ENGLISH]
.\macro\it.mtx@8@Instrument Test@Instrument Test@Run
the Instrument Test

The key words in square brackets specify the different language

sections. Within these sections each line represents a macro or
script. The different parts of the lines are separated by the "@"
character and have the following meaning:

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 Chapt. 14 Setup

.\macro\it.mtx@ Path and file name of macro or script

@8@ Number of menu

@Instrument Test@ Text for menu

@Instrument Test@ Text for tooltip

@Run the Instrument Test@ Text for status bar

14.6 Register OPUS

Registering OPUS is only required if:

• additional OPUS packages have been acquired
• Bruker libraries want to be used
• the 30-days’-trial period1 has expired

The data required (key, serial number etc.) to register OPUS in the
above mentioned cases can be obtained from the OPUS stick.

The registration has to be performed only once and is valid for all
users.

Note: To be able to register OPUS you need to have Admin-

istrator rights in Windows.

1. If you work without any spectrometer connected, you can use OPUS for 30 days
without registering, after the program has been installed.

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 Register OPUS Chapt. 14

To r e g i s t e r O P U S . . .

1 ...select the Register OPUS command.

2 Fill in the entry fields.
3 Confirm the settings by clicking OK.

The dialog of this command is described in the following.

D
Figure 490: Registration Dialog

A Fill in only those fields which you received registration data

for.
The OPUS serial, package and library number consist of fig-
ures only, whereas the key consists of both figures and capi-
tal letters. When entering the key for the first time it is
displayed in plain text, later it is hidden by "*".
B Select the option which corresponds to your registration data.
If you have registration data for OPUS 5.5 (or previous ver-
sions), a message pops up and asks you to define the
respective additional software packages from the Available
software packages and libraries drop-down list. These addi-
tional packages are defined as Extended packages in your
registration data.

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 Chapt. 14 Setup

To check whether the registration data are correct click Check

Registration Data. If they are correct, the selection field lists
all available OPUS packages and libraries.
C If additional software packages have been installed, they can
be deactivated using this option button. They will be deacti-
vated until you restart OPUS or open the Registration dialog
once again.
D If you click this button, the data are permanently registered.

14.7 Customize Toolbars

Definition Customizing toolbars in OPUS is similar to any other

software package based on Windows. OPUS pro-
vides the following options:

• Moving, adding, deleting, customizing or creating

toolbar
• Adding, deleting or copying icons
• Grouping icons in toolbar
• Creating user-defined icons

Principle There are different possibilities to modify the toolbar.

These possibilities are described in the following.

Note: In some cases it is required to have the

Customize dialog open to be able to make
changes in the toolbar.

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 Customize Toolbars Chapt. 14

14.7.1 Moving toolbar

1 The toolbar can be freely moved. Position the cursor over

the drag point ( ) at the beginning of the toolbar.

2 The cursor changes to .

3 Now, press the left mouse button and move the toolbar to
any position you like.

14.7.2 Adding toolbar

1 Select the Customize Toolbars command and click the
Toolbars tab.
2 Set a check mark in front of the toolbar name which you
want to add.

3 The toolbar is displayed on the OPUS interface. Press the

left mouse button and move it to the position desired.

14.7.3 Deleting toolbar

1 Position the cursor over the drag point ( ) at the beginning
of the toolbar.

2 The cursor changes to .

3 Now, press the mouse button and move the toolbar to the
lower edge of the OPUS interface.

4 Click the icon to delete the toolbar from the OPUS inter-
face.

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 Chapt. 14 Setup

14.7.4 Customizing toolbar

1 Select the Customize Toolbars command. The Customize
dialog opens.
2 Specify the settings.
3 The changes are immediately performed.

The different tabs of the Customize dialog are described in the

following.

B
A

Figure 491: Customize - Commands

A The list box includes the different menu categories. Depend-

ing on the menu selected from the list box, all commands
available for this menu are displayed in (B).
B The list box includes the single menu commands with the
appropriate icons. If you click any command in the list box, a
short text pops up describing this command.

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 Customize Toolbars Chapt. 14

C This button allows to open the online help of the respective

tab.

To a d d a c o m m a n d t o t h e t o o l b a r.. .

1 ...click the respective command in the Command list box (B

in figure 491).
2 The cursor changes to .
3 Drag the command to the desired position in the toolbar by
pressing the left mouse button.
4 If you release the mouse button, the appropriate icon of the
command selected is displayed in the toolbar.

To d e l e t e a c o m m a n d f r o m t h e t o o l b a r

There are two possibilities:

1 Click the appropriate icon in the toolbar and drag it from the
toolbar while pressing the left mouse button. If you release
the mouse button, the icon is deleted from the toolbar. Note:
Make sure that the Customize dialog is open.
2 You can also right click the icon and select the Delete com-
mand from the pop-up menu. Note: Make sure that the
Customize dialog is open, otherwise no pop-up menu
will be displayed.

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 Chapt. 14 Setup

To a d d s i n g l e m e n u s o r s u b - m e n u s t o t h e
t o o l b a r.. .

1 ...select the New Menu command from the Categories list

box (A in figure 491).
2 Drag and drop the New Menu entry displayed in the Com-
mands list box (B in figure 491) to the desired position in the
toolbar.

3 The new entry is displayed in the toolbar.

If you want to change the name of the entry, right click

onto the entry and select the Button Appearance command
from the pop-up menu. Enter the new name into the Button
text entry field.
The new menu entry has an arrow head on the right side.
Clicking this arrow head opens a small field in which you can
drag and drop single menu commands from the Commands
list box (B in figure 491).

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 Customize Toolbars Chapt. 14

14.7.5 C r e a t i n g Too l b a r

Click the Toolbars tab to open the following dialog:

B
A

Figure 492: Customize - Toolbars

A The Toolbars list box helps to define which toolbar is to be

displayed on the OPUS interface. Therefore, set a check
mark in front of the toolbar name. If you remove the check
mark, the toolbar will be hidden.
B These buttons allow to reset the toolbar to the standard con-
tent. If you have selected several toolbars in (A), you can to
reset single ones. In this case the Reset button will be
enabled.
C This button allows to generate new toolbars.
D Toolbars can also be displayed with their text labels. Set a
check mark in front of the name of the toolbar. Activate the
Show text labels check box. The toolbar will be displayed as
follows:

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To c r e a t e n e w t o o l b a r s . . .

1 ...click New (B in figure 492). A dialog opens.

2 Enter the name of the new toolbar into the Toolbar Name
entry field.
3 Confirm the name by clicking OK. The new entry will be dis-
played on the lower end of the Toolbars list box (A in
figure 492).
To rename or delete this new entry, select it and click the
Rename or Delete button.
Note: Toolbars which have not been created by the user
cannot be deleted. If you select such a toolbar the
Reset button will be enabled. This button allows to
reset the standard icons of the toolbar.

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O p t i o n s ta b

Further settings on the appearance of toolbars can be made on the

Options tab.

Figure 493: Customize - Options

A By default, the two check boxes are activated. This means

that screen tips (tooltips) will be shown as soon as you move
the cursor over an icon in the toolbar. The tooltip will also
include the short cuts for the icon.
B By default, the check box is activated. This means that the
toolbar icons will be double the normal size.

For details on the menu settings in this dialog refer to chapter 14.8.

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14.7.6 Adding or deleting icons

1 Close the Customize dialog. Click the arrow head at the end
of the OPUS toolbar. An edit field pops up.

2 Position the cursor on the edit field arrow head. Another edit
field is displayed.

3 Position the cursor on the arrow head of the second edit

field. All icons are displayed which can be added to the stan-
dard toolbar.

By default, a check mark is set in front of some icons.

These icons are activated and displayed in the toolbar.
To add further icons to the toolbar click the respective icon.
A check mark is set in front of the icon selected. Thus, the
icon is activated and displayed in the toolbar.
To delete an icon from the toolbar click the check mark. The
check mark is then deleted and the icon is no longer dis-
played in the toolbar.

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14.7.7 Copying icons

1 Open the Customize dialog by means of the Customize
Toolbars command.
2 Go to the toolbar and click the icon to be copied.
3 Drag the icon to the desired position by pressing the
CTRL+ALT keys on the keyboard. Otherwise, the icon will
only be shifted.

14.7.8 Depicting icons

In general, OPUS icons can be depicted as follows in the toolbar:

• Image:

• Text:

• Image and text:

Right click any icon in the toolbar and select the appropriate
depiction type from the pop-up menu. A check mark will be set in
front of the depiction type selected.

Note: Make sure that the Customize dialog is open. Other-

wise, the pop-up menu will not be displayed.

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14.7.9 Grouping icons in the toolbar

Icons which belong together regarding subject matter can be

grouped in the toolbar. In this case you can set a dividing line in
front of the first and after the last group element to differentiate
between this group and the other icons and menus in the toolbar.

To a d d a d i v i d i n g l i n e . . .

1 ...right click the desired icon while the Customize dialog is

open.
2 Select the Start Group command from the pop-up menu.
3 The dividing line is added to the left side of the icon.

On a vertically positioned toolbar the dividing line is

added above the icon.

To d e l e t e a d i v i d i n g l i n e b e t w e e n . . .

...right click one of the icon and remove the check mark at the Start
Group command in the pop-up menu.

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14.7.10 Creating user-defined icons

1 Right click a toolbar while the Customize dialog is open.
2 A pop-up menu is displayed.
3 Click Button Appearance from this pop-up menu. The follow-
ing dialog opens:

Figure 494: Button Appearance

4 Activate the Select User-defined Image option button and

click New. Another dialog opens:

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Figure 495: Edit button image

Similar to any other drawing program a color palette and dif-

ferent tools are available to create your own icon. The icon
drawn is displayed in the preview.
5 To store the newly created icon click OK. The icon will be
included in the icon list box.

Figure 496: Newly created icon

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If you want to create a name for the icon, click the icon and
activate the Image and text option button. The Button text
entry field will be enabled. Now, enter an appropriate name
for the icon.

Figure 497: Create icon name

14.8 Customize Menus

Definition Customizing menus in OPUS is similar to any other

software package based on Windows. OPUS pro-
vides the following options:

• Adding or deleting menu commands

• Moving or copying menu commands
• Moving or copying menus and menu commands in
toolbar
• Creating sub-menus
• Grouping menu commands

Principle There are different possibilities to configure the

menus. These possibilities are described in the fol-
lowing.

Note: To configure menus requires the Customize

dialog to be open.

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Click the Customize Menus command. In the following the Menu

and Options tabs are described.

The Commands and Toolbars tabs mainly refer to customizing tool-

bars and are described in chapter 14.7.

Figure 498: Customize - Menu

A Select the workspace for the menu to be customized from the

drop-down list. You can edit the menus for the following
OPUS workspaces:
- OPUS
- PLE (Plot Layout Editor)
- VBScript 
- GMacro
- Default Menu
B To undo the changes made click this button. The menus of
the workspace in question are displayed again with their stan-
dard icons and commands.
C Menus can be animated. Select one type of animation from
the Menu animations drop-down list. The following types of
animations are available:

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- Unfold
- Slide
- Fade
D The check box is activated by default and displays the menus
with a light grey shadow on the right side.
E This button allows to open the online help of the respective
tab.

Two additional general settings can be made on the Options tab.

These settings have an influence on the appearance of the user-
defined menus and toolbars.

Figure 499: Customize - Options

A If you activate the check box, only those commands are dis-
played in the menus which have been used recently. To open
the complete menu view click the double arrow ( ) below
the last command shown.
B You can have the complete menu view be displayed after a
short period of time. Activate the check box.
C If you click this button, all the default settings are restored.

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 Chapt. 14 Setup

D This button allows to open the online help of the respective

tab.

Note: The settings of the customized menus are stored in

the particular workspace. If you are not entitled to
customize a particular workspace (also see
chapter 14.10), the deactivated menus and com-
mands will remain deactivated.

To have all menus and commands displayed you may

have to load a different workspace.

14.8.1 A d d i n g o r d e l e t i n g m e n u c o m-
mands

In both cases first select the Customize Menus commands.

Note: Menus can only be configured, if the Customize dia-

log is open.

1 Open the menu which has to be edited.

2 On the Customize dialog, click the Commands tab. For fur-
ther information on this tab refer to chapter 14.7.2.
3 Use the Categories list box and select the menu which you
want to add the command from.
4 Click the respective command icon in the Commands list

box. The cursor changes to .

5 Drag and drop the icon to the desired position in the menu
you want to edit.

To delete a command from a menu, click the command and

remove it from the menu.

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14.8.2 M o v i n g o r c o p y i n g m e n u c o m-
mands

In both cases click the respective command with the Customize

dialog and the menu being open.

Move the command to the desired position while pressing the

mouse button.

To copy menu commands right click the respective command.

Press the Ctrl+Alt keys and drag and drop the command to the new
position.

14.8.3 Moving or copying menus and

menu commands in toolbar

Both single menu commands as well as complete menus can be

moved within or copied to the toolbar. In both cases the
Customize dialog has to be open.

When moving click the menu or menu command and drag and
drop it to the desired position in the toolbar.

When copying press the Ctrl key and drag and drop the menu
command or menu to the desired position in the toolbar.

14.8.4 Creating sub-menus

Menu commands which belong together regarding subject matter

can be sorted in sub-menus and subsumed under a main menu.

1 First, create the main menu. On the Customize dialog, click

the Commands tab .
2 From the Categories list box, select New Menu. The New
Menu entry is displayed in the Commands drop-down list.

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3 Open the menu which you want to edit and drag and drop
the New Menu entry into this menu. The new entry is now
displayed in the menu:

To c h a n g e t h e n a m e o f t h e m e n u e n t r y.. .

1 ...right click the menu entry.

2 Select the Button Appearance command from the pop-up
menu. The following dialog opens:

Figure 500: Change name of menu entry

3 Define an appropriate name for the new menu entry in the

Button text entry field. Click OK.

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The new menu entry has a small arrow head on the right side. If
you click this arrow head, a small field opens in which you can drag
and drop the sub-menu commands.

Select the respective command with the appropriate icon either

from the Commands list box in the Customized dialog or from the
menu itself. Drag and drop this command into the small entry field
next to the arrow head.

Figure 501: Example of a main menu command with sub-menus

14.8.5 Grouping menu commands

Menu commands which belong together can be grouped within a

particular menu, i.e. in front of the first and after the last element of
a group you can add a dividing line. This allows to distinguish the
group from other commands within a specific menu.

To a d d a d i v i d i n g l i n e . . .

1 ...right click the menu command with the Customize dialog

being open.
2 Select the Start Group command from the pop-up menu.
3 The dividing line is set above the menu command selected.

Figure 502: Example of grouping menu commands

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 Chapt. 14 Setup

To d e l e t e a d i v i d i n g l i n e . . .

1 ...right click the respective command.

2 Remove the check mark in front of the Sort Group command
from the pop-up menu.

14.9 Shortcuts

Definition The Keyboard tab in the Customize dialog allows to

assign shortcuts to frequently-used commands.

Principle The procedure is described in the following.

Note: Shortcuts have to start with STRG+, ALT+

or a function key (e.g. F4).

14.9.1 A s s i g n i n g s h o r t c u ts
1 On the Customize dialog, click the Keyboard tab .

Figure 503: Customize - Keyboard

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2 Select the OPUS option from the Set Accelerator for drop-
down list.

3 Select the OPUS menu which contains the respective com-

mand from the Category drop-down list.
4 In the Command list box, click the command definition (see
the following example).

5 Use the Press New Shortcut Key entry field to enter the
shortcut to be assigned to the command selected. Press e.g.
STR+ and the key desired. Note: If a shortcut has already
been available for the command selected, this shortcut
will be displayed in the Current Key list box. An existing
shortcut can also be deleted (see chapter 14.9.2).
6 Whether the shortcut has already been assigned to a differ-
ent command or not is displayed accordingly.

Note: When assigning an already existing shortcut to a

new command, this shortcut cannot be used for the pur-
pose originally intended.
7 Click Assign.

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14.9.2 D e l e t i n g s h o r t c u ts
1 From the Category drop-down list, select the OPUS menu
which contains the command with the respective shortcut.
2 In the Command list box, click the command definition. The
shortcut is displayed in the Current Keys list box.
3 First, click the shortcut and then Remove.

14.9.3 R e s e t t i n g s h o r t c u ts
1 Select the appropriate option from the Set Accelerator for
drop-down list, whose shortcuts you want to delete.
2 Click Reset All.

Note: When clicking Reset All the user-specific shortcuts

are deleted and the original shortcuts reset.

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14.10 User Settings

Definition OPUS user accounts can be created and managed

by means of the User Settings command. Make sure
that you have the necessary user rights to do so (see
figure 505).

Principle • Select the command.

• Define the user settings. Use the different tabs from
the dialog that opens.
• To confirm the settings click OK.

The different tabs of the User Settings dialog are described in the
following.

General

Figure 504: User Settings - General

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 Chapt. 14 Setup

A The user status is indicated.

B The paths for the OPUS system directories are displayed.
C If a lab journal is to be created in OPUS, the check box has to
be activated. For details on the lab journal refer to
chapter 3.21.

2 1 C F R 11 R i g h ts

Figure 505: User Settings - 21CFR11 Rights

A Define the specific rights for the user account. Activate or

deactivate the corresponding check box. Note: Make sure
that at least one administrator account includes all the
user rights which can be assigned to.
B If you activate the check box, you work in GLP1 (Good Labo-
ratory Practice) mode. The original data are saved. If you
have measured a spectrum in GLP mode, it is still possible to

1. GLP means Good Laboratory Practice and is some kind of quality assurance di-
rective.

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 User Settings Chapt. 14

modify and overwrite the spectrum data. To restore the origi-

nal spectrum data, click the respective data block of the spec-
trum file and select the Delete Data Blocks command from the
File menu. In this case the data block will not be physically
deleted, but only the changes made.

Preferences

Figure 506: User Settings - Preferences

A Define how to proceed in OPUS if you want to save a mea-

surement by using an already existing file name. Check the
respective option button.
B The default decimals for frequencies are 4 and for intensities
3. The number of decimals are displayed in the report view.
C If you want to have the number of decimals automatically set,
activate the Automatic check box for both frequencies and
intensities.

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Display

Figure 507: User Settings - Display

A The display limits are set by default. To change the limits

enter the appropriate figures into the entry fields.
B If you activate the check mark, define whether the axes
should have legends.

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Figure 508: Spectrum display with axis legend

C Annotations (wavenumber by default) to a spectra are dis-

played with an arrow. See also chapter 2.8.4.

Figure 509: Spectrum with annotation

If you deactivate the check box, the annotation will have no

arrow.
D The check box allows to display spectra, which have the
same basic file name, in one specific color during a particular

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 Chapt. 14 Setup

loading procedure. Usually, the spectral curve colors are

automatically assigned when loading spectra into the
OPUS browser window.
If you activate the check box, two additional option buttons
will be displayed.

If you activate the Whole file name option button, all spectra
with the same file name (without extension) will be displayed
in the same color.
Activate the File name check box if only a specific number of
file name characters has to be identical. Example: if a file
name has 12 characters and you enter 1 into the First charac-
ter entry field and 8 into the Length entry field, the first 8 char-
acters of any file name will be checked to see whether they
are conform with the file name series.
Click the Spectra Colors... button to assign a color sequence
to the spectra. The following dialog opens:

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Figure 510: Setup Color Palette

The standard range of colors include 16 colors defined by

default, whereby only those colors checked will be assigned
to spectra.
If you have checked a color, use the arrow buttons to move it
to the appropriate position, either upwards or downwards.
Note: The color sequence defined on the color palette
correlates with the spectra color displayed in the spec-
trum window. Therefore, the first color on the color pal-
ette corresponds to the color of the first spectrum
displayed, the second color corresponds to the color of
the second spectrum and so forth. To save the settings
click Set.

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New File

Figure 511: User Settings - New File

A Define how a new spectrum file loaded or measured is to be

integrated into the spectrum window. Activate the respective
option button. In some workspaces, the Add new spectrum to
window option is activated by default. In this case, a new
spectrum file loaded replaces the current spectrum displayed
in the spectrum window. This means, if a spectrum has
already been displayed in the spectrum window it will be
removed.
B This check box is activated by default. All spectra will be auto-
scaled.
C This option button is activated by default. All data blocks are
shown in the browser.
D If you activate this option button, the main data blocks only
(i.e. spectra data blocks) will be shown in the browser. In this
case the browser will not show data blocks generated after
manipulation or evaluation procedures.

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Evaluations

Figure 512: User Settings - Evaluations

On the Evaluations tab you define whether the result of the evalua-
tion performed should be directly displayed in OPUS, or printed.

Note: The analysis results of a multi evaluation (ME) are

added to the spectrum file in the form of data blocks.
After multi evaluation, the spectrum file does not
only contain the ME data block, but also the respec-
tive original data block of the type of analysis per-
formed (e.g. REPORT, QUANT etc.). The result view
only contains the results of the original data block(s).
Hence, the values corrected by multi evaluation are
not considered in the result view. This means, that
user-defined group or component names are not
listed in the result view, either. The QUANT result
view does not differentiate between different analysis
levels.

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Diagnostics

Figure 513: User Settings - Diagnostics

On the Diagnostics tab you define which warning indications or

alarms you want to set for which spectrometer component.

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C o m pa n y S e t t i n g s

Figure 514: User Settings - Company Settings

On the Company Settings tab you can optionally define standard

data for different company features. Once these entries have been
defined they will be written in each OPUS file when a measurement
is performed.

1 4 . 1 0 . 1 In s t r u m e n t Te s t ( o n l y i n c a s e o f
n o n - O V P s u p p o r t e d i n s t r u m e n ts )

For spectrometers which are not supported by OVP, e.g. 120/

125 HR there are two additional tabs for the instrument test. Each
of the Instrument Test 1 and Instrument Test 2 tab includes 6 test
channels. Each of these test channels can assign one program to
be used from within OPUS for validation purposes, and correlates
with an icon position on the second or third row of the Instrument
Status dialog, see chapter 7.8.

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Note: The Instrument Status dialog can be accessed by

clicking the status light in the bottom right corner of
the main OPUS spectrum window.

The test channels of the Instrument Test 2 tab correlate with the
third row of the Instrument Status dialog. Thus, a total of 12 differ-
ent test channels can be assigned, if required.

Note: Configuring 12 test channels is only possible in OPUS

5 and higher versions.

Figure 515: User Settings - Instrument test

First, activate the IT check box which represents the active test
channel, and either enter the path manually or click the Path but-
ton.

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N o t e s w h e n s e l e c t i n g t h e pa t h :

If you have selected a path, OPUS will be informed that you want to
assign the Instrument Test macro (which can be installed during
OPUS installation) to a particular channel.

OPUS assumes that the IT.mtx macro is located in this path. If the
macro cannot be found, a Runtime Error in Macro message pops
up when you attempt to run the test.

Example:

Assuming the instrument uses both a sample chamber and an

external port as measurement channel, to validate both configura-
tions you would assign OVP to 2 IT channels on the Instrument
Test tab.

Figure 516: Two configurations assigned for the instrument test

In this example we would arbitrarily designate the first position (IT)

to be used for all experiment files that use the sample compart-
ment. All experiment files that use the external port channel will be
designated for the second position (IT2).

If you have entered a path into the appropriate IT entry field on the
Instrument Test tab, an icon is assigned for that particular channel
on the Instrument Status dialog (see chapter 7.8).

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M e a s u r e m e n t e x p e r i m e n ts :

Use the XPMs button to register one or more measurement experi-

ment files to the validation channel. These are the experiment files
which you will use for normal daily measurement.

You can add as many XPM files as you like. It is important that you
only select experiment files which have the same basic spectrome-
ter configuration (source, beam splitter, measurement channel
etc.).

If you click the XPMs button the following dialog opens:

B C

A D

Figure 517: Assign XPM file(s)

A Clicking this button adds XPM files from particular directories

into the selection field.
B This icon allows to define a new XPM file.
C Clicking this icon cancels an existing XPM file.
D Use the arrow buttons to scroll up and down the entries in the
selection field.

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Confirm the selection by clicking OK. Undo the selection by clicking

Cancel.

If you load an experiment file,...

...OPUS checks all the experiment files registered. If the experi-

ment selected has been registered for a channel, this channel
becomes the active test channel. OPUS polls the spectrometer to
detect the status of that channel. That channel is set Active in the
spectrometer as well.

If you deactivate one of the IT check boxes, this particular channel

becomes inactive. OPUS does not update the status light (at the
lower right end of the OPUS interface) if that particular channel is
selected as the active channel.

The following summarized sequence of actions ensues:

• User loads an experiment file.
• The XPM lists for each channel are scanned for the first
position containing that experiment.
• If a particular channel has been found, this channel
becomes the active test channel.
• The status for the active channel is read from the spec-
trometer.
• The status light reflects the current status.

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14.11 O p en P l an n e r

Definition The Open Planner command allows to exactly sched-

ule appointments or events in a calender. Appoint-
ments are planned activities in your planner which
you can also define as recurring items at a daily,
weekly or monthly interval.

In this context an event is an activity that normally

takes place once (e.g. yearly) during at least one day
or several days.

Principle OPUS allows to schedule the following activities:

• Switching on and off the internal IR source of the

spectrometer
• Starting the instrument test
• Activating user-specific messages

Basically, the general planner setup in OPUS is simi-

lar to any other comparable planner feature based on
Windows.

Note: The Open Planner command can only be

accessed if you are entitled to change user rights
and add new workspaces (see also
chapter 14.10).

Basic Features

If you double click anywhere on the planner, you can start defining
the entry. It is also possible to colorize the entry to see at once
what kind of appointment or event it is about.

When a timer item starts a message pops up and reminds you of

the OPUS activity running soon.

OPUS has to run, before being able to start the scheduled item at
the pre-defined time. If you select the Open Planner command, the
following dialog opens:

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Figure 518: Planner view

1 4 . 11 . 1 Vie w O p t i o n s

OPUS provides different planner view options. By default, the

month panel is displayed which you can change at any time.

To c h a n g e a p l a n n e r v i e w. . .

1 ...right click the panel to open the following pop-up menu:

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Figure 519: Planner - Pop-up menu

2 Select the Go to Date command from the pop-up menu (A in

figure 519). Another dialog is displayed.

Figure 520: Planner panel selection

3 Select the desired planner panel from the Show in drop-

down list (A in figure 520). To undo the setting made select
the Go to Date command (A in figure 519) again and change
the panel, accordingly.

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Default planner view options

The following planner view options are set by default in the pop-up
menu:

• Show end time:

• Compress weekend days: i.e. Saturday and Sunday
are displayed in one column, one below the other

To change these default settings remove the check mark in front of

the respective command in the pop-up menu (see figure 519).

1 4 . 11 . 2 C r e a t i n g p l a n n e r i t e m s
1 Right click the respective day and select the New
Appointment command from the pop-up menu.
2 Define the settings in the dialog displayed.
3 Save the settings made.

In the following the Edit Appointment dialog is described in more

detail.

D
B

Figure 521: Edit Appointment

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A Select the OPUS activity desired from the Subject drop-down

list. The following options are available:
- SOURCE=OFF
- SOURCE=MIR
- RUN OVP PQ TEST
- COMMAND_LINE
B Single entries can be colorized to see at once in the planner
what kind of appointment it is about. Select the color desired
from the Label drop-down list. The entry will then be displayed
by an additional color bar in the planner view.
C Define the start and end time of an entry. Either enter the date
manually into the entry field or click the small arrow next to
the entry field. In the latter case a small month panel pops up
from which you can select the desired day for the respective
entry.

Starting from today’s date you can also use the arrow keys
to define the date desired. The time can be set either man-
ually or by using the arrow keys.
D If you activate the check box, the entry becomes an event that
lasts at least one day. Note: An all day event does not
occupy blocks of time in your planner. Instead, it is dis-
played at the top of the date which you have specified in
the planner. This kind of event can also be created by using
the New All Day Event from the pop-up menu (see
figure 519).
E The Show time as drop-down list allows to define the time sta-
tus of the entry. This is recommended if others have access
to your planner.
F To save your settings click Save and Close.

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Note: Each single appointment or event can be changed

into a recurring item, i.e. have it occurred repeatedly.
In this case click Recurrence (for details see the fol-
lowing chapter).

1 4 . 11 . 3 Creating recurring items

If single appointments or events are to be repeated, define these

appointments or events as recurring items. A typical example of a
recurring daily event is to start the instrument test at a fixed period
of time, or shut down the IR source inside the spectrometer.

To c r e a t e r e c u r r i n g i t e m s . . .

1 ...right click the planner view and select the New Recurring
Appointment or New Recurring Event command. The dialog
that opens is the same for both commands.
2 Define the settings.
3 Confirm the settings made by clicking OK.
4 At last, define the name of the recurring appointment or
event.

In the following the Appointment Recurrence dialog is described.

Bruker Optik GmbH OPUS Reference Manual 771

 Chapt. 14 Setup

D
Figure 522: Appointment Recurrence

A Define the start and end time of the actual appointment or

event, either manually or use the arrow keys.
B The recurrence pattern helps to exactly set up at what inter-
vals the appointment or event recurrence has to take place.
Activate the respective option buttons.
C The range of recurrence refers to the duration of a complete
appointment or event recurrence. Define the start and end of
the recurrence. Recurring items are always indicated in the
planner by the symbol.
D As soon as you confirm your settings by clicking OK, the Edit
Appointment dialog (figure 521) is displayed. Enter the name
of the recurrence into the Subject drop-down list, or select the
corresponding activity from the Subject drop-down list.

1 4 . 11 . 4 Editing planner items

1 Double click the respective entry. The Edit Appointment
dialog (see figure 521) is displayed.
2 Make all the changes desired.
3 Save the changes made.

772 OPUS Reference Manual Bruker Optik GmbH

 Open Planner Chapt. 14

You can also right click the appointment or event and select the
Open command from the pop-up menu to have the Edit
Appointment dialog displayed.

To r e n a m e s i n g l e a p p o i n t m e n ts o r e v e n ts
i n t h e p l a n n e r. . .

1 ...click the name (not the time) of the respective entry.

2 A small white entry field opens in which you can change the
current name.

Note: To copy or delete particular entries right click the

appointment or event and select Copy or Delete from
the pop-up menu.

1 4 . 11 . 5 Editing recurring planner items

Editing recurring appointments or events is similar to editing single

appointments or events. However, a warning pops up indicating
that this kind of entry selected is a recurring item.

Figure 523: Warning in case of recurring items

You can either change any aspect of a recurring appointment for

the entire series, or edit a single instance of an appointment
without affecting the entire series of items. Activate the

Bruker Optik GmbH OPUS Reference Manual 773

 Chapt. 14 Setup

corresponding option button (figure 523) and confirm the setting by

clicking OK.

The Edit Appointment dialog (figure 521) is displayed. If you want

to change the complete recurrence pattern, click Recurrence.

Note: Recurring items can also be copied or deleted. In the

latter case a warning pops up again indicating that
the entry in question is a recurring item.

14.12 N e w Wor k s pa c e

Definition This command allows to create a new workspace,

and is only available if the user has the right to do so
(see chapter 14.10).

The following settings are stored in an OPUS work-

space:

• All user rights

• Configuration of toolbar and windows
• Parameters (settings) of all commands
• Configuration of menus and pop-up menu

Principle • Select the New Workspace command. A copy of the

workspace recently used will be created.
• At the same time the User Settings dialog opens
(see chapter 14.10).
• Define the settings required for the respective work-
space.
• Save the workspace by using the Save Workspace
As command (see chapter 14.13).

774 OPUS Reference Manual Bruker Optik GmbH

 Save Workspace As Chapt. 14

14.13 Save Wo rkspace As

Definition This command allows to store the workspace by

using a specific name.

Note: By default, workspaces are stored in the

C:\Users\Public\Public Documents\Bruker
\OPUS_<version> directory.

Principle • Select the Save Workspace As command.

• If you have changed a workspace, e.g. by re-posi-
tioning toolbars, this modified workspace will be
stored when you exit OPUS.
• If you have created a new workspace, a dialog
pops up requesting the name of this new workspace
when you exit OPUS.

1 4.14 Cl o se Wor k s pa c e

Definition This command allows to close the current workspace.

Note: Unload all files or stop all active tasks

before closing the workspace. Otherwise the data
will get lost.

Principle • Select the Close Workspace command.

• The workspace will be closed completely.

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 Chapt. 14 Setup

1 4.15 S en d Wo rk s pa c e

Definition This command allows to send the OPUS workspace

by e-mail. In this case the e-mail addressee accepts
all OPUS settings valid on your computer. The
addressee has to store the OPUS workspace file on
his computer, and open the file by OPUS. Make sure
that each path correlates with the OPUS settings.

Note: Therefore, sending workspaces does only

make sense if the computer configuration is iden-
tical with regard to the installation paths.

Principle • Select the Send Workspace command.

• Follow the on-screen instructions.

776 OPUS Reference Manual Bruker Optik GmbH

15 H e l p
The OPUS Help commands are available either from the Help
menu or by clicking any Help button on a dialog box.

Figure 524: Help menu

15.1 H elp To pics

If you click this command, the OPUS online help starts. The online
help can also be started by the F1 key on the PC keyboard.

Note: To be able to use the online help function make sure

that you have installed the Microsoft Internet
Explorer.

15.2 O nline Docs

If you position the cursor on this command, the names of the online
manuals available in OPUS are displayed. The online manuals are
provided as PDF files.

Note: To be able to read these PDF files you have to install

the Acrobat Reader from the OPUS stick.

Bruker Optik GmbH OPUS Reference Manual 777

 Chapt. 15 Help

15.3 FT- IR Tutorial

This command imparts basic knowledge about FT-IR spectroscopy

in the form of a tutorial.

15.4 A bout OPUS

If you select this command, a dialog opens and displays the OPUS
version used, the user name registered and the OPUS software
package available (see also chapter 1).

778 OPUS Reference Manual Bruker Optik GmbH

Appendix A
Kramers-Kronig-Tr ansformation
The o ry

The real and imaginary parts of complex physical quantities

describing the interaction between radiation and sample, e.g. the
complex refractive index
n = n + ik (B-1)

complex dielectric constant

 =  + i (B-2)

and the logarithm of the amplitude-reflectivity

ln  re i  = ln  r  + i (B-3)

depend on each other due to the causality principle. The two parts
can be transformed into each other by the so-called Kramers-Kro-
nig Transformation (KKT). OPUS uses KKT to first calculate the
phase rotation angle     as function of the wavenumber v from
the measured reflectance spectrum R    = r 2    of an optically
thick sample. Then, the reflectivity of the air/sample edge (vertical
incidence) is calculated from r    and     using the Fresnel
equation:
i   
   e =  n  – 1   n  + 1 (B-4)

The real and imaginary part of the refractive index are calculated
as follows:
12
n    =  1 – R       1 + R    – 2R    cos        (B-5)
    = 2R 1  2    sin         1 + R    – 2R 1  2    cos        (B-6)

Bruker Optik GmbH OPUS Reference Manual 779

 Chapt. 16 Appendix A

If desired, the dielectric function is calculated:

 = n 2 –  2 (B-7)
 = 2n (B-8)

From the imaginary part of the refractive index, the so-called

absorption coefficient     , the absorptivity A    of a layer with a
thickness d can be calculated by:
A    = log  e 2d    (B-9)

In principle, KKT enables to determine all important optical sample

properties on the basis of one single measurement (reflectance
spectrum R    ). At least two measurements are required to deter-
mine the real and imaginary part of the complex quantities (B-1) to
(B-3).

Equation (B-9) is implemented such that OPUS does not calculate

A    from a given thickness d but selects d, with the maximum of
A    being 1.0. This results in comparable intensities similar to
absorption spectra measured in transmission. Therefore, the inten-
sities of A    are only defined up to a freely selectable scaling fac-
tor.

A    according to equation B-9 is not directly comparable with the

measured A g    absorption spectrum of a layer of thickness d as
the absorptivity only describes the absorption of the pure medium
without any reflection losses. In contrast, the measured A g   
absorption spectrum is always a combination of absorption and
reflection at the two boundaries of the sample. In case of simple
reflection this can be considered by the additional factor  1 – R  2 ,
with multiple reflections and interference being neglected.
2 –A  v 
A g    = – lgT = – lg   1 – R  10  (B-10)

780 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Performing KKT

1 On the Manipulate menu, click Kramers-Kronig-

Transformation. A dialog opens.
2 Select the result function desired in the Compute group field.
The Refractive index (complex) and Dielectric function (com-
plex) commands both produce two data blocks, with the real
part being stored in the ABR reference data block ( ) and
the imaginary part in the ABI sample data block ( ). One
data block only is created in case of the Absorbance ( )
and Phase ( ) command.
3 Define the frequency limits used to perform KKT, by clicking
the Frequency Range tab.
4 Click KKT to start the transformation.

Frequency Range tab

Figure 525: Kramers-Kronig-Transformation - Frequency Range

Bruker Optik GmbH OPUS Reference Manual 781

 Chapt. 16 Appendix A

A Activating this check box allows to specify the entire fre-

quency range. In this case the other options in the Select fre-
quencies group field will be disabled.
B To select a particular part of the frequency range either click
the Interactive or Get Display Limits button.
C You can also enter the frequency range manually, using of
the X-Startpoint and X-Endpoint entry fields.

Note: When selecting the frequency range make sure that

the spectrum is as flat as possible at the edges, and
does not abruptly break off at high intensity changes.

Preconditions and Restrictions

KKT can only be used reasonably if the following preconditions are

met as best as possible. Thus, a large number of errors can be
avoided.

Limited Frequency Range

Strictly speaking, KKT is only valid on condition that the function to

be transformed is known for the entire spectral range from v = 0 to
v =  . This can, however, never be achieved in practice. There-
fore, KKT of the logarithmized reflectance spectrum is only an
approximation of the   v  phase.

When selecting the frequency range make sure that the reflectance
spectrum is flat at the edges. Avoid any significant structures at the
edges of the spectrum.

The KKT software in OPUS extrapolates the ln  R  spectrum in

horizontal direction at the edges, which is a suitable approximation
for insulators. In case of semiconductors, however, this kind of
approximation cannot be used as their reflectivity with v  0 tends
to 1. You can only extrapolate to v  0 correctly in case of semicon-
ductors if you have appropriate information on the effective mass
and concentration of free charge carriers.

782 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Furthermore, you have to be able to measure far enough in the FIR

range such that R    monotonously tends to 1 again and can be
fitted by a model function. At present, an automatic v  0 extrapola-
tion in case of semiconductor reflectance spectra is not yet possi-
ble with OPUS.

Measuring Accuracy

In general, calculating optical constants by KKT on the basis of

reflectance data requires a very reliable measuring accuracy.
Therefore, noise, insufficient water vapor and CO2 compensation,
non-linearities or baseline drifts have an adverse effect on the
measuring accuracy.

The reflectance spectrum should not contain any zero lines as oth-
erwise the  ln R  KKT integrand becomes singular. In case of
highly absorbing material, e.g. NaCl, SiO2, the reflection decreases
–3 –4
in some positions from 10 to 10 which may lead to the fact that
the measuring errors are greater than the wanted signal.

The result of KKT substantially depends on the correct spectrum

intensity within these critical ranges. Wrong intensities in the reflec-
tance spectrum can frequently be detected by a sometimes nega-
tive absorption coefficient k    . In this case spectral noise effects
can be minimized by smoothing. Furthermore, at least the reflec-
tance value can be set to the correct order of magnitude by adding/
subtracting a linear offset.

Incorrect Model

The sample used has to correspond to the model of an optically

thick sample (half-space reflection), i.e. no radiation, which has
been reflected on a rear boundary, may emit from inside the sam-
ple. If, e.g., the reflectance spectrum contains interference pat-
terns, the sample has certainly be too thin.

If the sample you use is not thick enough, roughen the sample to
avoid back reflection. Strictly speaking, the calculation of optical

Bruker Optik GmbH OPUS Reference Manual 783

 Chapt. 16 Appendix A

constants outlined before on the basis of the reflectance spectrum

is only valid in case of vertical incidence. Therefore, this kind of cal-
culation should only be used in case of measurements which have
been performed by using almost vertical incidence (10° reflection
unit).

Examples

KKT can be verified quite well by theoretical reflectance spectra

which have been acquired from the following oscillator model for
dielectric function:
2
    =  +     2    2 – v – iv rj   (B-11)
pj tj

With  pj ,  tj and  rj being the intensity, resonance frequency

and line width of the jth oscillator.   is a linear contribution to the
dielectric function. Based on the real and imaginary part of the
above model with the dielectric function  and  the real and
imaginary part of the refractive index
2 2 0 ,5 0 ,5
n =  0 ,5  + 0 ,5   +    (B-12)
2 2 0 ,5 0 ,5
k =  – 0 ,5  + 0 ,5   +    (B-13)

can be calculated. This yields to the reflectivity R (for vertical inci-

dence, optically thick sample) with
2 2 2 2
R = n – 1 + k   n + 1 + k  (B-14)

and the phase shift  with

2
 = arc tan  2k   n – 1 + k   (B-15)

784 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Figure 1 shows a reflectance spectrum  R  of NaCl, which has

been calculated by the following model parameters (3 oscillators,
with all  values being cm-1):

  (2.3)

j =1 j =2 j=3

 tj 164 233 254

 pj 284 60 40

 rj 5.5 28 16

The corresponding phase spectrum  Phi  , real and imaginary part

of the refractive index  N ,K  and dielectric function  , have
been calculated both on the basis of the model parameters (equa-
tions B-10 to B-14) and per KKT, as well as compared with each
other. In both cases the data points have been quite conform.

Bruker Optik GmbH OPUS Reference Manual 785

 Chapt. 16 Appendix A

786 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Figure 2 shows a measured reflectance spectrum of NaCl as well

as the refractive index and dielectric function both derived by KKT.
Compared to figure 1 considerable errors can be detected (strong
negative parts in the K and  spectra).

This erroneous result is mainly due to the inaccuracy of the mea-

sured spectrum in the range of the lower limit at about 340cm-1.

Bruker Optik GmbH OPUS Reference Manual 787

 Chapt. 16 Appendix A

Figure 3 is the same as figure 2, however, the experiment spec-

trum has been smoothed first, to get a more even band in the range
of the lower limit.

Afterwards, a linear offset has been deducted to reduce the inten-

sity in the range of the lower limit from 0.008 to the value of the the-
oretical spectrum R in figure 1 (0.002). Thus, the erroneous parts
of the K and  spectra could be substantially decreased as
shown in figure 3.

788 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Figure 4 shows the influence of extrapolation at the low-frequent

end of the spectrum. The theoretical spectrum of figure 1 has been
cut at 50cm-1 and transformed by KKT. Compared to figure 1 there
are insignificant amounts of negative parts and higher intensities in
the K and  spectrum, however, these effects are less distinctive
than in figure 2.

Bruker Optik GmbH OPUS Reference Manual 789

 Chapt. 16 Appendix A

Figure 5 and figure 6 are further examples to verify KKT on the

basis of the theoretically calculated reflectance spectra of SiO2 and
polystyrene (PS), analog to figure 1. The results received by KKT
are again quite conform. The following model parameters have
been used:

  (2.4)

j =1 j =2 j=3 j=4

 tj 1445 800 1075 1190

 pj 422 240 867 266

 rj 30 70 20 70

Polystyrene (5 oscillators):

   2 ,4 

j =1 j =2 j=3 j=4 j=5

 tj 542 699 763 1452.5 1493.5

 pj 57 100 65 40 50

 rj 60 7 12.5 5 10

790 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

Bruker Optik GmbH OPUS Reference Manual 791

 Chapt. 16 Appendix A

Figure 7 shows both a measured reflectance spectrum  Rxp  of

polystyrene  PS  and the absorption coefficient  Kxp  as well as
the absorptivity  Axp  calculated therefrom by KKT.

To enable a direct comparison both the theoretical reflectance

spectrum  Rth  and the spectra  Kth  and  Ath  , calculated there-
from by KKT, are also displayed. This comparison makes it possi-
ble to assess the error to be expected in practice.

792 OPUS Reference Manual Bruker Optik GmbH

 Chapt. 16

When calculating the absorptivity A from the absorption coefficient

k according to equation B-9 the intensities are scaled proportion-
ally to the wavenumber. This means that noise and interferences in
the reflectance spectrum in case of high wavenumbers additionally
increase by transformation.

Bruker Optik GmbH OPUS Reference Manual 793

 Chapt. 16 Appendix A

794 OPUS Reference Manual Bruker Optik GmbH

Index B
Beam Path 173
Black Body 296
Browser 4, 7, 13, 142
Numerics C
3D Window 146 Check Signal 169
Clone Entry 89
A Clone Original 89
Abcissa Conversion 335 Command Line Parameter 55
About OPUS 778 Compound Information 537
Access Control 11 Connecting to Spectrometer 51
Acquisition Mode 187 Convert Spectra 279
Add Information 117 Method 280
Analysis Report Correlation coefficient 504
Evaluation Results 566 Correlation mode 189
Generate 568 Crosshair 32, 548
Global Result Options 565 Curve Fit 386, 608
Multi Sample Report 563 Cut 271
Output 571
Sample-Specific Data 564 D
Set up Template 556 Data Block 48
Setting Options 558 Change 97
Spectrum Frame 559 Copy 96
Standard Template 570 Decimal 51
Structure 559 Derivative 286
Types 558 Dialog Box 7
Apodization 194, 300 Direct Command 199
Atmospheric Compensation 349 Drag & Drop 7
ATR Corection 329
Attach Video Image 113 E
Auto Sampler 239
Extended ATR Correction 329
Automatic Accessory Recognition
Extrapolation 325
696
ATR Accessories 702 F
External Accessory 701
Fiber Probe 704 File
Automatic Peformance Test 700 Scan 85
Averaging 341 File Name Extensions 53
Theory 343 Fourier Self-Deconvolution 313
Theory 316
Frequency Calibration 288

Bruker Optik GmbH OPUS Reference Manual

 Index

Frequency Range 40 Library

FT-IR Tutorial 778 Status 536
Logout 710
G Low Pass Filter 186
GRAMS 73
M
H Macro
H18 521 Compile 618
High Pass Filter 186 Debuggen 611
Hit Spectrum 537 Edit 612
Run 611
I Macro Converter 610
Macro Editor
Icons Adding Variables 615
Creating 739 Command Lines 613
Information Mask 121 Interface 612
Information View 143 Syntax Errors 613
InStep 74 Macro Structure
Instrument Status 5, 52 Editing 625, 627, 628, 633
Instrument Test Macro Wizard 619
Channel Setting 761 Make Compatible 276
Integration 400 Method 277
Integration Modes 402 Make Monotone 369
Interferogram to Spectrum 299 Material identification 507, 508
Interleaved Measurement 220 Material verification 507, 508
Inverse FT 309 Maximize All 545, 546, 547
Measurement experiment file 639
J
Measurement Parameters 178
JCAMP/OPUS Conversion 711 Menu
Customizing 741, 744, 745, 747
K Edit 109
Kramers-Kronig-Transformation Merge Spectral Ranges 344
320, 779 Minimum Hit Quality 533
Kubelka Munk 280 Mixture analysis 530
Moving Mean 368
L Multi Evaluation 469
Adding Method 477
LabJournal 100
Analysis Sequence 470
Language Parameter 61
Component 483
Laser Wavenumber 640
Expected Reference 476
Layer Thickness 516
First Steps 471
Theory 520
Formulae 479

OPUS Reference Manual Bruker Optik GmbH

 Index

Group Names 475 Energy Distribution 662

Method 470 Linearity 663
Next step QUANT 2 485 Photometric Accuracy 662
Report 494 Position 663, 674
Setup 472 Ratio 663, 674
Storing Method 492 Reproducibility 663
Test 493 Resolution 662
Variables 480, 494 Scan Time 662
Multi Sample Report 558, 569 Sealing 663, 674
Sensitivity 662
N Water Vapor 663
New Layout Wavenumber Accuracy 662
Creating 575 Overview Window 5
Spectral Frame 590 OVP
Noise Generation 367 Non-Ethernet Based Instru-
Normalization 273 ments 216
Method 274, 532 Resetting accessory in test
Min/Max 274 channel 706
Vector 275 Test Run 676
Test Spectra 678
O Trend Chart 688
OVP configuration
Offset Correction 275 Deleting 640
Online Docs 777 OVP test
Online Help 5 Status 677
Open Planner 766
Recurring Items 773 P
View Options 767, 769
OPUS Language 60 Paths 12
OPUS View 5 Peak Picking 444
OQ Test Interactive 449
Alignment 672 Theory 451
Energy Distribution 667 Phase Correction 193, 303
Linearity 673 Plot Layout
Photometric Accuracy 664 Creating 572, 578, 579, 580,
Reproducibility 674 582, 583, 584
Resolution 670 Icons 575
Scan Time 670 Spectrum Frame 585, 589, 592,
Sensitivity 665 593, 595, 596
Water Vapor 671 Table Frame 601, 603
Wavenumber Accuracy 668 Text Frame 597, 598, 600
OQ-Test 661 Pop-up Menu 7
Alignment 663 Post Zerofilling 310

Bruker Optik GmbH OPUS Reference Manual

 Index

PQ-Test Registering 726

Energy 649 Report
Energy Distribution 653 Output 571
Ice Band 655 Report Data 558
Interferogram Peak Amplitude Report Types 558
652 Rubberband Correction 254
Photometric Accuracy 659 Concave 254
Position 660
S/N Ratio 650 S
Sealing 656 Scattering Correction 254
Wavenumber Accuracy 656 Search algorithm
Preamplifier 184 Peak table 531
Preview Window 64 Spectrum correlation 531
Print Setup 606 Standard 530
Procedure Setup OVP 637
Edit 633 Shortcut 8
Run 634 Signal-to-Noise 438
Pull-down Menu 4 Theory 443
Pump Control 235 Single Peak Pick 544
Single Sample Report 558, 562,
Q 569
Quality Test 462 Smooth 282
QUANT Interactive 284
Analysis 434 Spectral Range
Setup Method 413 Deleting 529
QUANT Builder 426 Moving Interactively 528
Query Spectrum 537 Selection 174
Quick compare 497 Zooming In 30
Material identification 507 Zooming Out 29
Material verification 507 Spectral range
Query spectrum 510 File limits 502
Result 508 Spectrum
Quick Identity Test 458 Activating Crosshair 32, 33
Quick Print 572 Adding Annotations 34
Changing Color 33
R Copying 35
Radiometric calibration Copying All Spectra 35
Standard procedure 376 Crosshair 33
Raman Correction 292 Deleting Single Peak 36
Method 294 Editing Annotations 34
Reference spectra 498 Maximizing 31
Registered Window 148 More than one spectrum in

OPUS Reference Manual Bruker Optik GmbH

 Index

spectrum window 27 Algorithm 362

Performing Single Peak Pick 35 Structural Formula 537
Removing Annotations 35 Structure
Removing From Spectrum Attach 129
Window 33 Create 125
Scaling Ordinate 31 Edit 125
Shifting Curve 32 Structure Editor 127
Undoing Shift Curve 32 Structure Search
Spectrum Calculator 267 Internet Search 537
Spectrum correlation 531 Switch gain 185
Spectrum Display 542, 544, 754 Symmetric Fourier Transformation
Spectrum from Interferograms 324 319
Spectrum Search 526
Adding Spectral Range 528 T
Auto Subtraction 538 Temperature Control 218
Defining Spectral Range 527 Time Resolution 221
Defining Spectral Range Limits Title Bar 64
527 Toolbar 4, 8, 47, 141
Generating Library List 535 Creating 733
Libraries 533 Customizing 728, 731, 735,
Loading Library List 535 736, 737, 738
Removing Library List 535 Tooltip 8
Selecting Library 533 Trend Chart
Starting search by using diffe- Hiding Line 694
rential spectrum 538 Twister 229
Spectrum search Macro 233
Deleting spectral range 529
Moving spectral range 528 U
Parameters 529
User Database 713
Spectrum Subtraction 259
User Group 13
Interactive 262
User Interface 4
Spectrum Window 5, 26, 145
User Macro List 724
Activating Crosshair 32, 33
User Management 713
Axes 111
User Password
Deactivating Crosshair 33
Changing 721
Enlarging 27
User Record 11, 714
Fixing Size 27
Creating 714, 717, 719
Reducing 27
User Rights 13, 752
Split Interferograms 322
User Settings 751, 753, 758, 760,
Status Bar 5, 142
761
Stepper Motor 172
Straylight Correction 357

Bruker Optik GmbH OPUS Reference Manual

 Index

V
Valve Control 241
VisualBasic Script 82

W
Window
Cascade 150
Window Display 540
Wizard 8, 142
Workspace 8, 11
Close 775
New 774
Send 776

Z
Zerofilling 300

OPUS Reference Manual Bruker Optik GmbH