Operation Manual

Version 2.0.1
May, 2017
 Warranty, Exclusions and Limitations

CHOPIN Technologies warrants workmanship and materials to be free from defects for a
period of one year from the date of shipment.

Excluded from the warranty coverage are products a) which have been subjected to
mechanical, electrical or other misuse or abuse b) which have been disassembled or
repaired or attempted to be, by other than CHOPIN Technologies authorized servicing
agents.

The foregoing warranty shall be in lieu of all other warranties, expressed or implied, and the
Corporation expressly disclaims any warranty for merchant ability or fitness for a particular
purpose.

Unless otherwise agreed in writing by the Corporation, repairs and replacement parts
provided by the Corporation under its warranty shall be guaranteed only for the non-expired
portion of the original warranty on the repaired product.

The liability of CHOPIN Technologies to any purchaser or user of its products shall not in any
case exceed the cost of correcting defects in a product as herein provided and, upon
expiration of one year from the date of sale, all such liability shall terminate. In no event 2
shall the Corporation be liable for interruption of operations, loss of profit, or special or
consequential damages.

CHOPIN Technologies
20 avenue Marcellin Berthelot
92390 Villeneuve La Garenne – France

Phone: + 33 1 41 47 50 48

Email: [email protected]

Visit us on the web at www.chopin.fr

CHOPIN Technologies UScan Quick Start Guide Version 1.0.1

 Contents

Contents ....................................................................................................................................... 3
1 Introduction .......................................................................................................................... 5
1.1 Supported Hardware ..................................................................................................... 5
1.2 Scope of UScan Software ............................................................................................. 6
1.1 Accessory/Companion Programs ................................................................................ 6
1.4 Multi-Language Support ............................................................................................... 6
2 UScan User Interface............................................................................................................ 7
3 Configuration ........................................................................................................................ 9
3.1 Introduction ................................................................................................................... 9
3.2 Entering Configuration Mode ..................................................................................... 11
3.3 Scan Method Configuration........................................................................................ 11
3.3.1 Create a new Scan Method ................................................................................. 12
3.3.2 Rename a Scan Method ...................................................................................... 14
3.3.3 Edit a Scan Method ............................................................................................. 14 3
3.3.4 Delete a Scan Method ......................................................................................... 15
3.4 Calibration Method Configuration .............................................................................. 16
3.4.1 Create Calibration Method based on PRD, MLR or CVF file .............................. 16
3.4.2 Create a Conformity Calibration Method ............................................................ 23
3.4.3 Create an MLR Calibration Model ....................................................................... 29
3.4.4 Create a Calculated Variable Calibration Model ................................................ 32
3.4.5 Rename a Calibration Method ............................................................................ 37
3.4.6 Edit a Calibration Method .................................................................................... 38
3.4.7 Delete a Calibration Method ............................................................................... 38
3.5 Define Product Configuration ..................................................................................... 39
3.5.1 Create a Product .................................................................................................. 39
3.5.2 Rename a Product ............................................................................................... 47
3.5.3 Edit a Product ...................................................................................................... 48
3.5.4 Delete a Product .................................................................................................. 48
3.6 Global Settings Configuration .................................................................................... 49
3.6.1 UIF Settings ......................................................................................................... 49

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 3.6.2 Demo Setup ......................................................................................................... 50
3.6.3 LIMS Configuration ............................................................................................. 51
3.6.4 System Settings................................................................................................... 52
4 Routine Analysis ................................................................................................................. 52
4.1 Analyzing a Sample .................................................................................................... 53
4.1.1 Sample Analysis Flow ............................................................................................... 53
4.1.2 Results View ............................................................................................................. 54
4.1.3 History View............................................................................................................. 54
4.1.4 SPC View .................................................................................................................. 55
4.1.5 Spectrum View ......................................................................................................... 56
4.2 Sample Management.................................................................................................. 56
4.2.1 Sample Selection ...................................................................................................... 57
4.2.2 Sample Search .......................................................................................................... 57
4.2.3 Managing Sample Data ............................................................................................. 58
4.2.4 Exporting Data ......................................................................................................... 58
4.2.5 Exporting Spectra ..................................................................................................... 60
4.2.6 Deleting Samples ...................................................................................................... 61 4
4.2.7 LIMS Exports ............................................................................................................ 61
5 Diagnostics ......................................................................................................................... 62
5.1 TAS .............................................................................................................................. 62
5.1.1 TAS Instrument Status ............................................................................................. 62
5.1.2 TAS Alignment ......................................................................................................... 62
5.2 Instrument diagnostics ............................................................................................... 63
5.2.1 Lamp Health ............................................................................................................. 63
5.2.2 Instrument Health .................................................................................................... 63
6 Appendix ............................................................................................................................. 64
6.1 Glossary....................................................................................................................... 64
6.2 Calculated Constituent Expression Formula Guidelines ........................................... 66
6.2.1 Expression Formula Design ................................................................................ 66
6.2.2 Operators ............................................................................................................. 67
6.2.3 Functions ............................................................................................................. 68

CHOPIN Technologies UScan Quick Start Guide Version 1.0.1

1 Introduction

The UScan™ program serves as the primary user interface for routine quantitative analysis
applications for the CHOPIN Technologies Spectralab . The primary objective in the
development of the UScan software was to make it as intuitive and easy to operate as
possible without compromising any of the vital features or functionality needed for
demanding NIR analysis.
UScan is designed with a graphical interface for easy operation via touch screen. This
design makes for easy training and operation in both laboratory and at-line process control
operations.
Configuration of the software is protected with a password for secure and reliable operation
in multi-user environments. The configuration is based on re-usable blocks of settings
termed Methods, which are versioned and stored in a database. These settings are linked to
each sample record for complete traceability.
UScan also supports TAS™; True Alignment Spectroscopy technology. TAS is a technology
that allows a customer to recalibrate the instrument to factory alignment using certified
reference standards based on first principles. As such, TAS based instruments are
inherently spectrally compatible with each other and future instrumentation, making data
collection future-proof.
5
This first section of the manual provides introductory information about the UScan product.
Section 2 provides a description of the components of the main UScan screen and an
overview of the fundamental capabilities of the UScan program. Section 3 describes various
UScan configuration options which are typically customized according to application
requirements, user preferences, instrument model, and sampling accessories being used.
Section 4 describes routine operation and diagnostic tests using the UScan program.
Section 5 provides information on miscellaneous other aspects of the software such as
language selection and practical guidelines. Additional useful information can be found in
the Appendix sections. Please note that detailed information about a particular model of
Spectralab spectrometer and its accessories can be found in the operation manual that
corresponds to it.

1.1 Supported Hardware

UScan is primarily intended to be run on the internal computer embedded in Spectralab and
has been developed to work in conjunction with the Spectralab touch screen (a standard
feature of all Spectralab instruments). Additionally, UScan can be installed on a Windows®
computer and operated in Demo mode for training and demonstration purposes. Please
see the appendix for installation and configuration instructions for demo installations.

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1.2 Scope of UScan Software

It is important to recognize that, while UScan is a vital part of successful implementation of

the Spectralab family of instruments, it is not used for developing new calibrations.
Calibration development is ordinarily done on a separate computer with a chemometric
software package or calibrations are obtained from outside sources. The role of UScan is to
use pre-existing quantitative calibrations (or models) to compute and report analytical
results. UScan compatible calibrations can be developed in UCal™, a comprehensive
chemometric package available from CHOPIN Technologies. It can also utilize MLR
calibrations generated/available from various sources, often including calibrations that were
originally developed for use with filter-based NIR analyzers.
UScan serves the additional important role of measuring and storing spectra that can be
utilized by UCal for purposes of developing new calibrations, or by 3rd party calibration
providers. All sample records and spectra are stored in the UScan database and can be
exported in a variety of formats for calibration development and / or external predictions.

1.1 Accessory/Companion Programs

6

As mentioned above, UCal chemometric program is an optional program that can be

purchased and used to create, maintain and validate custom calibrations. Please ask your
CHOPIN Technologies account manager for more information

1.4 Multi-Language Support

Although English language text is used in the screen images in this manual, UScan supports
the display of text in a number of additional languages. As this is the first version of UScan,
translated versions of the software are in progress. Please check with your local distributor
for information on translated versions.

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2 UScan User Interface

UScan is designed around a central graphical user interface (UI) that can easily be operated
with a touch screen for routine operations. Sample analysis and routine diagnostics are
performed from the main UI, with configuration and other advanced operations accessible
behind a password protected icons.

The main UI is presented below, along with a description of its function. Each item is
described in detail in later sections of this manual under the Configuration and Operation
sections.

Descriptions

Section Icon Description

Status Product Active Product Name
Cup Type Required Cup Type

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 UScan Help

Configuration

Quit UScan

Views Result View

History View

SPC View

Spectrum View

Operation TAS

8
TAS Diagnostics

Lamp Health

Choose Product

Scan Sample

Print Sample

Instrument Health

Scan Reference

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3 Configuration

3.1 Introduction

Configuration of UScan for routine analysis involves creating re-usable blocks of settings
termed Methods and combining these methods to create Products. The Products are then
selected and used for routine analysis.

There are two types of methods – Scan Methods and Calibration Methods.

Scan Methods contain settings related to sample cup type and all the scanning settings that
are used to analyze that cup type. UScan installations generally have at least one Scan
Method per cup type that they use.

Calibration Methods contain settings related to a calibration model and how the calibration
model should be used. The calibration model might be a quantitative PLS based model, an
MLR model, or a Calculated Constituent model.

Every Product must have one Scan Method and at least one Calibration Method. More than
one Calibration Method can be combined into one Product.

This modular design for Product configuration has several implications. First, it allows for 9
easy creation and maintenance of important analytical settings. For example, the settings
for using a Forage cup can be created once, saved in a Scan Method and re-used for all
products that require this cup type. If a change is needed to the settings for the Forage cup,
the Scan Method can be updated, and all products using this Scan Method will be
automatically updated with the new settings.

Secondly, it allows for easier tracking of all settings used create each method, and likewise
link these settings to each sample record. UScan creates unique versions when a Method is
created or updated, and links the Methods and Versions to each sample record. In this way,
each sample record can be linked to all analytical settings that were in place at the time of
analysis for a completely traceable analytical record.

A diagram of Product Configuration is below:

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3.2 Entering Configuration Mode

To enter configuration mode, select the icon from the upper right section of the main
user interface (UI). A password dialog will open.

The default user and password are both ‘admin.’ The advanced configuration screens will
now be available from buttons across the top of the main UI.

11

To log out from the administrator user, press the icon present in the upper right of the
UI.

To return back to the routine analysis screen, press the Main button from the top buttons
present in the main UI.

3.3 Scan Method Configuration

The Scan Method contains all of the analytical settings that an instrument needs to collect a
spectrum from a sample. These settings include cup type, cup rotation settings, reference
method and settings, and sample scan settings. In general, most installations have one
Scan Method per cup type.

The Scan Method settings are versioned, meaning that each time a Scan Method is changed,
a new version is created. All Sample records are traceable to the Scan Method and version
in place at the time of analysis for complete traceability.

Below are the settings for the Scan Method configuration. The actual options present are
specific to the instrument configuration, and thus not all options might be present in your
installation.

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3.3.1 Create a new Scan Method

To create a new Scan Method, press the Add button. Place a name for the Scan
Method in the dialog below. It is suggested that the name refer to the cup type being
configured.

Configuration of a Scan Method should follow this order:

3.3.1.1 Sample Cup Settings

Adapter Type
12
Select the Adapter Type that describes the sample cup adapter that is present on the
instrument. A list of compatible cup types will be displayed based on the adapter chosen.
Depending on the adapter selected, additional settings for cup movement might be
available.

Cup Type

Next, select the Cup Type appropriate to your sample and calibration. In general, finely
ground samples can be analyzed in smaller cups like ring cups and powder cups, while
coarse or unground materials should be analyzed in larger cups with more surface area to
reduce sampling errors. Please consult your CHOPIN Technologies specialist for further
information.

Cup Rotation Settings

Depending on the Adapter type and Cup chosen, Cup Rotation, Sample Steps and / or Platter
Speed might be displayed. In general, Stepped rotation with 1 rotation and 12 scans is
recommended. Please consult with your CHOPIN Technologies specialist for specific
recommendations.

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3.3.1.2 Scan Settings
The Scan Settings determine the number of sample scans, reference scans and reference
method used to collect the sample spectrum.
13
Reference Method

A reference every sample means that the reference is scanned before every sample. This
method is good in some situations where the environment is changing but makes the
scanning sequence longer. A timed reference setting is best in situations where the
environment is stable as the scanning sequence is shorter.

Scanning Parameters

The Number of Sample Scans refers to the number of complete scans that are averaged to
make up a sample scan. Increasing the number of scans lengthens the scanning sequence
but lowers the noise. It is recommended to use the default value here unless circumstances
dictate otherwise.

Number of Scans for Internal Reference refers to the number of reference scans that are
averaged to make up the reference scan. This is set in the Global Settings, System Settings
and is listed here only as an indication.

Internal Reference Expiration Time (min) is only used when the Timed reference method is
selected, and is also set in the Global Settings, System Settings.

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When finished, press the Save button to save the Scan Method

3.3.2 Rename a Scan Method 14

To rename a Scan Method, right click on the name in the list at the right and choose Rename
Scan Method.

Enter the new name and press Save .

3.3.3 Edit a Scan Method

Scan Methods may be edited, with the new settings being used for all new sample analysis
based on Products using that method. Editing a Scan Method will create a new version.
Some important considerations of editing a Scan method are:

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  All Products that are configured to use this Scan Method are immediately updated to
use the newest version of the Scan Method.
 All Samples scanned are traceable to the specific version of the Scan Method that
was in place at the time of analysis.

To edit a Scan Method, select the method desired from the list on the left of the screen and

press the Edit icon. The warning below will indicate that a new version is being created.
Press OK.

The Scan Method dialog will now be editable. Make the desired changes and press the Save

button to save the updated Scan Method. Pressing the Cancel button will cancel the 15
edit session and leave the Scan Method as it was.

3.3.4 Delete a Scan Method

To Delete a Scan Method, select the Scan Method from the list at the left of the screen and

press the Delete icon. The warning below will ask you to confirm the deletion:

Press OK.

If the Scan Method is currently part of a Product configuration, it cannot be deleted and the
following warning will be displayed:

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3.4 Calibration Method Configuration

The Calibration Method contains all of the analytical settings that an instrument needs to
predict constituent values from a sample spectrum, calculate additional constituent values
from available data, or perform a qualitative conformity analysis on a sample spectrum.
Every Product must have at least one Calibration Method, but more than one Calibration
Method can be combined into a Product to produce the desired analytical results.

Quantitative calibration Methods can be based on PLS (Partial Least Squares) calibrations
present in a .PRD file or an MLR (Multiple Linear Regression) calibration present in a .MLR
file. Calculated Variables can be configured and are found in CVF files. Qualitative models 16
for performing a conformity test are present in PRC files. For more information on these
calibration types, please see the Glossary in the Appendix.

Below are the settings for the Calibration Method configuration.

3.4.1 Create Calibration Method based on PRD, MLR or CVF file

PLS calibrations in PRD files are the most common Calibration Method input type. PRD
calibrations include CHOPIN Technologies calibrations, calibrations from CHOPIN
Technologies partners, and custom calibrations created with UCal. MLR files are manually
created linear calibrations, usually transferred from filter instruments. CVF files are
Calculated Variable equations. Each type of file returns one or more constituent results.

To create a Calibration Method, press the Add button. Place a name for the Calibration
Method in the dialog below.

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3.4.1.1 Calibration File
The first tab of the Calibration Method dialog is the Calibration File. Press the Browse

button to browse in your PRD calibration file and then give it a description that is
informational.

NOTE: If you are configuring a Calibration Method based on an MLR or CVF model, please
change the file extension filter to the proper extension and select the appropriate file.

17

3.4.1.2 Constituents
Click on the Constituents tab to verify the Constituent names. If the incoming constituents
have already been registered in UScan, they will be matched automatically. If any of the

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incoming constituents are new, UScan will automatically create constituents from the
constituents present in the PRD.

The dialog below shows the incoming constituents from the PRD and how they are matched
to the constituents registered in UScan.

18

3.4.1.3 Editing Constituents

Each constituent is registered in UScan and has properties that include Display Name,
Decimals, Display Priority, and whether to force negative predicted values to zero. These
properties are global to UScan and will affect all products configured in the software.

The properties for constituents are accessed from the Edit icon on the Constituents
tab.

Display Name – the name displayed in the UScan program and for reporting. The display
name can be useful when working in languages other than English or for customizing the
displayed constituent name as desired, for example Fat to Oil.

Decimals – the number of decimals displayed in UScan.

Display Priority – the highest priority constituents appear to the top and to the left when
displayed in UScan. Priority can also be used in reports.

Force Zero – negative numbers will be displayed as 0. This can be useful for constituents
that routinely have values close to 0.00 to prevent negative numbers from being displayed.

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3.4.1.4 Moisture Correction
The moisture correction tab allows a user to display constituent values in a moisture basis
that is different from the moisture basis in the PRD file.

NOTE: For a definition of moisture basis, dry matter, as received etc., please see the
Glossary in the Appendix.

For example, many calibrations are made using reference values having a dry matter basis.
This means that the constituent values are expressed as a percentage of the sample weight
with all of the moisture removed. Dry matter based values can be useful as the constituent
values remain constant across various sample moistures. However, many customers need
to know how much of a constituent is in the sample as it is or as received. Moisture
correction allows you to display the constituents in the desired moisture basis.

To use moisture correction, the check box at the top of the dialog must be checked. This
enables the moisture correction dialog. 19

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The following guidelines apply to moisture correction:

 Any calibration moisture basis can be displayed as any other moisture basis
 There must be a Moisture constituent or a Dry Matter constituent present to base the
correction on.
 Constant Moisture with a value of 0 is the same as Dry Matter

To configure moisture correction, please follow the instructions below:

1) Determine which constituent will be used to base the corrections on. This must be a
moisture or a dry matter constituent. Locate this constituent in the list of
constituents and select the proper Input basis and Output basis. If it is a moisture
constituent, select Moisture Variable in both input and output. If it is a dry matter
constituent, select Dry Matter Variable in both input and output.
2) For all the constituents that you wish to be corrected, use the dialog to select the
proper Input Basis, Input Moisture (if Constant Moisture is selected), Output Basis
and Output Moisture (if Constant Moisture is selected).
3) Some constituents should not be corrected. An example might be a property like
digestibility or hardness. The input and output basis should be the same for these
constituents.

An example converting from Dry Matter (Constant Moisture = 0) to As Received is below:

20

An example converting from As Received to Dry Matter (Constant Moisture = 0) is below:

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Finally, it is possible to convert from one constant moisture basis to another, for example
from dry matter to 12.5% moisture as shown below:

21

3.4.1.5 Transfer File

A transfer file is a file that corrects or standardizes the raw spectra from this instrument to
match that of a master instrument where a calibration was developed. As a result,
calibrations transfer with little or no biases and outlier indications are more precise.

NOTE: UScan stores spectra unstandardized or uncorrected. When exporting spectra

collected with a configured STF transfer file, the user can export the spectra data with or
without the standardization applied.

A transfer file is created after scanning standards on both your instrument and the master
instrument. The collected spectra are compared, and a standardization file containing the
correction is saved with an extension of .STF. Please follow the calibration originator’s
instructions on the use and scope of the STF file.

Transfer files are added to the Calibration Method. Place a check mark in the Use Transfer
File check box, browse in the STF file and enter a description. The transfer file will then be
used during routine analysis.

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3.4.1.6 Outlier Limits
Outlier limits determine the acceptable range of various outlier indicators that are calculated 22
during sample analysis. The outliers are various statistical calculations that determine how
the unknown sample compares to the samples that were used to create the calibration.
Each outlier has a Warning value and an Action value and these are used to determine pass /
fail indications in the Result view and History view.

The types of outliers are listed below (Please see the Glossary in the Appendix for more
information):

Term Outlier Name Description

GD Global Distance An indication of how well the spectrum of the
unknown compares to the calibration samples
ND Neighbor Distance An indication of how close the spectrum of the
unknown sample is to its nearest spectral neighbor
in the calibration set.
T T Statistic Indicates how the predicted value for that
constituent compares to the range and distribution
of reference values used in the calibration set.
X X Residual An indication of how well the spectral variation in
the calibration set can model or explain the
unknown spectrum

When a PRD calibration is imported, default values are entered for all of the outlier types. It
is recommended that these values be used initially as outlier criteria. The Outlier limits may

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be changed at any time by editing the Calibration Method, and double clicking in the table
below.

23

When the above tabs of the Calibration Method are properly filled in, press the Save
icon to save the Calibration Method.

3.4.2 Create a Conformity Calibration Method

Conformity models test then unknown Sample’s spectrum against a training library and
determines the similarity or conformity to the library. Sophisticated math treatments can
yield very powerful models that can either be used to determine if a sample fits the profile of
a “Good Sample” or a “Bad Sample.” Models can also be used to detect adulteration or
contamination of a sample by some unknown material.

As Conformity Calibration Methods do not return a standard quantitative result, the

configuration of the Method is slightly different. Please follow the steps below to configure
a Conformity Calibration Method:

To create a Calibration Method, press the Add button. Place a name for the Calibration
Method in the dialog below.

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3.4.2.1 Calibration file
The first tab of the Calibration Method dialog is the Calibration File. Press the Browse

button to browse in your PRD calibration file and then give it a description that is
informational. 24
NOTE: Please change the file extension filter to the proper extension (PRC) and select the
appropriate file.

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3.4.2.2 Constituents
Click on the Constituents tab to verify the Constituent names. The constituent listed will be
the name given to the Conformity model. You can change the Display Name if desired by

clicking the Edit icon on the Constituents tab.

At the bottom of the Constituents tab, there are radio buttons to select the Conformity Value
to use for the Conformity test. This is a very important setting and will determine what value
will be used globally in UScan for the Conformity evaluations. This is the value that will be
displayed on the Result and History Views, and this is the value that will determine the
Sample PASS or FAIL based on the Product Limits set. The two options are:

Probability Value: A Probability value gives the probability that your newly scanned sample is
the same as some standard value. Intuitively, a probability of 1.0 would indicate that your
unknown will CERTAINLY be a match for the standard value.

Standardized Value: In the Standardized value system, perfection occurs when the
standardized value is 0.0. Values above (or below) zero, are presented in standard deviation
terms.

Click to select the Conformity Value to use. Depending on your application and users, you
might prefer Probability Value or Standardized Value. Please ask your CHOPIN
Technologies Product Specialist if you have questions.
25

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3.4.2.3 Moisture Correction
Moisture correction is not used for Conformity evaluations.

3.4.2.4 Transfer File

A transfer file is a file that corrects or standardizes the raw spectra from this instrument to
match that of a master instrument where a calibration was developed. As a result,
calibrations transfer with little or no biases and outlier indications are more precise.

NOTE: All Calibration Methods in a Product must have the same Transfer file or not use a
transfer file at all.

A transfer file is created after scanning standards on both your instrument and the master
instrument. The collected spectra are compared, and a standardization file containing the
correction is saved with an extension of .STF. Please follow the calibration originator’s
instructions on the use and scope of the STF file.

Transfer files are added to the Calibration Method. Place a check mark in the Use Transfer
File check box, browse in the STF file and enter a description. The transfer file will then be
used during routine analysis.

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3.4.2.5 Default Limits

Default limits have a special use for Conformity Calibration Methods. These are the
suggested limits for either Probability or Standardized Values that should be used as
Product limits to determine Pass or Fail. These values are placed in the PRC model when
the model was created and reflects the calibration sample variation that was present at the
time of calibration.

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Based on your Conformity Value selection on the Constituents tab, write down the
suggested Warning and Action limits and enter these in the Define Product, Product Limits
tab. You might need to adjust the values slightly to obtain your desired sensitivity and
detection limit.

An example dialog is below.

27

When the above tabs of the Calibration Method are properly filled in, press the Save
icon to save the Calibration Method.

3.4.2.6 Special Considerations for Product Limits for Conformity Values

When defining a Conformity Calibration Method, the user must select to use either a
Probability Value or a Standardized Value. This value is then used globally in UScan for
evaluating the Conformity test. These two types of values have different evaluations and
thus must be entered into the Product Limits differently.

Probability Value

A Probability Value range is 0 to 1, with perfection being 1. Thus a Warning Limit must be
less than 1, with an Action Limit lower than the Warning Limit. Probability Value Limits are
added using the Lower Action and Lower Warning Limits as shown below.

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Standardized Value

The range of Standardized Value results from a Conformity test is 0 to ∞, with 0 being
perfection. Thus a Warning Limit must be above 0, with an Action Limit above the Warning 28
Limit. Standardized Value Product Limits are added using the Upper Warning and Upper
Action Limits as shown below.

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3.4.3 Create an MLR Calibration Model
UScan can manually create MLR (Multiple Linear Regression) models and use them to
predict constituent values. MLR calibrations are typically from filter-based instruments,
where the response from a small number of filters are used in a linear equation such as the
one below:

𝐶 = B0 + B1X1 + B2X2 + B3X3 …BiXi where i = # of filters or coefficients

The wavelengths and coefficients of the calibration must be known to create an MLR
calibration.

These MLR calibrations define a relationship between a spectrum and a constituent value
based on only a few datapoints and frequently must be modified with a bias and / or slope
correction to obtain good values. Filter instruments also have a large degree of variability
with the wavelength and quality of light passing through them. It is recommended that full
spectrum PLS calibrations be created for more difficult constituents and more robust
predictions.

Creating an MLR Calibration Method involves 2 steps: Creating the MLR File and then
creating the Calibration Method to use that file.

To create an MLR Calibration file, please follow the instructions below.

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3.4.3.1 Create MLR File
From the Calibration Method tab, click the Model Types button.

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Press the New Button to start a new MLR calibration.

Click to select an existing Constituent name, or enter in a new Constituent name and press
Add New Constituent.

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Added Constituents can be modified with Decimals, Display Priority etc.

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The dialog below will open to create the MLR calibration. Press the Add button to add
in a term to the calibration. Click in the table to edit the wavelength and coefficient as
shown below. Continue adding terms as needed, and finish by adding in the Intercept Value.
31

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Press the icon and enter in a name for the MLR model as shown below.

It is recommended that you save the file in the default C:\Unity\models directory. Save the
file with a .MLR extension. The MLR calibration is now ready for configuration in a
Calibration Method.

3.4.3.2 Configure an MLR Calibration Method

Configuring an MLR Calibration is the same as with a PLS PRD models with the exception of
32
Outlier Limits. As the MLR calibration is based on only a few wavelengths, outlier
identification is not possible and thus there are no limits. Please follow the steps in CREATE
CALIBRATION METHOD BASED ON PRD, MLR OR CVF file to configure a Calibration Method
based on the MLR file.

3.4.4 Create a Calculated Variable Calibration Model

Calculated Variables are models that allow mathematical and / or logical evaluations of
existing predicted constituent values in a product. Examples where calculated variables are
useful include:

 Calculations for sample properties like Energy that are based on other constituent
values
 Evaluations of constituents for further processing ie if a constituent is below a
threshold then apply a correction factor. These are useful for forage evaluations and
other applications
 Estimating growth rates or potentials
 Displaying additional moisture bases on the results screens

Creating a Calculated Variable Calibration Method involves 2 steps:

1. Creating the CVF (Calculated Variable File) and

2. Creating the Calibration Method to use that file.

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3.4.4.1 Create CVF File
To create a CVF file, please follow the instructions below.

From the Calibration Method tab, click the Model Types button.

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Click to select the Calculated Variables tab, then press the Select button as shown below to
select the name of the Calculated Variable result. To edit an existing CVF file, press the

button and browse in the existing CVF file.

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In the dialog below, select the Constituent name for the Calculated Variable. If the desired
name is not present, enter the name in the text box at the top and press Add New

Constituent. Press the save button to Save your selection.

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Now that the Name of the Calculated Variable is set, the constituents used in the calculation

must be selected. Press the Add button and select the Constituents from the dialog
below. Multiple constituents can be selected by holding down the <ctrl> key. An example is

shown below. Press the Save button to Save your selection.

35

The selected Constituents will be present in the table to the left. These are the constituents
that are available for building the equation. It is recommended that you double click the Test
Value column for each constituent and place an example value as shown below. These
values will be used to test the equation. Choose values that make the result easy to predict.

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Finally, create the expression. Double click in the Constituent table or the Function table to
enter the selection in the formula. Enter in numeric values from the keyboard.

NOTE: Decimal values must be added with a . period as the decimal. For detailed guidelines
on syntax for numeric and logical expressions, please see the Appendix 6.1 Calculated
36
Constituent Expression Formula Guidelines.

Note the Result value in the lower right as you are creating the equation. If the expression is
invalid, an error will be displayed. Make sure that the result is what you expect based on the
Test Values that you entered above.

When the equation is complete, press the icon and enter in a name for the CVF model
as shown below.

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The CVF file is now saved and ready to be incorporated into a Calibration Method.

3.4.4.2 Configure a CVF Calibration Method

Configuring an CVF Calibration is the same as with a PLS PRD models with the exception of
Outlier Limits. As the CVF calibration is based on calculations between constituent values,
outlier detection is not possible and thus there are no limits. Please follow the steps in 37
CREATE CALIBRATION METHOD BASED ON PRD, MLR OR CVF file to configure a Calibration
Method based on the MLR file.

3.4.5 Rename a Calibration Method

To rename a Calibration Method, right click on the name in the list at the right and choose
Rename Calibration Method.

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Enter the new name and press Save.

3.4.6 Edit a Calibration Method

Calibration Methods may be edited, with the new settings being used for all new sample
analysis using that method. Editing a Calibration Method will create a new version. Some
important considerations of editing a Calibration method are:

 All Products that are configured to use this Calibration Method are immediately
updated to use the newest version of the Calibration Method.
 All Samples scanned are traceable to the specific version of the Calibration Method
that was in place at the time of analysis.

To edit a Calibration Method, select the method desired from the list on the left of the screen

and press the Edit icon. The warning below will indicate that a new version is being
created. Press OK.

38

The Calibration Method dialog will now be editable. Make the desired changes and press
the Save button to save the updated Calibration Method. Pressing the Cancel button will
cancel the edit session and leave the Calibration Method as it was.

3.4.7 Delete a Calibration Method

To Delete a Calibration Method, select the desired method from the list at the left of the

screen and press the Delete icon. The warning below will ask you to confirm the
deletion:

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If the Calibration Method is currently part of a Product configuration, it cannot be deleted
and a warning will be displayed.

3.5 Define Product Configuration

A Product is the collection of settings and calibrations that a UScan user selects to analyze
a sample. The Product was designed to be a versatile container that would allow users to
create custom configurations of a wide collection of settings yet be nimble to maintain and
use.

A Product must have one (1) Scan Method, and one (1) or more Calibration Methods. These
methods may be updated individually, or be swapped in and out during Product updates.

When a sample is analyzed, all the settings in place at the time of analysis are traceable to
the sample record in the database.

When a Product is saved, it may be placed in a Main Category, or in custom categories that
allow Products to be placed in logical groups for more intuitive use by routine operators. All
Products and Categories have associated icons for easy operation with a touch screen.
Users can choose from an included library of icons or import their own image files.

Below are the settings for the Product configuration.

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3.5.1 Create a Product

To create a Product, press the Add button. Place a name for the Product in the dialog
below.

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Press Save to continue creating the Product.

3.5.1.1 Add Scan / Calibration Methods

The Add Scan / Calibration Methods screen will list all of the Scan Methods and Calibration
Methods registered in UScan. Click to highlight the Scan Method and Calibration Method(s)
you wish to be part of this product. The highlighted methods will be configured with the
Product.

NOTE: There must be exactly one (1) Scan Method and one (1) or more Calibrations
Methods in each product. If more than one Calibration Method is configured, the following
rules apply:

 All Constituent names must be unique. It is not valid to add in Calibration

Methods that have the same constituents.
 All Calibration Methods must have the same Transfer File settings. Thus all
Calibration Methods must have no transfer files or use the same transfer file
settings.

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3.5.1.2 Product Settings

Settings on this tab determine how the samples are identified, if sample re-packs should be
used, and if the data should be exported to an external system such as a LIMS.

The following options are available for Sample Naming conventions:

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Enter Name for Each Sample – System will prompt the user to enter a sample name prior
to each sample measurement. If this option is selected, then the “Clear Entry for Each
Sample” check box immediately below it will become available for use. If checked, then the
“Sample Name” and “Sample Comment” fields will be cleared when a new sample is
analyzed in preparation for entry of a new sample name and comment. If not checked, then
the previously-entered sample name and comment will persist (for editing). The latter is
advantageous if sample names are similar and it is easier to edit the previous name than to
enter the entire new name for a new sample. If global sample naming is enabled, having this
box checked will have no impact on the sample name but it will cause the sample comment
field to be cleared prior to each analysis.

Use Date and Counter – A field is provided to the immediate right of this option to enter the
initial counter value. A name will be automatically generated using a date code prefix
followed by the next value in the counter sequence. The date is formatted according to the
“Short Date Format” configured within the Date tab of the Windows Control Panel’s Regional
Options. Any “/” characters within the date are replaced with the “-” character. InfoStar will
automatically reset the counter to 1 when generating the name of the first report file for a
new day. The maximum value for this counter is 999999. Example sample number would
be “06-03-2010_1” for the first sample analyzed on the date of June 3, 2010 with a regional
“Short Date Format” of MM/dd/yyyy or MM-dd-yyyy.

Use Base Name and Counter – Allows a base name to be specified, and provides a
counter that will automatically increment and append to the base name. A field is provided 41
to the immediate right of this option to enter the initial counter value. A field below is
provided for entry of the base name. For file and/or sample name sorting purposes, it is
sometimes helpful to set the counter to a large value, such as 1000. This will cause the next
8999 measurements to have names with the same number of characters. The maximum
value for this counter is 999999.

Sample Full Name – If one of the automatic sample naming schemes is in use, this
provides an example of what the name of the next sample in the sequence will be. If “Enter
Name for Each Sample” is selected, then this field will indicate “Manual Entry”

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Enable LIMS Output
42
Place a check mark in this field to export Sample data based on the LIMS configuration in
the 3.6.3 Global Settings section.

Enable Repacks

Repacks are useful with inhomogeneous samples. If the product is inhomogeneous,

unground, or coarsely ground, then accuracy may be improved by running multiple repacks
(i.e. two or more repeated packs of the sample cup). Repacks allow an operator to place
multiple subsamples on the instrument, and the software will report a result based on all the
repacks.

If a value of three were used for this setting, then the final spectrum would be an average of
the three spectra measured, one per repack, and the final results for the sample would be
the average of the three separate NIR predictions, one corresponding to each repack.

NOTE: The reported value for a repack sample might be slightly different than what would
be predicted using the calibration and the average spectrum because the reported value is
based on an average of the predictions.

3.5.1.3 Slope / Intercept

Slope and intercept values are maintained at the Product level in UScan. This allows for fine
tuning of each Product if desired.

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To enter a simple bias, keep the slope value as 1.0. This value should be the difference
between the reference value and the predicted value (Ref – NIR).

NOTE: Slope adjustments have a significant and sometimes unexpected effect on predicted
values and are rarely needed in most NIR installations. Please contact a CHOPIN
Technologies product specialist if it appears that you require a slope adjustment.

To enter a bias, double click on the Intercept field next to the Constituent name and enter the
bias value.

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3.5.1.4 Product Limits

Product Limits are constituent values that define the range of acceptable values for the
sample and product to pass. Product Limits are used in the Result View, History View and
SPC view to flag samples as passing or failing the Product Limit specifications. Finally, the
Product Limits affect the scale of the y-axis in the SPC view. If no limits are entered, the SPC
view y-axis always starts at y = 0.

There are 5 Product Limits:

Product Limit Definition

Lower Action Constituent values below this value cause the sample to fail.
Lower Warning Constituent values below this value are flagged as a warning.
Target The target value for the product.
Upper Warning Constituent values above this value are flagged as a warning.
Upper Action Constituent values above this value cause the sample to fail.

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Enter the appropriate values in the table for Product Limit evaluations to be performed.

NOTE: Conformity Values have special rules for Product Limits. Please see 3.4.2.6 Special
Considerations for Product Limits for Conformity Values for more information.

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3.5.1.5 Display Parameters

The Result View can be customized to display just the predicted values or to include outlier
and other indicators. The Display Parameters are saved as a set that can be then selected
and used for other Products. When a Display Parameter set is updated, all linked Products
are updated.

To select a Display Parameter set, click Edit icon. The dialog below will open.

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Click to select the Display Parameter set desired. To create a new Display Parameter set,

press the Add button and enter in a name for the Display Parameter set. Place a check
45
mark in the checkboxes of the items you wish displayed. Press Save to save the
Display Parameter set.

For an explanation of each statistical term, please see the Glossary in the Appendix.

3.5.1.6 UIF Field Selection

UScan allows for a custom set of User Information Fields to be configured for each Product.
User Information fields are used to track Sample information known at the time of analysis
and that may be useful in printouts or reports.

Place a check mark in the check boxes next to the UIFs that you wish to have linked to this
Product.

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3.5.1.7 Groups
UScan uses both an icon and a text description to identify Products for quick, intuitive use 46
on the touch screen display. Additionally, Products may be grouped in Categories for ease
of use during routine operations.

Product Categories

UScan has a Main product category that can be used to organize Products. If the UScan
installation is to have many Products, it might be useful to create additional categories. For
example, a flour mill might want to have a category for finished flours and a category for by-
products.

To select the Category, simply click to highlight the desired category.

To add a Category, press the Add button and enter a name for the Category. Browse in

an image icon file and press Save .

UScan has a library of typical Category images in C:\Program Files\Unity

Scientific\UScan\Icons\Category that may be used. Alternatively, files of JPG, GIF or PNG
may be browsed in and used.

Product Image

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UScan has a default library of typical Product images loaded in the database. Click to select
one of these images. For additional options, alternate versions of the default icons are
available in C:\Program Files\Unity Scientific\UScan\Icons\Product or image files of JPG,

GIF or PNG may be browsed in and used. To add a Product image, press the Add
button and enter a name for the Product Image. Browse in an image icon file and press

Save .

47

Once the category and image are selected, the Product can be saved and is ready for routine
analysis.

3.5.2 Rename a Product

To rename a Product, right click on the name in the list at the right and choose Rename
Product.

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Enter the new name and press Save .

3.5.3 Edit a Product

Products may be edited, with the new settings being used for all new sample analysis.
Editing a Product will create a new version.

To edit a Product, select the Product desired from the list on the left of the screen and press

the Edit icon. The warning below will indicate that a new version is being created.
Press OK.
48

The Define Product dialog will now be editable. Make the desired changes and press the

Save button to save the updated Product. Pressing the Cancel button will cancel the
edit session and leave the Product as it was.

3.5.4 Delete a Product

To Delete a Product, select Product name from the list at the left of the screen and press the

Delete icon. The warning below will ask you to confirm the deletion:

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WARNING: Deleting a Product will also delete the samples analyzed with that Product. Do
not delete a Product containing sample data you wish to keep.

3.6 Global Settings Configuration

The Global Settings tab contains settings that have a program-wide effect on the
configuration of UScan.

3.6.1 UIF Settings 49

User Information Fields or UIFs are accessory information fields that can be used to track
additional Sample information beyond the sample number. An example might be a
Purchase Order, technician, production line, retest, supplier, shift etc. UIFs are stored with
the Sample record and can be exported to reports, printouts or an external LIMS.

UScan has 8 UIFs available, and the configuration of each one is the same. Products can
then be configured to use any combination of the 8 UIFs, depending on need. Each UIF can
be made a required field, meaning that the Sample record cannot be saved until the operator
fills in that UIF. Making a UIF required ensures that the field is filled out with every sample
analyzed.

UIFs can be configured in two ways: Manual Entry and Select Values. The examples below
explain each one. Each UIF needs to be configured and saved individually.

Manual Entry

UIFs configured for manual entry present a text box for the user to fill in. These fields are
useful to capture information that is unique or always changing, like a Purchase Order or
Sales Order.

To configure a UIF for manual entry, simply click Manual Entry and fill in the name as shown
below. If this field is to be required, place a check in the Check Box for Required field. Press
save to save the UIF configuration.

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The second type of UIF configuration is Select Values. Select Values presents a list to the
operator and only allows them to pick from that list. This type of configuration is useful 50
when there are a defined set of alternatives, such as technician, internal / external, yes/no
type questions or production line.

To configure a UIF for Select Values, click this selection and fill in the UIF name as shown
below. If this field is to be required, place a check in the Check Box for Required field.

To add items to the list, press the Add button to create an entry in the list box, and then
click on this entry to edit it. Repeat for each item in the list. Items can be deleted from the

list as well. When finished, press Save to save the UIF configuration.

3.6.2 Demo Setup

The Demo Setup tab allows a user to browse in an SVF spectra file for demo installations. In
Demo mode, the spectra file serves as the spectrum source, taking the place of an
instrument. This allows for demonstrations and training without connecting to an actual
instrument.

For more information on creating a demo setup, please see the UScan Quick Start Guide.pdf
in C:\Program Files\Unity Scientific\UScan\Help .

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3.6.3 LIMS Configuration
UScan has the ability to export Sample data automatically to a designated file. This feature
can be used to automatically transfer data to a LIMS, PLC or other external data system.

Enabling the LIMS export function is configured in the Product Settings tab of Define
Product. Thus each Product can have the LIMS export enabled individually.

The LIMS Configuration tab contains the global settings that define the fields and format of
the LIMS export file.

Settings

The Settings tab defines where the LIMS output file will be stored and format settings.

Press the browse button and select the directory and filename of the LIMS output file.
Place a check in the check box if you wish the file to be appended with each sample record
(recommended in most situations).

Select the Start Character and Delimiter for the data format. These settings help the external
data system properly parse the file. Consult your IT professional if you have questions on
the proper format.

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Parameters

Place a check in the check boxes next to the parameters that should be exported to the LIMS
file.

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When finished, press Save to save the LIMS Configuration settings.

3.6.4 System Settings

System settings are global to the UScan installation. The default settings are recommended
for most installations.

Internal Reference Expiration Time: (min)

This setting keeps the internal reference scan current for reliable and consistent data
collection. 30 minutes is the default and good for most installations. For extremely variable
environments, 15 or 20 minutes (or a reference setting of before every sample in the Scan
Method) might be appropriate.

Number of Scans for Internal Reference

20 scans is the recommended default.

4 Routine Analysis

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UScan was designed for intuitive, easy routine analysis of samples. The information below
describes the procedures and options related to routine analysis.

4.1 Analyzing a Sample

UScan is designed to offer a flexible user interface for operators so that the analytical flow
and data presentation are optimized for the particular analytical situation. The setup of
UScan is addressed in the Configuration section of this manual. Please refer to that section
for more complete information on configuration options.

There are 2 methods for maintaining a current reference scan: timed reference and a
reference before each sample. This is configured in the Scan Settings the Scan Method. At

any time, the reference scan can be updated by pressing the Scan Reference button.

4.1.1 Sample Analysis Flow

UScan is designed to support routine scanning operations and present the results in various
pre-defined views. The Sample Analysis flow is the same for all views and is as follows:

1. Click to select the Choose Product icon to select the Product to 53

analyze. This step is only required if the active Product is not the Product desired.
The Choose Product button will bring up the Product Selection dialog. Please click
to select the Category and then Product desired.

2. Place the sample on the instrument in the proper sample cup. The sample cup type
is displayed in the status section of the main window below the Product name.

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 3. Press the Scan button to initiate the analysis. The scanning will start immediately.
4. If the Product is configured for manual sample number entry, a sample registration
screen will be displayed. Fill in all appropriate fields. If any User Information Field
is required, the operator will be required to enter a value in that field before the
sample data are displayed.
5. The sample data are displayed in the view selected.

4.1.2 Results View

The Results view is designed to display detailed results for one sample. The columns of this
view are configured in Product, Display parameters.

54

Pressing the print sample icon to get a hard copy of the results. The document
will be sent to the Windows default printer.

4.1.3 History View

The History View is designed to display the data from the current sample in a table that
contains the previous samples for that product. This allows the operator to instantly view
and compare the data to previous samples. This is also the View that is used for Sample
Management tasks.

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4.1.4 SPC View
The SPC or Statistical Process Control view is a specialized view for displaying the data
from a current sample and comparing it graphically to previous samples to determine trends
and pass / fail status when compared to set constituent limits. 55

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Pressing the Prev and Next buttons cycle through the Constituents present in the Product so
that the operator can choose the primary constituent and secondary constituents to display.
The Constituents are ordered per the Display order in the Calibration Method setup.

In Options, the operator can define how to select the samples to display, display options and
moving average options.

The Product Limits for each product determine the scaling of the y-axis. If no Product Limits
are configured, the y-axis starts at y=0.

4.1.5 Spectrum View

The Spectrum View presents the raw data from the Sample scan to the operator. It is
possible to use a mouse and expand sections of the plot for detailed examination. It is also

possible to overplot other sample spectra by pressing the button and selecting
Samples to plot.

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4.2 Sample Management

UScan stores all sample data in one central database, with all sample records traceable to
the exact configuration settings in place at the time of analysis. UScan has a collection of
tools available for managing and reporting sample data.

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Sample Management is performed from the History View.

4.2.1 Sample Selection

Sample selection is performed from the History View. Single samples are selected with a
touch to the touch screen or a click of the mouse. Multiple Samples may be selected using
the standard Windows conventions of <Ctrl> click for multiple selections or <Shift> click for
bracketed selections. For more powerful or automated selection, please use the search
dialog below.

4.2.2 Sample Search

The Sample Search dialog is used to select the samples visible on the History View. This
can be used to narrow the search for a specific sample or group of samples for further
processing such as report generation or exporting spectra.

To activate the Sample Search, press the Search button on the History View. The dialog
below will be presented:

57

Each of the fields in the dialog above acts as a filter to all the samples in the database.

Enter in the number of samples, sample name or date range to select samples from the
listed product. To change Products, click the Change Product icon and select the Product
desired.

When using Sample Name as a filter, use % as a wildcard. For example, 114% will select

 114
 11456778
 114 Retest
 114943#1

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Press the button to filter the History View based on the selected criteria. The selected
samples will now be present in the History View and are available for the following
operations.

4.2.3 Managing Sample Data

All of the sample data can be displayed in UScan. From the History view, click to select the
Sample of interest and press Sample Details.

Sample labels such as Sample Number, Comment and User Information Fields (UIFs) can be
edited in the Sample Record. These fields are outlined in red below. Simply click in the field
of interest and edit the data. Other data such as the Sample DateTime of analysis and
Product type are fixed and cannot be changed.

The Configuration Methods are also displayed in the Sample Details. Each Method is listed
along with the version in place at the time of analysis. For example, the sample below was
analyzed with version 5 of the Puppy Chow product.

58

When finished, press Save to save the updated information or to cancel the
update.

4.2.4 Exporting Data

UScan can create reports from the stored Sample data in the program. The Sample data are
formatted and exported based on Crystal Reports report templates. Several default report

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templates are provided. For custom reports, please contact your CHOPIN Technologies
support specialist.

To Export Sample data, select the samples to export using one of the methods above. Press
Export to initialize the export, and the dialog below will appear:

59

Select the report template from the list at the left and press View Report. The sample data
will be exported based on the template selected and the Window below will be displayed:

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 60

From this dialog is it possible to export the report to a variety of formats including XLS, PDF,
RTF, TXT or CSV. It is also possible to print the report from the icon circled in red. It is also
possible to send this report to any Windows printer. Controls across the top allow for
navigating within the report.

If more than on sample is selected, the sample data will be exported to an XLSX file in
C:\Unity\Reports. This file can be opened by Microsoft Excel or Open Office from Apache
(https://www.openoffice.org/ ).

4.2.5 Exporting Spectra

Sample spectra or raw data can also be exported from UScan. This can be useful for
calibration work, validation work or for sending to calibration providers for remote
predictions or calibration updates.

To export spectra, select the samples to be exported with the methods described above.
Press the Export Spectra button and the dialog below will appear:

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First select the format for the spectral export. Unity SVF format as well as SPC, NIR/Cal and
JCamp formats. If you wish to export the spectra to Excel or other generic program, select
CSV.
61

Next, press the destination folder icon and enter in the filename for the export. Press
OK and the file will be exported to the destination entered.

4.2.6 Deleting Samples

To delete samples, select the desired samples in the History View using the methods above.
Press the Delete button. A dialog will ask you to confirm the deletion. Sample deletion is
permanent and cannot be undone.

4.2.7 LIMS Exports

UScan can be configured to automatically export sample data after each sample analysis.
The format of the export as well as the destination folder are configured in the System
Settings, LIMS CONFIGURATION section.

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5 Diagnostics

UScan has a complete set of instrument hardware and performance diagnostic procedures
to ensure proper performance and functionality of your instrument. Many of these
diagnostic tests are instrument specific, and thus are covered in detail in the instrument
operating manual. Please consult this manual for more information. A summary of each
diagnostic test is presented below.

5.1 TAS

TAS, or True Alignment™ Spectroscopy, is a patent pending technology for aligning and
maintaining instrument calibration. TAS routines include a procedure to evaluate instrument
status and performance, as well as a procedure to align the instrument back to factory
specifications.

5.1.1 TAS Instrument Status

The TAS Instrument Status evaluation is accessed from this button:

62

The TAS Instrument Status evaluation will prompt the user to place specific standards on
the instrument. When done, a status page with pass / fails will be displayed. If any tests fail,
proceed to run the TAS Alignment procedure below.

5.1.2 TAS Alignment

The TAS Alignment is accessed from this button:

The TAS Alignment procedure will prompt the user to place specific standards on the
instrument. After scanning the samples, the computer will calculate the optimal alignment
settings. When done, a procedure complete message will be displayed.

NOTE: The final section of the alignment procedure can take 4 – 5 minutes of computer
time, and it might appear that the program is not doing anything. Please do not interrupt this
process. The program will tell you when it is done.

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5.2 Instrument diagnostics

5.2.1 Lamp Health

The Lamp Health is accessed from this button:

Press this button to diagnose the lamp. The elapsed hours, current and other settings are
displayed.

NOTE: The hours remaining are approximate based on the estimated lifetime of the lamp.

5.2.2 Instrument Health

The Instrument Health diagnoses the electrical components of the instrument and is
accessed by this button:

63

The Instrument Health button will test various electrical and mechanical parts in the
instrument and return pass/fail indications for each test. If any component fails, please call
your CHOPIN Technologies product specialist.

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6 Appendix

6.1 Glossary

The terms and definitions below are simple definitions based on the usage with UScan and
CHOPIN Technologies products. For more complete definitions, please consult reference
sources.

As Received A moisture basis for reporting constituent values which

includes the moisture present in the original sample. Also
called as-is basis.
Calculated Constituent A constituent that is calculated from other constituents
or Variable and constants according to a mathematical or logical
formula.

Conformity Test A conformity test is a qualitative evaluation that

determines how closely an unknown sample fits a selected
population. These can be used for Good Product / Bad
Product determinations or adulteration type evaluations.
64

Constant Moisture A moisture basis for reporting where the constituent

values are expressed as a percentage of the sample with
the constant moisture described. An example is constant
moisture basis of 0 – also known as dry matter basis –
where the constituent is expressed as a percentage of the
sample without moisture.
Dry Matter A moisture basis for reporting where the constituent is
expressed as a percentage of the sample without
moisture.
GD (Global Distance) The GD is an indication of how well the spectra of
unknown sample fits with the calibration population. A GD
below 4 or so indicates that the sample is well represented
by the calibration.
MLR Multiple Linear Regression. A calibration made with
several terms and an intercept, usually based on filter data.
Moisture Basis Moisture basis indicates the amount of moisture in the
sample when the constituent content is expressed.
Common moisture bases include as-received, dry matter or
constant moisture.
ND (Neighbor Distance) The neighbor distance is the spectral distance from the
unknown to the closest calibration sample. A high ND with

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 an acceptable GD indicates a sample that should be added
to a calibration set.
NIR Near InfraRed. A region of the electromagnetic spectrum
classically defined as 1100 – 2500 nm.
Outlier A sample that does not fit. A spectral outlier (GD, ND)
indicates that the spectra do not fit with the calibration set.
A product outlier indicates that the constituent’s values are
not within limits.
PLS Partial Least Squares. A regression technique that relates
spectral variance with reference constituent values and
produces a mathematical relationship (calibration).
Product Outlier A product outlier indicates that the constituent’s values are
not within limits.
Spectrum The raw data from a spectrophotometer, usually expressed
as log 1/r.
T Statistic The T statistic is also known as the Z-test. UScan uses
this statistic to express how well the constituent value
compares with the range of reference values in the
calibration. Below 2.5 is well represented.
X Residual The X residual is a spectral outlier indication that describes
the amount of spectral variation that cannot be explained
with the modeling. 65

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6.2 Calculated Constituent Expression Formula Guidelines

6.2.1 Expression Formula Design

The "expression formula" here refers to the algebraic formula that is used to produce the
calculated variable result. The expression formula may contain one or more of the following
items:

(1) Numerical items (“numerics”) (1.0, 2, -0.003, etc.) Note that numerics cannot
contain any commas. If a decimal marker is to be used, it must be a period “.”.
For integers, the decimal marker is optional.
(2) Constituent Names - any constituent name on the internal constituent list can be
used. There is some logic in the software that does arrange the computational
order so that each calculated variable can be computed. Even with that logic in
place, it is still possible to compose an expression that cannot be computed. In
general, .prd constituents, .mlr constituents , and .prc constituents are
determined prior to any calculated variable constituent. The exact spelling of
constituents must be observed. Since constituent names are always forced to
upper case, the constituent names in expression are not case sensitive. For best
results, avoid internal spaces in constituent names (use the underscore "_"
instead).
(3) Operators - operators include + - * / % (for modulus) ^ (for exponents). UScan
also recognizes some logical operators (== != >= <= < > & |). See section below
for more on operators.
(4) Functions - There is a limited selection of Functions. There are unary (one
66
argument) functions, binary (two arguments) functions, and one ternary (three
arguments) function. Functions that start with "I" are logical functions that return
either 1 or 0 as a result. See section 4 for more on Functions.
(5) Parenthesis - Parenthesis must come in pairs. For each left parenthesis, there
must be a corresponding right parenthesis. Note that functions also include
paired parenthesis.

When entering the expression formula, do not use an equal sign unless it is part of a logic
operator. Do not begin an expression formula with an equal sign. Note that an equal sign
can only be used as part of a double-character operator (== != >= <= ).

Order of operations - Parenthesis contents are evaluated first. Since all functions contain
parenthesis, expressions within function parenthesis are evaluated as if they were simple
parenthesis expression.

The Operator order of operations are: Logical operations, then ^ / % * - +.

Feel free to overuse parenthesis to enforce the operation order that you desire.

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6.2.2 Operators
There are unary operators "op argument" and binary operators "argument1 op argument2".

The unary operator "-" (numerical negate) converts the op argument to -1*argument.

The unary operator "!" converts the op argument to either 0 (when argument is ,0.5) or 1
(when argument>=0.5).

Binary operations must lie between two sub expressions that evaluate to numerics.

^ (exponential) A^B A raised to the power of B

% (Modulo) A%B A mod B, A - int(A/B)*B,

/ (Division) A/B returns quotient of A/ B

* (Multiplication) A*B returns product of A , B

- (Subtraction) A-B returns difference A-B

+ (Addition) A+B returns sum of A , B

Logical Comparisons

> Greater than A>B returns 1 if true, 0 if false

< Less than A<B returns 1 if true, 0 if false 67

>= Greater than or equal to A>=B returns 1 if true, 0 if false

<= Less than or equal to A<=B returns 1 if true, 0 if false

== Equal to A==B returns 1 if abs(A-B)>=.000001, 0 otherwise returns 1 if true, 0

if false

!= Not equal A!=B returns 1 if abs(A-B)<.000001, 0 otherwise

Logical Math

& Logical And A&B returns 1.0 if BOTH A and B are greater than 0.49999999, 0
otherwise.

| Logical OR A|B returns 1.0 if Either A or B are greater than 0.49999999, 0

otherwise.

Order of operations

Each operation is assigned a rank. In expressions or sub expressions that contain no

parenthesis, this order is followed:
Logical operations (< > >= <= == != & |) in the order that they appear in the expression
^ (exponential), % (modulo), / (division), * multiplication, - subtractions, + addition

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6.2.3 Functions
There are a variety of Mathematical and logical functions that can be used. Functions can be
unary, binary, or ternary. Arguments of functions can be numerics or “sub-Expressions”. A
sub-Expressions is a series of text characters that fulfills the requirements of an expression
if it were entered as an expression. For example, the expression MAX(PROTEIN-
1,(FAT+PROTEIN)*2) contains two subexpressions. Both “PROTEIN-1” and
“(FAT+PROTEIN)*2” could have stood alone as legal expressions.

Unary functions have one argument.

ABS(argument) returns the positive version of the argument

EXP(argument) returns natural number e (2.17..) raised to the argument power

INT(argument) returns the positive version of the argument

LOG(argument) returns base 10 logarithm of the absolute value of the argument

LNE(argument) returns base e logarithm of the absolute value of the argument

SQR(argument) returns the square root of the absolute value of the argument

Binary Functions have two arguments (with one comma in between)

68
MAX(arg1,arg2) returns the larger of Arg1,arg2

MIN(arg1,arg2) returns the smaller of Arg1,arg2

Binary Functions (Logical Functions)

IGT(arg1,arg2) returns 1 if Arg1>Arg2, 0 otherwise

IGE(arg1,arg2) returns 1 if Arg1>=Arg2, 0 otherwise

ILT(arg1,arg2) returns 1 if Arg1<Arg2, 0 otherwise

ILE(arg1,arg2) returns 1 if Arg1<=Arg2, 0 otherwise

ICZ(arg1,arg2) returns 1 if (Arg1-Arg2)<0.0000001, 0 otherwise

INE(arg1,arg2) returns 1 if (Arg1-Arg2)>=0.0000001, 0 otherwise

Ternary Function

IBT(Arg1,arg2,arg3) returns 1 if arg1>=arg2 AND arg1<arg3 ("between")

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