VisionWorks Acquisition and Analysis Software User Guide

Software
Installation and User Guide

VisionWorks® Acquisition and Analysis Software

Analytik Jena US Ultra-Violet Products Ltd.

2066 W. 11th Street Unit 1, Trinity Hall Farm Est., Nuffield Rd.
Upland, CA 91786 USA Cambridge CB4 1TG UK
(909) 946-3197 +44(0)1223-420022
Fax: (909) 946-3597 Fax: +44(0)1223-420561
Email: [email protected] Email: [email protected]
Web site: us.analytik-jena.com

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 Table of Contents
Contents
Welcome to VisionWorks Acquisition/Analysis Software Guide.............................................................................. 1
What's New in Version 8 ..................................................................................................................................... 1
Getting Started ................................................................................................................................................... 1
Minimum System Requirements ........................................................................................................................... 3
Operating System Requirements ......................................................................................................................... 3
Registering the Software (optional) ...................................................................................................................... 4
User Administration ............................................................................................................................................ 5
About Secure User Accounts.............................................................................................................................. 5
Users Rights ...................................................................................................................................................... 6
Configure User Accounts ..................................................................................................................................... 8
User Names and Passwords .............................................................................................................................. 8
Add a New User ................................................................................................................................................. 8
Edit a User ......................................................................................................................................................... 9
Change a Password or Other Settings ............................................................................................................. 10
Deactivate/Reactivate a User.......................................................................................................................... 10
View the Login History of a User ..................................................................................................................... 11
Technical Support ............................................................................................................................................... 12
License Agreement............................................................................................................................................. 13
End User License Agreement ........................................................................................................................... 13
VisionWorks® Software ................................................................................................................................... 13
Navigate the Software ........................................................................................................................................ 15
Navigating the Software ..................................................................................................................................... 15
Main Window ................................................................................................................................................... 15
Action Tabs ...................................................................................................................................................... 15
Image Windows ................................................................................................................................................. 17
Organize Image Windows ................................................................................................................................. 17
Information Provided by the Image Window ..................................................................................................... 18
Show the Image in Actual Size .......................................................................................................................... 18
Fit the Image to the Window ............................................................................................................................ 18
Context Menu Commands................................................................................................................................. 18
Status Bar ........................................................................................................................................................ 18
Obtain Image Information .................................................................................................................................. 19
Overview .......................................................................................................................................................... 19
Display Image Information................................................................................................................................ 19
Enter Notes ...................................................................................................................................................... 19
Calibrate Image Scale ....................................................................................................................................... 20
Menu Buttons .................................................................................................................................................. 21
Menus and Action Tabs Overview ....................................................................................................................... 21
Main Menu Buttons.......................................................................................................................................... 21
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Action Menu Tabs ............................................................................................................................................ 21

File Menu Overview ........................................................................................................................................... 23
Open and Save Images........................................................................................................................................ 24
Open Images .................................................................................................................................................... 24
Save Images ..................................................................................................................................................... 24
Image File Types............................................................................................................................................... 25
Print ................................................................................................................................................................... 26
FTP Transfer ....................................................................................................................................................... 27
Edit Menu Button Overview................................................................................................................................ 29
Copy ................................................................................................................................................................... 30
Copy an Entire Image........................................................................................................................................ 30
Copy a Selected Region Within an Image........................................................................................................... 30
Paste .................................................................................................................................................................. 31
Paste an Image................................................................................................................................................. 31
Paste Special .................................................................................................................................................... 31
Undo and Redo ................................................................................................................................................... 33
Region of Interest (ROI) ..................................................................................................................................... 34
About the Selection Tools ................................................................................................................................. 34
Select a Region ................................................................................................................................................. 35
Adjust a Region ................................................................................................................................................ 35
Cancel a Region ................................................................................................................................................ 35
Image Enhancement Filters ................................................................................................................................ 36
Sharpen ............................................................................................................................................................. 37
Remove Noise ..................................................................................................................................................... 38
Enhance Exposure .............................................................................................................................................. 39
Adjust the Image ................................................................................................................................................ 40
Rotate Function .................................................................................................................................................. 41
Rotate an Image ............................................................................................................................................... 41
Rotate an Image by an Exact Number of Degrees .............................................................................................. 41
Align the Image .................................................................................................................................................. 43
Flip Image .......................................................................................................................................................... 44
Flip Horizontally ............................................................................................................................................... 44
Flip Vertically.................................................................................................................................................... 44
Resize Image ...................................................................................................................................................... 46
Reduce Image to Monochrome ........................................................................................................................... 47
Change Image Depth .......................................................................................................................................... 48
Advanced Menu Overview .................................................................................................................................. 49
Log Viewer ......................................................................................................................................................... 50
Display Loaded Modules ..................................................................................................................................... 51
Configure Application ......................................................................................................................................... 52
Rulers................................................................................................................................................................. 53
Show or Hide the Rulers ................................................................................................................................... 53

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Using Macros ..................................................................................................................................................... 54

Overview .......................................................................................................................................................... 54
Macros Navigation ........................................................................................................................................... 54
Record Macros.................................................................................................................................................. 54
Edit Macros ...................................................................................................................................................... 55
Play a User-Defined Macro ............................................................................................................................... 55
Help Menu Overview .......................................................................................................................................... 56
Display Help Topics ............................................................................................................................................. 57
Application Information...................................................................................................................................... 58
Acquire Images .................................................................................................................................................. 59
Acquisition Action Tab Overview ......................................................................................................................... 59
Image Acquisition............................................................................................................................................... 61
Capture an Image ............................................................................................................................................. 61
Using the UVP iBox® Explorer Imaging Microscope ............................................................................................. 63
Emission Filters ................................................................................................................................................ 63
Magnification ................................................................................................................................................... 64
Fine Focus ........................................................................................................................................................ 64
Bookmarks ....................................................................................................................................................... 65
Lighting/Darkroom/Lens .................................................................................................................................. 67
UVP eLITE MultiSpectral Light Source ................................................................................................................. 67
Using the UVP eLITE Functions ......................................................................................................................... 67
Darkroom Control .............................................................................................................................................. 69
Hardware Settings Selection ............................................................................................................................. 69
Tray Height ...................................................................................................................................................... 69
Lens Control ....................................................................................................................................................... 71
Lens Control ..................................................................................................................................................... 71
Camera ............................................................................................................................................................ 72
Camera Functions............................................................................................................................................... 72
Integration ....................................................................................................................................................... 72
Exposure Time ................................................................................................................................................. 73
Gain ................................................................................................................................................................. 73
Post Capture ..................................................................................................................................................... 74
Binning ............................................................................................................................................................ 74
Saturation Preview ........................................................................................................................................... 75
Preferences ...................................................................................................................................................... 75
CCD Temperature ............................................................................................................................................. 75
Camera Integration ............................................................................................................................................ 76
Manual Integration .......................................................................................................................................... 76
Sequential Integration .................................................................................................................................... 76
Image Integration ........................................................................................................................................... 78
Binning Modes ................................................................................................................................................... 79
Perform 1D Analysis ........................................................................................................................................... 80

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1D Analysis Action Tab Overview ........................................................................................................................ 80

Lanes and Bands .............................................................................................................................................. 83
Finding Lanes and Bands .................................................................................................................................... 83
Define Region of Interest (ROI)......................................................................................................................... 83
Perform Automatic Finding of Lanes and Bands ................................................................................................ 83
Adjust Lanes and Bands Search Parameters ...................................................................................................... 85
Lane and Band Information ................................................................................................................................ 86
Lane and Band Properties................................................................................................................................. 86
Information Found in the 1D Analysis Image Window ....................................................................................... 88
Add Lanes and Bands ......................................................................................................................................... 89
Add Lanes Method No. 1: From the Find Lanes and Bands Window .................................................................. 89
Add Bands Method No. 1: From the Find Lanes and Bands Dialog Window ....................................................... 89
Add Lanes Method No. 2: From the Image Window .......................................................................................... 89
Add Bands Method No. 2: From the Image Window .......................................................................................... 90
Delete Lanes and Bands ..................................................................................................................................... 92
Delete Lanes .................................................................................................................................................... 92
Delete Bands .................................................................................................................................................... 92
Edit Lanes and Bands ......................................................................................................................................... 93
Move Lanes and Bands ..................................................................................................................................... 93
Resize Band Extents ......................................................................................................................................... 93
Place Bands Exactly .......................................................................................................................................... 94
Lane Profile ...................................................................................................................................................... 96
Lane Profile Overview ........................................................................................................................................ 96
Perform Molecular Weight Calibrations .............................................................................................................. 98
Overview .......................................................................................................................................................... 98
Apply a Molecular Weight Standard to a Lane .................................................................................................... 99
Calibrate a Lane ............................................................................................................................................... 99
Stretch Factor ................................................................................................................................................. 100
Manual Placement of Weights ........................................................................................................................ 101
Exact Placement of Bands ............................................................................................................................... 101
Changing Molecular Weight Settings ................................................................................................................ 102
Add Molecular Weight Standard to the Library................................................................................................ 102
Edit Molecular Weight Standard in the Library ................................................................................................ 103
Remove Molecular Weight Standard in the Library ......................................................................................... 103
Copy Molecular Weight Standard in the Library............................................................................................... 103
Background Correction ..................................................................................................................................... 104
Background Correction Options ....................................................................................................................... 104
Lane Profile Graph ........................................................................................................................................... 107
Use the Lane Profile Graph ............................................................................................................................. 107
Display Lane(s)............................................................................................................................................... 107
Axis Options ................................................................................................................................................... 108
Display Options .............................................................................................................................................. 108

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Move Bands Using the Lane Profile Graph ...................................................................................................... 109

Resize Bands Using the Lane Profile Graph ..................................................................................................... 110
Concentration Calibration ................................................................................................................................. 111
Change Unit Type ........................................................................................................................................... 112
Select Unit Type.............................................................................................................................................. 112
Add, Edit or Delete a Unit Type ....................................................................................................................... 112
Select Data Points ......................................................................................................................................... 113
Select Curve Type ........................................................................................................................................... 115
Remove Concentration Calibration .................................................................................................................. 115
Retardation factor (Rf) Lines ............................................................................................................................ 116
Automatic Rf Line Determination .................................................................................................................... 116
Adjust an Automatic Rf Line ........................................................................................................................... 116
Add Rf Lines Manually .................................................................................................................................... 117
Move Rf Lines ................................................................................................................................................ 117
Delete Rf Lines ............................................................................................................................................... 117
Dendrogram Analysis...................................................................................................................................... 119
Performing Dendrogram Analysis ..................................................................................................................... 119
Overview ........................................................................................................................................................ 119
Generate Dendrogram Graphs ........................................................................................................................ 119
Modify Dendrogram Graphs............................................................................................................................ 120
Dendrogram Standards ................................................................................................................................... 120
Create Clusters ............................................................................................................................................... 121
Linkage Rules ................................................................................................................................................... 122
1D Analysis Settings ......................................................................................................................................... 124
Results ........................................................................................................................................................... 126
Viewing and Printing 1D Gel Analysis ............................................................................................................... 126
Overview ........................................................................................................................................................ 126
Results Data Explorer........................................................................................................................................ 127
Filtering Data ................................................................................................................................................. 127
Printing Data Explorer Tabular Reports ............................................................................................................. 128
Print Data Explorer Reports ............................................................................................................................ 128
Export Data Explorer Reports.......................................................................................................................... 128
Report Types .................................................................................................................................................. 129
Fixed Image and Analysis Reports ................................................................................................................... 129
Clear .............................................................................................................................................................. 131
Clear Lane and Band Information ..................................................................................................................... 131
Perform Area Density Analysis .......................................................................................................................... 132
Area Density Action Tab Overview .................................................................................................................... 132
Perform Area Density ....................................................................................................................................... 134
Overview ........................................................................................................................................................ 134
Perform Area Density Analysis ........................................................................................................................ 134
Use MagicWand to Define ROI ........................................................................................................................ 136

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Select Multiple Bands and Regions in the Image ............................................................................................. 136

Modify Regions in the Image .......................................................................................................................... 137
Area Density Settings ....................................................................................................................................... 138
Define Area Density Background....................................................................................................................... 139
Define Background ......................................................................................................................................... 139
Delete Background Region .............................................................................................................................. 140
Modify an Existing Background Region ........................................................................................................... 140
Estimate Region Volume ................................................................................................................................... 141
Calibration Curves ............................................................................................................................................ 143
About Intensity Calibration Curves .................................................................................................................. 143
Optical Density ............................................................................................................................................... 143
Grey Level ...................................................................................................................................................... 144
Types of Calibration Curves ............................................................................................................................. 144
Apply Pre-Defined Intensity Calibration Curve ................................................................................................. 144
Add New Intensity Calibration Curve ............................................................................................................... 144
Set Amount Calibration Curve ......................................................................................................................... 145
Change Calibration Curve Graph ..................................................................................................................... 147
Reporting and Printing Area Density Results ..................................................................................................... 148
Area Density Results and Data ........................................................................................................................ 148
Save the Results ............................................................................................................................................. 149
Print the Results ............................................................................................................................................. 149
Export the Results .......................................................................................................................................... 149
Perform Colony Counting .................................................................................................................................. 150
Colony Count Action Tab Overview.................................................................................................................... 150
Colony Counting Settings .................................................................................................................................. 152
Label Type...................................................................................................................................................... 152
Count Colonies ............................................................................................................................................... 154
Counting Colonies - Options ............................................................................................................................. 154
Automatic Counting .......................................................................................................................................... 155
Click and Add Counting ..................................................................................................................................... 157
Set-Up Colony Counting Templates ................................................................................................................... 159
Counting Using a Predefined Template ............................................................................................................. 162
Add Colonies .................................................................................................................................................... 163
Delete Colonies................................................................................................................................................. 164
Split Colonies.................................................................................................................................................... 165
Manual Split Colonies ..................................................................................................................................... 165
Auto Split Colonies ......................................................................................................................................... 166
Merging Colonies ............................................................................................................................................. 167
Identify by Color Counting ................................................................................................................................ 168
Identify by Color Counting Step 1: Select ........................................................................................................... 170
Identify by Color Counting Step 2: Finish ........................................................................................................... 173
Spiral Counting ................................................................................................................................................. 174

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Perform Spiral Count ...................................................................................................................................... 174

Adjust Grid Size and Volume ........................................................................................................................... 175
View, Save and Print Spiral Plate Results......................................................................................................... 176
User Tips ........................................................................................................................................................ 177
Colony Counting Results ................................................................................................................................. 178
Colony Counting Reports .................................................................................................................................. 178
Export and Print Colony Results ........................................................................................................................ 179
Exporting to Excel .......................................................................................................................................... 179
Printing Colony Results ................................................................................................................................... 179
Reporting Colony Class Information .................................................................................................................. 180
Reporting General Colony Information ............................................................................................................. 181
Reporting Colony Statistical Information ........................................................................................................... 182
Reporting Colony Distribution Information ....................................................................................................... 183
Modify Images ................................................................................................................................................. 184
Image Action Tab Overview .............................................................................................................................. 184
Display Control ............................................................................................................................................... 185
Image Corrections ............................................................................................................................................ 185
Corrections ..................................................................................................................................................... 185
Change Brightness, Contrast, Gamma Or Invert ............................................................................................... 186
Histogram Controls .......................................................................................................................................... 188
Apply a Histogram .......................................................................................................................................... 188
Pseudocolor ..................................................................................................................................................... 190
Pseudocolor Spectrums................................................................................................................................... 190
Apply or Remove a Pseudocolor ...................................................................................................................... 191
3D Plots ........................................................................................................................................................... 192
Using the 3D Plot Function ............................................................................................................................. 192
Viewpoint Tab ................................................................................................................................................ 193
Output Tab ..................................................................................................................................................... 193
Annotations ................................................................................................................................................... 195
Annotations ..................................................................................................................................................... 195
Overview ........................................................................................................................................................ 195
Annotation Navigation ................................................................................................................................... 195
Types Of Annotation ....................................................................................................................................... 195
Annotation Tools ............................................................................................................................................ 196
Draw Annotations ............................................................................................................................................ 197
Draw a Text Annotation.................................................................................................................................. 197
Draw Line Annotations ..................................................................................................................................... 198
Draw Shape and Highlight Annotations ............................................................................................................ 199
Draw a Rectangle, Ellipse, Highlighter Annotation .......................................................................................... 199
View or Hide Annotations ................................................................................................................................. 200
Modify Annotations .......................................................................................................................................... 201
Select Annotations ......................................................................................................................................... 201

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Edit Text Annotation ...................................................................................................................................... 201

Move and Resize Annotations ......................................................................................................................... 202
Rotate Text Annotations ................................................................................................................................. 202
Format Annotations ....................................................................................................................................... 202
Delete Annotations ......................................................................................................................................... 203
Synchronize Annotations .................................................................................................................................. 204
Measurement Tools .......................................................................................................................................... 205
Line Measure ................................................................................................................................................. 205
Area Measure ............................................................................................................................................... 205
Angle Measure ............................................................................................................................................... 206
Layer Actions .................................................................................................................................................... 207
Multi Image Actions ....................................................................................................................................... 208
Multi-Image Actions ......................................................................................................................................... 208
Background Filters .......................................................................................................................................... 208
Background Correction ................................................................................................................................... 208
Background Subtraction.................................................................................................................................. 208
Image Compositing .......................................................................................................................................... 209
Create a Composite Image .............................................................................................................................. 209
Player (Image Sequences) ................................................................................................................................ 210
Purpose of the Player...................................................................................................................................... 210
Using the Player ............................................................................................................................................. 210
Merge Functions ............................................................................................................................................ 211
Player Features .............................................................................................................................................. 212
Player Options ................................................................................................................................................ 212
Extract or Delete individual Image files (frames) ............................................................................................. 213
Saving .AVI Files ............................................................................................................................................. 214
Create Templates .............................................................................................................................................. 215
Set-Up Hardware Master Templates ................................................................................................................. 215
Create a New Template .................................................................................................................................. 215
Edit, Synchronize and Delete Templates ............................................................................................................ 217
Edit a Template .............................................................................................................................................. 217
Synchronize a Template.................................................................................................................................. 217
Delete a Template .......................................................................................................................................... 217
Open and Save Images...................................................................................................................................... 218
Open and Save Images...................................................................................................................................... 218
Open Images .................................................................................................................................................. 218
Save Images ................................................................................................................................................... 218
Image File Types............................................................................................................................................. 219
Print Reports .................................................................................................................................................... 221
Print ................................................................................................................................................................. 221
File Print Command .......................................................................................................................................... 222
Print Image History .......................................................................................................................................... 223

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Reports .......................................................................................................................................................... 223

Preview and Print a Report ............................................................................................................................. 223
Print an Image................................................................................................................................................ 224
Support 21 CFR Part 11 Compliance ................................................................................................................. 225
Supporting 21 CFR Part 11 Compliance ............................................................................................................ 225
Purpose .......................................................................................................................................................... 225
Features ......................................................................................................................................................... 225
Usage ............................................................................................................................................................. 225
Image History .................................................................................................................................................. 228
View Image History ......................................................................................................................................... 228
Add Notes in the Image History ...................................................................................................................... 228
Glossary ........................................................................................................................................................... 229
Glossary ........................................................................................................................................................... 229
Index ................................................................................................................................................................ 231

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Welcome to VisionWorks Acquisition/Analysis Software

Guide

Analytik Jena's VisionWorks software allows users to acquire, enhance, analyze and document images in a
simple and efficient way. Plus generate extensive reports and export them to Excel.

VisionWorks software is available as:

 VisionWorks® Acquisition and Analysis or VW (includes 1D, Area Density and Colony Counting
Analysis)

Note: If a software function is grayed out, the function is not available with the version of software loaded on
the user’s computer.

The VW software is designed to image electrophoresis gels (DNA, RNA, and Protein), blots, membranes,
plates, plants, and animals. Once an image has been captured with an application-specific camera, it can be
saved for documentation and presentations, manipulated for analysis, and annotated to point out key
features in the image.

What's New in Version 8

VW software release 8 new features include:
 New master template interface
 Updated workflow user interface
 Windows 7, 8, 10 compatibility
 Image interpolation for increased resolution
 Enhanced auto exposure capabilities
 Automatic histogram adjustment
 Automatic noise subtraction
 Automatic dark frame subtraction

Getting Started
 Minimum System Requirements
 Registering the Software (optional)
 User Administration
 Configure User Accounts

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Capturing Images
 Acquisition

Performing Analysis Functions on Images

 1D Analysis
 Area Density
 Counting Colonies

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Minimum System Requirements

Operating System Requirements

 Windows 7, 8 and 10, (32-bit or 64-bit)
 Internet Explorer 8 or higher [To determine the version of Internet Explorer, open Internet
Explorer and click on Help > About]
 Intel Pentium Processor or equivalent, 1.6 GHz or higher
 2 GB of RAM or greater (4 GB recommended)
 200 MB of available hard disk space for the program, more for data
 To avail the functionality of 21 CFR Part 11 support, the disk partition must be formatted with
NTFS.
 Computer equipped with minimum of three USB ports; additional ports required for peripheral
equipment (mouse, keyboard, etc.)
Note: Firewalls may impede successful installation and use of VW software, specifically for networked
applications. Contact your organization’s IT or network administrator to determine if a firewall or other
protection needs to be modified prior to installation of the software.

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Registering the Software (optional)

 Optional registration

1. It is optional to register your new software. If you register, you will receive free software update
notifications at the email you assign.
2. When you open the software by double-clicking on your desktop VisionWorks® icon, you will be
prompted with the window for registering (see below).
3. You can choose to exit the window by selecting “not now” or you can disable it by checking the lower
left box, “Don’t show this again”.

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User Administration

 About Secure User Accounts

 User Rights
 Configure User Accounts

About Secure User Accounts

The concept of User Accounts for individual users is central to the software by providing security of user’s data
from being tampered with by other users, accidentally or otherwise.
 VW system of usernames and passwords is not to be confused with the login required to open the
computer. VW users must provide a separate login and password to enter the VW software.
 Setting up user accounts is mandatory if support for CFR 21 Part 11 is required from the
software.
 If individual accounts are not required, create just one account for all users and give full
permissions to that account.

Enable Secure User Accounts

 Request a System Administrator to log into the Windows computer.
 For Windows XP and 3, 32-bit: Navigate to C:\Documents and Settings\All Users
 For Windows 7,8, and 10, 64-bit, Navigate to C:\ProgramData
 Locate the Application Data folder.

 If the Application Data folder is not present in the All Users window, go to the Tools menu and
select Folder Options. (If the Application Data is present, skip the next step.)
 A Folder Options window appears. On the View tab, select Show hidden files and folders.
Select Apply then OK.

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 Go to the UVPSettings folder inside the Application Data folder.

 Have the System Administrator select Allow for all permissions listed for each user or group for
either the UVPSettings folder, or for each file within the folder (depending on the Network
Security Policy where the VW software will reside).

Definitions of the User Administration Columns

Column Heading Description

User Name Unique Identification name for a particular user. This could be a name or
a word that makes it easier to identify the user.
Date Created Date the user name was created.
Last Login Date of last login.
Login Count Number of times the user has logged in.
Idle Time Lock Indicates the maximum idle time. To change the idle time, click Edit User
> Set Idle Time. Zero means no idle time.
Password Date the password expires.
Expiration Date
View Enables user to view images. To change this setting, click Edit User >
Edit Rights. Click or unclick the View option.

Change Enables user to change images. To change this setting, click Edit User >
Edit Rights. Click or unclick the Change option.
Has Admin. Gives user administration permissions. To change this setting, click Edit
Rights User > Edit Rights. Click or unclick the Has Administrative Rights
option.

Users Rights
Depending on the privileges for the user that has logged onto windows, the following rights are available to
that user for the software:

Login Privileges Rights

Install Un- Open User Use the
Install and Run Administration Camera
Restricted X* X
Standard/Power X* X
Admin X X X X X
X = Supported rights.

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Note that even though a user may be able to do things with the
software which are outside of this matrix, Analytik Jena neither
recommends it, nor supports it. For example, the user may try
(successfully or otherwise) to uninstall the software as a Power User,
but Analytik Jena does not provide support for problems arising during
or due to that action.

Related Topics:

Configure User Accounts

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Configure User Accounts

 User Names and Passwords

 Add a User
 Edit a User
 Change a Password or Other Settings
 Deactivative/Reactivate a User
 View the Login History of a User

User Names and Passwords

 Start the software. It will bring up a Login window.
 The administrator user name will show.
 Click Login.

 A Reset password window appears. Enter the new password. Confirm the new password.
 Click OK.

Add a New User

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 From the menus, click the Advanced menu button then select Configure user accounts to open the
User Administration window.
 Click the Add User button.
 Type in the new user name and password. Note: Each time the new user logs in, use that new user
name and password.
 Click OK.

Edit a User
 Highlight the user name in the User Administration window.
 Click the Edit User and select from the Define User Permissions screen to allow users to view
images, modify images, change templates, or assign administrative rights.
 Click OK when changes to the user are complete. Note: The Administrator's rights cannot be
edited.

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Change a Password or Other Settings

 To change a password, click the Advanced menu button then select Configure user accounts
to open the User Administration window.
 Click on the appropriate user to change.
 Right-click > Reset Password and enter the new password. Enter the password again to confirm
the change.
 Click OK. The change in password will be noted in the User Administration > History box.

Deactivate/Reactivate a User
 To deactivate/reactivate a user, click the Advanced menu button then select Configure user
accounts to open the User Administration window.
 Select that user name and right-click > Deactivate. A red X will indicate the user is deactivated. To
reactivate, right-click > Activate.
 Click OK to close.

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NOTE: Never disable the Administration Account.

View the Login History of a User

 Select a user name in the User Administration table. The lower half of the window displays the login
history associated with the selected user.
 Click OK to close the window.

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Technical Support

Analytik Jena offers expert technical support on all of our products. If there are questions about the product’s
use, operation or repair, please contact our offices at the locations below.
If located in North America, South America, East Asia or Australia:
 Call (909) 946-3197, and ask for Technical Support during regular business days, between 7:00
am and 5:00 pm, PST.
 E-mail your message to: [email protected] or [email protected]
 Fax Technical Support at (909) 946-3597
 Write to: Analytik Jena US 2066 W. 11th Street, Upland, CA 91786 USA

If located in Europe, Africa, the Middle East or Western Asia:

 Call +44(0) 1223-420022, and ask for Customer Service during regular business days between
8:30 am and 5:30 pm.
 E-mail your message to: [email protected]
 Fax Customer Service at +44(0) 1223-420561
 Write to: Ultra-Violet Products Ltd. Unit 1, Trinity Hall Farm Estate, Nuffield Road, Cambridge
CB4 1TG UK

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License Agreement

End User License Agreement

PLEASE READ THE FOLLOWING AGREEMENT CAREFULLY

This Agreement is between Analytik Jena US of 2066 West 11th Street, Upland, California 91786
(hereinafter "Licensor") and the end user of Analytik Jena software (hereinafter "Licensee").

Licensor has developed and offers to Licensee on a non-exclusive basis pursuant to the terms and conditions
set forth hereinafter, the following software, including related copyrighted instructional materials,
(collectively referred to hereafter as "The Software"):

VisionWorks® Software
The terms of this Agreement apply without regard for the method by which the Software is acquired by
Licensee. While the most common medium for acquiring the Software from Licensor is by CD-ROM, the
Software may, in some instances, be acquired by download; from a Licensor thumb drive acquired from
Licensor; from a CD ROM acquired from Licensor from a network location; or may be pre-installed on the
Licensee’s computer.
By using the Software, you are agreeing to be bound by all terms of this License. If you do not agree to the
terms of the License, you are not authorized to use the Software in any manner.

License
In consideration of payment of the License fee, which is a portion of the price you paid, the software,
including any images incorporated in or generated by the software, and data accompanying this
License and related documentation are licensed (not sold) to you by Licensor. Licensor does not
transfer title to the Software to you; this License shall not be considered a "sale" of the software and
Licensor retains full and complete title to the Software and all intellectual and industrial property
rights therein. It is to be understood that this non-exclusive and personal License only gives you the
right to use and display the software. You must treat the software like any other copyrighted material.
You may not copy the Software or the written material accompanying the software without the
express written consent of Licensor.

Restrictions
The Software contains copyrighted materials, trade secrets, and other proprietary material. You may
not re-sell, decompile, reverse engineer, disassemble or otherwise reduce the Software to a human-
perceivable form. Except as provided for in this License, you may not copy, modify, network, rent, lease,
or otherwise distribute the Software; nor can you make the Software available by "bulletin boards", on-
line services, remote dial-in, or network or telecommunications links of any kind; nor can you create
derivative works or any other works that are based upon or derived from the Software in whole or in
part. You may not transfer the license rights to the Software to another party.

Termination
This License is effective until terminated by either party. You may terminate this License at any time by
returning the Software to Licensor or destroying any permanent form of the software and all related
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documentation and all copies and installations thereof, whether made under the terms of this

License or otherwise. This License will terminate immediately without notice from Licensor if you fail to
comply with any provision of this License. Upon termination, you must destroy or return to Licensor any
permanent form of the software and related documentation.

Limited Warranty and Disclaimer

Licensor warrants the software and related documentation to be free from defects in materials and
workmanship, under normal use for a period of ninety (90) days from the date of purchase as evidenced
by a copy of the sales receipt or packing slip. Licensor’s entire liability and licensee’s exclusive remedy
will be replacement of the defective software and related documentation or refund of the purchase price
(at licensor’s election) upon return of the software and related documentation to licensor with a copy of
proof of purchase. This warranty gives you specific legal rights and you may also have other rights which
vary from jurisdiction to jurisdiction. You expressly acknowledge and agree that use of the software is at
your sole risk after the ninety (90) days. The software and related documentation are provided without
warranties and/or conditions of any kind either express or implied, except as provided above. Licensor
expressly disclaims all other warranties and/or conditions, express or implied, with respect to software
and related documentation including, but not limited to, the implied warranties and/or conditions of
merchantability and fitness for a particular purpose. Licensor does not warrant that the functions
contained in the software will be uninterrupted or error-free, or that defects in the software will be
corrected after the ninety (90) days. Furthermore, after the ninety (90) days, licensor does not warrant
or make any representation regarding the use or the results of the use of the software and related
documentation in terms of their correctness, accuracy, reliability, or otherwise. The limitations of
liabilities described in this section also apply to the third party suppliers of materials used in the
software. No oral or written information or advice by licensor or by representatives of licensor shall
create warranties, and/or conditions, or in any way increase the scope of this limited warranty. Licensee
assumes the entire cost of all necessary servicing, repair or correction after the ninety (90) days. Some
jurisdictions do not allow the exclusion of implied warranties, so the above exclusion may not apply to
you.

Limitation of Liability
Under no circumstances, including negligence, shall licensor be liable for any special or consequential
damages that result from the use of, or the inability to use, the software or related documentation,
even if licensor or authorized representative of licensor has been advised of the possibility of such
damages. Some jurisdictions do not allow the limitation or exclusion or liability or consequential
damages, so the above limitations or exclusion may not apply to you. In no event shall licensor’s total
liability to you for all damages, losses, and causes of action (whether in contract, tort (including
negligence) or otherwise) exceed the amount paid by you for the software.

Governing Law and Severability

This License shall be governed by and construed in accordance with the laws of the State of California,
without giving effect to any principles of conflicts of law. Any actions, suits or proceedings instituted in
connection with this License, the Software and/or related documentation shall be instituted and
maintained exclusively in the Superior Court for the State of California, County of Los Angeles, or in the
United States District Court for the Central District of California. By entering this License you hereby
consent to the venue and jurisdiction of the aforesaid courts. If any provision of this license shall be
unlawful, void, or for any reason unenforceable, then that provision shall be deemed severable from this
License and shall not affect the validity and enforceability of any remaining provision. This is the entire
agreement between the parties relating to the subject matter herein and shall not be modified except in
writing, signed by both parties.
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Navigate the Software

Navigating the Software

 Main Window
 Action Tabs
 Menu Buttons

Main Window
After the software is opened, the menu bar will look similar to the one shown below. The main window
contains the Action Tabs, Menu Buttons and modules (not shown) down the left side. Action tabs are shown
across the top row and are for functions used the most. Below each Action Tab is a set of corresponding
menu buttons. When a specific menu button is clicked, a module will display in the left column (not shown)
with additional function options. The example below shows Acquisition Action Tab
> Camera module.

The File and Edit menus always display on the screen. To the far right, Advanced menu and Help menus are
available.

Action Tabs
The purpose of the Action Tabs is to enable quick selection of major tasks.
 Acquisition: Functions to capture images and change camera, darkroom, lens etc. settings
 Image: Functions to apply image filters, brightness & contrast, pseudocolors, annotations, and
other tools to apply to an image
 1D Analysis: Functions to perform 1D Analysis on a captured image
 Area Density: Functions to perform Area Density on a captured image
 Colony Counting: Functions to perform Colony Counting on a captured image
Action tabs are shown in the top row. Each Action tab has a unique set of menu buttons with the
corresponding menu buttons displayed in the row below. The example below shows the Acquisition Action
Tab highlighted with yellow and its corresponding menu buttons. When selected menu buttons are clicked,
modules will open to provide function options.

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Note: For users with a UVP iBox® Explorer2™ Imaging Microscope, the menu buttons display differently.
Learn more about capturing images using the iBox Explorer, go to http://www.uvp.com/iboxexplorer2.html

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Image Windows

Each open image in the software workspace will appear in a separate Image Window. Several Image
Windows can be opened at one time. The window below shows several images open, layered with tabs for
selection of images.
 Organize Image Window
 Information Provided in Image Window
 Show the Image in Actual Size
 Fit the Image to Window
 Context Menu Commands
 Status Bar

Organize Image Windows

Images can be visible in the workspace area with either tabbed layout, shown above, or cascaded
images.
 To change from tabbed layout to cascaded layout, on the menu, go to Advanced > Configure
Application > Main Settings and uncheck the Tabbed Interface checkbox.
 To bring an Image window to the forefront, click on the image's title bar above the image.
 To close an image window, click onto the X in the image title bar.
 To resize a Cascaded Image window, drag the lower right corner (or an edge) to the desired size.

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Information Provided by the Image Window

Besides displaying an image, the Image tab includes the filename of the image. A caption of "Untitled" means
that the image has not been saved.

Show the Image in Actual Size

To show the image in actual size (no scaling), right click on the image and select View Original Size.
Images taken at high resolution will look large on the screen.

Fit the Image to the Window

To show the entire image in the window (scaled up or down as required to make it fit), right click on the image
and select View Best Fit.

Context Menu Commands

A context (shortcut) menu appears when the user clicks on the image itself with the right mouse button. It is a
shortcut menu that lets the user sidestep the menu buttons. Once brought up, treat it as a regular menu by
selecting features from the list. Click on the image with the right mouse button, a menu with the following
commands opens:
 Undo
 Redo
 Copy
 Paste
 Paste Special
 View Best Fit
 View Original Size
 Print
 Image Information

Status Bar
The Status Bar, located at the bottom of the software, shows:
 The current pointer position in an image
 The intensity of the image at the pointer position
 Status messages during operations
 Zoom and magnification options
The mouse position (POS) is displayed in pixels (X and Y). The Intensity is displayed as a single value if the
image is monochrome and has three values (Red, Green and Blue) if the image is colored. In both cases, the
value is reported as a percentage value of the maximum intensity. The ROI (Region of Interest) is also
reported.

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Obtain Image Information

 Overview
 Display Image Information
 Enter Notes
 Calibrating Image Scale
 Image History

Overview
The software maintains information about an image. Access the image information by right clicking on the
open image and left clicking Image Information. This Image Information includes:
 Overall Sample Width: Described as the number of metric units in the image's width, this
information is used to calibrate Rulers and Measurement Annotations. Image Scale is also
described under Spatial Calibration.
 Resolution: The width and height of the image in pixels.
 Bit Depth: The number of bits used to represent intensity. VW Software supports 8-bit, 12-bit and
16-bit image depth.
 Background: Indicates the color of the image background.
 Notes: Enter notes about an image.
 File Properties: Shows the file name, path, create date and size. All fields will be "N/A" if the
image has not yet been saved.
 Image History: The Image History tab provides a list of material changes to the image, when they
occurred and any notes to add about why or how the change was made are shown in the Image
History window.
The Image Information window is organized into two tabs. All information except History is on the first tab
Properties; image History is on the second tab.

Display Image Information

 Right click onto the image to obtain its image information. A shortcut menu will appear.
 Click onto Image Information at the bottom of the shortcut menu. The Image Information window
will appear.
 To switch between Properties and History, click the appropriate tab at the top of the window.

Enter Notes
 Display the Image Information window as described above.
 In the Properties tab, type information into the Notes text box.
 Click OK.

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Calibrate Image Scale

Each image in VW software has a scale associated with it. Scaling information is used to display rulers,
measure length and measure area annotations. Refer to Spatial Calibration for information on using this tool.

Images scanned into the system from a scanner or imported from another program are not calibrated. In these
two cases, therefore, the image's scale should be set.

Note: An uncalibrated image will have "Pixels" as the unit type. If the unit type is Pixels, the number of
units is the number of pixels in the image width and cannot be changed.

Related Topics:
 Spatial Calibration
 Image History

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Menu Buttons

Menus and Action Tabs Overview

Main Menu Buttons

There are four menu buttons that are always available (not dependent on what Action Tab is selected) these
are:
 File Menu: Contains commands to open, save, and print files. Also contains a FTP (file transfer
protocol) window to assist in using the file transfer function.
 Edit Menu: Contains the following functions: Copy/Paste, Undo/Redo, Define Region, Filters, and
Adjust (such as rotate, align and crop).
 Advanced Menu: Contains option for saving and playing Macros, displaying the log file,
configuring user accounts and viewing options.
 Help Menu: Contains access to the software help guides, information on the software version,
contact numbers and a link to the registration process.

Action Menu Tabs

Each Action Tab has an associated menu for providing software functionality. In many cases, the Action Tab
must be selected before the menu buttons under the Action Tab can be opened. The software is organized
with five Action Tabs:
 Acquisition Action Tab
 Image Action Tab
 1D Analysis Action Tab
 Area Density Action Tab
 Colony Counting Action Tab

Acquisition Action Tab and Menu Buttons

Image Action Tab and Menu Buttons

1D Analysis Action Tab and Menu Buttons

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Area Density Action Tab and Menu Buttons

Colony Counting Action Tab and Menu Buttons

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File Menu Button

File Menu Overview

File menu options are available at any time. The File menu does not need to be accessed through any
specific Action Tab.

Select from common file actions:

 Open image from file
 Open demo image
 Save
 Save as
 Close image
Select from printing options:
 Print preview
 Print
 Print a report
Access FTP (file transfer protocol) functionality.

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Open and Save Images

 Open Images
 Save Images
 Image File Types

Open Images
The software will open images in standard file formats including JPEG, TIFF, GIF, PNG, TGA and BMP. Video
files can be saved as AVI and SQV. If the image was previously saved using this software, then other image
details such as the image's scale, history and annotations will be loaded as well. Many demo images are
included with this software to increase user familiarity.

Open a Previously Saved Image

 From the File menu, choose Open image from file.
 Select the type of file to open. If unsure of the file type, select "All Supported Formats."
 Navigate through the drives to the file folder in which the image is stored.
 Select the desired image file.
 Click Open. An Image window containing the desired image will appear.

Open a Demo Image

 Go to File menu and click on Open Demo Image. The software keeps a folder "Images" that
shows by default where the demo images are stored.
 Select the desired demo image file from the list of available files.
 Click Open.

Save Images
Save images acquired in the software so they can be used in later sessions. To save a new image:
 Click on the File menu and select Save or Save As. The Save window will appear.
 Select the file type to use from the drop-down list. TIFF is the default file type. It is ideal to save
images in the TIFF format to maintain the most image data for analysis purposes.
 Navigate through the drive, folder or network structure to the desired location to save the image.

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 Enter a filename for the image.

 Click Save.

NOTE: If analysis, annotation, etc. is performed on an original image, the file must be opened with
VW software to view or modify this information. To view the analysis/annotation in a different
program, use the Flatten Layer tool and save the image as a NEW file. Once the flatten layer tool is
applied, the analysis cannot be modified in the new image.

Save Using a Different File Folder, Name or Type

 From the File menu choose Save As. The Save window will appear.
 Select the file type to use from the drop-down list near the bottom of the window.
 Navigate through the drive, folder and network structure to the location to save the image.
 Enter a filename for the image.
 Click Save.

NOTE: Analytik Jena’s imaging systems and software support network connectivity for saving and
sharing image files.

Image File Types

The software supports the following formats:
 TIFF: Tagged Image File Format, a common image format. Depending on settings, TIFF can be
either a lossy or a lossless compression format. In the software, it is used in the lossless mode to
reduce image file size without losing integrity. TIFF files generally have TIF or TIFF extensions.
 JPEG: Joint Photographic Experts Group. A common lossy compression image format used to
store images on disk. JPEG files generally have JPG or JPEG extensions.
 TGA: Truevision Targa image format. TGA is a lossless compression format that reduces file size
somewhat. TGA files generally have a TGA extension.
 BMP: Microsoft Bitmap image file format. BMP is a lossless format which provides
some compression to reduce file size. BMP files generally have a BMP extension.
 PNG: Portable Network Graphics, a common image format. PNG is a lossy compression format
that results in very small files. Files stored in PNG usually have a PNG extension.
 GIF: Graphic Interchange Format, a proprietary Xerox image compression format. GIF is a lossy
compression format that results in very small files. Files stored in GIF usually have a GIF
extension.
JPEG, PNG and GIF are lossy compression formats. TIFF, TGA and BMP are lossless compression
formats (at least, as used by this software; TIFF can actually be either lossy or lossless). Lossy
compression makes small, usually non-visible changes to an image in order to make the file size
smaller. Typically, formats that use lossy compression store in much less space than lossless
compression formats. By comparison, a lossless format does not store as compactly, but also does
not change the image in any way.

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Print

 Printing Image History

 File Print Command
 Printing Colony Count Results
 Viewing and Printing 1D Gel Analysis
 Reporting and Printing Area Density Results

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FTP Transfer

The FTP Transfer function allows the user to transfer files from one computer to another.

NOTE: The computers must be connected to a network to use the FTP transfer functionality.
 Click on File menu button > FTP Transfer. This will bring up a separate window that shows
the FTP Transfer plug-in.
 Click the Preferences button to open the Preferences FTP Transfer window.
 Enter the IP address of the system acquiring the image and the username and password. Click
Apply and OK.
 Start the software and take pictures.
 Press the Connect button on the FTP module.

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Edit Menu Button

Edit Menu Button Overview

Edit options are available at any time. The Edit menu does not need to be accessed through any
particular Action Tab.

Copy / Paste
 Copy
 Paste, Paste Special and Paste Special Options
Undo and Redo

ROI Tools (Region of Interest)

 New
 Rectangle
 Ellipse
 Polygon
 Freeform
 MagicWand
Filters
 Sharpen
 Remove Noise
 Enhance Exposure
Adjust
 Rotate
 Align
 Flip Horizontally
 Flip Vertically
 Crop
 Resize
 Reduce to Monochrome
 Change Image Depth

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Copy

Used on an image, the Copy command copies all or part of the image to the clipboard.

Copy an Entire Image

 Click Copy to copy the entire image. If a Region of Interest (ROI) is present on the image, adjust the
ROI to select the desired copy area.
 Choose Copy from the Edit menu button.

Copy a Selected Region Within an Image

 Select a Region of Interest (ROI) on the image using one of the selection tools.
 Choose Copy from the Edit menu.

Note: Copy can also be used on text, in which case it acts in the standard Windows fashion. Copied
images or sections of images will include annotations if the annotations were displayed when Copy
was used. If annotations were used, image must be flattened or they will not be included.

Related Topics:
 Paste
 Region of Interest (ROI)
 Layer Actions - Flatten Layers

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Paste

This command takes an image from the clipboard and imports it into the software, displaying it in a new
Image window.

Note: Paste can also be used on text, in which case it acts in the standard Windows fashion.

Paste an Image
 From the Edit menu button choose Paste. The image will be displayed in a new Image window.
Note: Paste is only available if there is an image on the clipboard.

Paste Special
This command allows an image on the clipboard to be merged into the current image. It is useful for adding
comparison or reference information into an image, for making composite images and for testing two
images against one another for motion.
 To modify the Paste Special options, go to Edit > Paste Special Options

Preview Frame Only functions shows where the Paste Special image will display and Apply with blend
check boxes.
The following three merge modes (Blend, Add, Subtract) are available in the Software:

 Blend: mixes the incoming image with the current image in a selected proportion. Click the Apply
with Blend check box to apply this function. If the Source proportion (Src%) is set to 100%, pixels
in the incoming image replace those in the existing image without mixing (i.e. the incoming image
is copied entirely over the existing image wherever it lands). Blend is used primarily to place
comparison information into an existing image, especially when using high proportions.

 Add: adds pixels in the incoming image to those in the existing image up to maximum intensity.
Add is used primarily to build composite images with little or no overlap. This feature requires no
additional settings.

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 Subtract: subtracts pixels in the incoming image from those in the existing image. Subtract is used
primarily to test for differences in or motion between two otherwise similar images. This feature
requires no additional settings.

Related Topics:
 Copy

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Undo and Redo

The Undo command will undo the last material change made to an image. Material changes include all
manipulations and the Paste Special command. The Redo command reverses the last Undo. To see what the
last material change did in detail, alternate between Undo and Redo. Changes made through the modules do
not permanently change the image.

Related Topics:
 Paste Special

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Region of Interest (ROI)

 About the Selection Tools

 Select a Region
 Adjust a Region
 Cancel a Region

About the Selection Tools

Select the Define region tools from the Edit button.

These tools allow users to mark part of the image for use in other operations. VW software provides several
Region of Interest (ROI) selection tools:

View Rectangular ROI View Elliptical ROI selects

selects rectangular regions. elliptical (oval) regions.

View Polygon ROI selects View FreeForm ROI selects

Polygonal regions. irregular regions.
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Select a Region
 Choose the desired selection tool from the Edit menu button.
 Rectangular and Elliptical ROI: To define a rectangular or elliptical type of ROI, start with the upper-
left corner of the desired region and drag the mouse downward and to the right until the desired
area is marked.
 Polygonal ROI: To define a polygonal ROI, click the left mouse button in the upper left area of the
desired ROI, then continue clicking the left mouse button to encompass the remainder of the desired
ROI. When the area is defined, right mouse click anywhere on the image to join the first and last
points and close the ROI.
 FreeForm ROI: To define a ROI with the mouse pointer, keep the left mouse button pressed and
draw around the region of interest. Lift the mouse button to automatically complete and enclose the
area.
 MagicWand ROI: To mark the ROI automatically on the image, click once inside the region of
interest and the software marks that area by identifying the edges. Zoom in on the image to get a
better outline of the ROI. The MagicWand slider allows adjustment of the sensitivity of the area
defined by the MagicWand.
Apart from Analysis features, Copy also uses the region of interest tool. Copy will copy the selected
region to the clipboard. If there is no selected region, the entire image will be copied.

Adjust a Region
If the selection is not quite right, move or resize it without having to start over:
 To change height or width: drag any of the white corner markers to the desired size.
 To move the selection: click on and drag the interior of the ROI to the new location.

Cancel a Region
 Click once anywhere on the image outside of the current ROI. The selection markers will
disappear. Once a region has been cancelled it cannot be undone.

Related Topics:
 Copy

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Image Enhancement Filters

Image enhancement tools allow users to highlight important features and remove unwanted signal in the
image.
 Sharpen
 Remove Noise
 Enhance Exposure

These functions are accessed from the Edit menu > Filter module.

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Sharpen

This filter enhances edges in an image, making them more visible. It is easier to see fine detail after an image
has been sharpened.

 Click onto Sharpen from the Edit menu button.

 Sharpening a large image may take a few seconds.

Image before Sharpen applied

Image after Sharpen applied

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Remove Noise

This filter removes periodic (patterned) noise from an image. Patterned noise is removed by creating a
frequency-space mapping (Fourier transform) of an image and removing frequency spikes away from the
graph's origin.

There are two issues to be aware of with noise removal. First, if the image has actual (desired) pattern
information, the operation will not be able to discern these from actual noise and it will remove them.
Second, the mathematics of the operation can cause some edges to be identified as patterns, resulting in
blurring on some images.

Remove noise is also referred to as Starfield Subtraction. The Image History indicates the noise removal as
Starfield Subtraction.

 Click onto Remove noise from the Edit menu button.

 Removing noise in a large image may take ten or fifteen seconds.

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Enhance Exposure
This filter option brightens the image without reaching complete saturation. However, image will not reach full
saturation. This function is not a linear increase of all pixels.

 Click onto Edit menu, then Enhance Exposure, and you will see the image become brighter.

Before

After

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Adjust the Image

 Rotate: Rotates the image around its center, useful for aligning images taken with a crooked gel.
 Align: Aligns the image to an adjustable grid.
 Flip horizontally: Mirrors the image right for left, correcting for an upside-down gel.
 Flip vertically: Mirrors the image top for bottom, also correcting for upside-down gels in the other
direction.
 Crop: Use the crop tool to select the part of the image you want to keep.
 Resize: Enlarges or reduces the image in size, uses less space and memory, and enables the image to
be seen on the entire screen.
 Reduce to monochrome
 Change image depth

These functions are accessed from the Edit menu > Adjust module.

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Rotate Function

Rotate an image by an arbitrary number of degrees. Rotate is helpful to correct for a misaligned gel. Graphically
select the degree to align the image based on an internal image feature.

Rotate an Image
 Click onto Rotate from the Edit menu.
 The Rotate window will appear and a grid will be overlaid on the image.

 Drag the grid so the yellow arrow moves in the direction you would like the image rotated.
 Once the grid is oriented to the desired position, click OK on the Rotate window.

Rotate an Image by an Exact Number of Degrees

 Rotate the image by an exact number of degrees. For example, correct for an upside-down gel by
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rotating it by 180 degrees.

 Click onto Rotate from the Edit menu. The Rotate window will appear and a grid will be overlaid on
the image. For this operation, you will ignore the grid.
 On the Rotate window, type the desired number of degrees into the Angle text box.
 Click OK.
Tip: Rotations by 90, 180 or 270 degrees do not degrade the image. These
operations can be completely reversed by a rotation of the same amount in
the opposite direction.

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Align the Image

Align the image to a grid by clicking onto the Edit Menu then select Align from the Adjust category of functions.

An Align Window will appear that will allow manual entry for moving the grid. As an entry is entered, the grid
moves into position in real time.

 Select OK.

 The image will align to the grid.

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Flip Image

Flip Horizontally
This filter provides a right to left mirror-image. Two clicks of the flip button will return the image to its starting
orientation.
 Click onto Flip horizontally from the Edit menu.

Image before Flip Horizontally

Image after applying Flip Horizontally

Flip Vertically
This image filter mirror-images an image, top for bottom. Unlike most image filters, it does not degrade the
image and may be used repeatedly with no ill effect. Two uses of the filter will return the image to its starting
orientation.

 Click onto Flip vertically from the Edit menu.

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Image before Flip Vertically

Image after applying Flip Vertically

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Resize Image

The Resize filter allows the image to be changed in size. It replicates or merges pixels as appropriate to arrive
at the new size. Resize most commonly would be used to create a smaller version of a very large image to
allow users to increase response time when applying filters or to import the image into another software
package that does not accept large images.

Tip: There is little point to increasing an image's size, although the filter does support it. Such an image
would have more physical pixels after the operation, but it does not gain any new information content.
 Click onto Resize from the Edit menu. The Resize window will appear.

 Select the desired new size from the drop-down list of suggested sizes.
OR
 Select the Enter custom size option and type either the desired new width or the desired new
height.
Note: To distort the image, clear the Maintain Aspect Ratio check box and type the new width and
height. This should be used only to reverse a similar distortion created in the image capture
process.
 Click OK. Resizing a large image may take a few seconds.

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Reduce Image to Monochrome

The Reduce to Monochrome filter reduces a color image to monochrome. This is primarily useful when colors
in an image are distracting rather than informative. For example, if light strikes certain surfaces from some
angles, a "rainbow effect" (prism) will appear. Another use is to adapt for some software packages and
techniques that require monochrome images or which are less reliable on color images.

The Reduce To Monochrome function uses a weighted mix of colors to arrive at each pixel's monochrome
intensity. Green is very heavily weighted while blue is almost disregarded.

 Click onto Reduce to monochrome from the Edit menu button.

 Reducing a large image to monochrome may take a few seconds.

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Change Image Depth

The Change Image Depth adjustment converts an image bit and color depth when needed.

 Click onto the Edit menu button and click onto Change Image Depth. Reducing a large image to
monochrome may take a few seconds.
 Click onto the new depth desired from the drop down menu and select OK.

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Advanced Menu Button

Advanced Menu Overview

The Advanced menu button contains additional software functions:

 Advanced Options
 Show Log File
 Configure User Accounts
 Display Loaded Modules
 Configure Application
 Macros
 Record Macros
 Administration Options
 View Options
 View Annotations: In the View Options menu, click to show or hide annotations on the screen. Click
here for more details on using Annotations.
 View Rulers: In the View Options menu, click to show or hide rulers on the screen. Click here for more
details on using Rulers.

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Log Viewer

The Log Viewer displays a log of user actions and presents the action list to the user in a log box.
 To access the Log Viewer, go to the Advanced menu button and click on Show log file.

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Display Loaded Modules

This window is typically used for technical support. Analytik Jena's technical support department can view this
window and diagnose and prevent future system failures.
 To access, click onto the Advanced menu button and select Display Loaded Plugins (Modules).

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Configure Application

The function Configure Application shows global application default settings (Preferences). A
Preferences - Main Settings window will pop up with the following settings:
 Switching between tabbed/windowed interface for images
 Setting the number of recently-opened images to show in the "open" dialog.
 Examine/modify the analysis/hardware settings.
To access, click onto the Advanced Menu Button and select Configure Application.

The Preferences window allows users to set functions for various analysis, camera and hardware as well as
other settings. Click each category in the left column to see the respective settings. After adjusting settings,
click Apply and OK to save the settings.

Note: Changes made to the preference settings apply only to the current user logged in and not applied
globally.

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Rulers

Rulers are located at the top and left of each Image window.

The rulers show the width and height of the visible portion of the image either in metric units (if calibrated)
or in pixels (if un-calibrated). When zooming in and out of the image the software updates the rulers to
show the actual size and position of the visible portion of the image. As the user moves the mouse over the
image, markers show the position on each ruler.

The units are shown in the upper-left corner. Pixels (uncalibrated) are abbreviated "px;" all other values
use standard abbreviations. When the rulers are calibrated to a standard measure, they may change units
as zoom is applied to the image detail. For example, an image calibrated in centimeters may switch to
millimeters when zoom is used. The measurements are still completely accurate; the rulers switch units
because they are designed to show a useful number of units at every point.

Note: The scale information used by the rulers also is used by measurement annotations. Length
measure annotations can be used to see the length of a feature that is not square to the rulers.

Show or Hide the Rulers

 Rulers may be hidden or shown individually for each Image window. Hiding the rulers provides
slightly more space in which to view the image.
 From the Advanced menu click onto View Rulers.

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Using Macros

 Overview
 Macros Navigation
 Record Macros
 Edit Macros
 Play a User-Created Macro

Overview
Macros are user-defined functions that group a series of commands into a single command. Macros allow
users to replicate image capturing conditions or image analysis functions which require multiple steps.
Typically a macro is created by recording steps the first time the user performs a series of actions. Details can
be edited or added to the recorded script, saved, and stored to be recalled and executed at a later time.

Macros Navigation
There are three main options: Macros, Record, Edit. To access these functions, click the Advanced menu
button. The Macros option allows users to manage all the information about the created macros. The
location of the file containing the macro scripts can be changed and loaded here. The created macros are
listed here and can be run, deleted, renamed or edited by accessing the macros script file. The recently ran
scripts will be listed under the macros options. As discussed later, the Record option allows users to create
macros and Edit allows users to modify a created macro.

Record Macros
 To record a macro, click onto Record from the Advanced menu.
 A Record Macro window appears.

 Provide a Macro Name and Shortcut Key. NOTE: The macro name must begin with an alpha
character.

 Select a Shortcut Key to execute the macro and provide a Description of the macro, if

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necessary.
 Click onto OK.
 A Recording window appears. Select Template Mode or Show Recording. To ensure the creation
of the macro, click onto Show Recording to display the software code of the macro as it is
formulated.
 Click onto any available command from the main screen or menu buttons to be saved into the
macro.
 Select Stop Recording when finished recording the macro.
NOTE: Template Mode allows variable user input from dialog boxes. For example, a user may want to
perform analysis on several different captured images. To do this, an image from the "Open" dialog box must
be selected by the user. The macro will wait for the user to provide input on which image to open in the "Open"
dialog box before continuing to the next step.

Edit Macros
 To edit a macro previously created, select Manage from the Advanced menu.
 A window appears with various options: Add, Run, Edit, Rename, and Delete.
 Click the Macro you want to edit, then select Edit. The following editing window will appear.

Play a User-Defined Macro

To playback a macro, select Macros from the Advanced menu then move the cursor down to the desired
macro and click on the macro name.

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Help Menu Button

Help Menu Overview

The Help menu contains the following features:

 Display help topics
 Application information
 Report an issue…
 Check for updates

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Display Help Topics

These are some of the help topics available. Simply click through the help topics or search for a word for
assistance using the help files.

To access, go to the Help Menu Button and select Display Help Topics.

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Application Information

The Application Information function brings up a window which describes the:

 Name of the software
 Version of software (useful when calling Analytik Jena's technical services department)

To access, click onto the Help Menu button and select Application Information.

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Acquire Images

Acquisition Action Tab Overview

The Acquisition Action Tab provides the menus to capture images with an Analytik Jena imaging system. The
Acquisition Action Tab > Camera menu is shown below.

Menu buttons contained in the Acquisition Action Tab are:

 Lighting and Other Hardware
 Lens Controls
 Lighting and Filters
 Tray Height
 Preferences
 UVP eLITE
 Microscope (for use with UVP iBox® Explorer only)
 Camera
 Integration
 Exposure Time
 Gain
 Post Processing (some cameras will have this feature)
 Binning
 Saturation Preview

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 Preferences
 CCD Temperature (for cooled cameras)
 Preview, Capture and Auto Exposure buttons
 Template Presets (initial button name says default)
 Close all Devices - Click this button to disconnect all hardware from the software. To reconnect
devices, click the Scan for Devices button.

Getting Started: Capture an Image

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Image Acquisition

To access the preview and capture buttons, click the Acquisition action tab.

Capture an Image
To capture an image:
 Place the gel, blot, plate (sample to be captured) into the darkroom.
 Click the Preview button in the Acquisition action tab to see a preview of the sample. The
Preview function is useful to ensure that the camera sees the sample clearly before taking the
actual picture. A Preview window will appear. Note: The Preview button now reads Stop
Preview.

 Set the optimal hardware settings (for the lens, camera, eLITE (optional), darkroom) from the
Lighting and Camera modules. Ensure that the Saturation Preview check box is selected.
 When the optimal settings have been selected, click the Capture button.
 Auto Exposure drop down button, located in the menu buttons, can be used for automatic
exposure settings. Select from:

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 Best (longer exposure): Exposes the image to the maximum value of the histogram
(65,000 gray levels).
 Better: Exposes to fill the histogram 50% so the brightest portion image is at 32,000 gray
levels.
 Good: Exposes to fill the histogram to 25% or 16,000 gray levels.
 Minimum (fast exposure): Exposes to fill the histogram to 10% over background.
Minimum and Good settings are particularly useful for chemiluminescent imaging applications and
allow for quicker image capture overall.

Note: If the captured image is black, increase the exposure time and/or check the Compensate exposure for
binning check box under Camera > Binning.
Note: If using a UVP iBox® Explorer Imaging Microscope, to select the hardware setting via the software go to:
Microscope

Related Topics:
 Set-Up Templates (also described as Presets): Save and reuse settings for repeat experiments.
 Set Standard Preference Settings

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Using the UVP iBox® Explorer Imaging Microscope

The Microscope menu will appear when the software connected to a UVP iBox® Explorer Imaging
Microscope. The functions in the menu control emission filters, magnification and location bookmarks. This
section discusses:
 Selecting emission filters
 Setting magnification levels including fine focus settings
 Setting location bookmarks

Emission Filters
Emission filter names are pre-set at the Analytik Jena factory. The names indicate the emission filter
wavelength and position in the filter tray.
To select an emission filter:
 Click a button in the Emission Filter menu. The selected button will be bordered in red. To
change the name of a filter or filter set:
 Click the double right arrow above the emission filter buttons. A pop up window will open.

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 Click the Edit button. A Filter Set Edit Form window will open.
 Change the Filter Name(s) in any of the four positions.
 To modify the color of the button, make the selection from the Color drop down menu for each
filter. The Preview button will show the selected color.
 The default name for a filter set is "Standard." To change the filter set name, type in a new name in
the Name field.
 Click OK to save.
If using more than one filter set, it is possible to create customized buttons for each set. To add a new filter set:
 Click the double right arrow above the emission filter buttons. A pop up window will open.
 Click the Add new set button. A Filter Set Edit Form window will open.
 Enter the Filter Name(s) in the four positions.
 To select a color for the button, make the selection from the Color drop down menu for each filter. The
Preview button will show the selected color.
 Enter a new filter set name in the Name field.
 Click OK to save.
To select a filter set:
 Click the double right arrow above the emission filter buttons. A pop up window will open.
 Click on the name of the filter set to be displayed in the Emission Filter module.

Magnification

To select a desired magnification level, click the radio button next to one of the settings. For further discussion
on using the magnification settings, refer to the UVP iBox® Explorer2 Imaging Microscope product manual.

Fine Focus
The Fine Focus plus and minus buttons are used for minor vertical adjustments of the platform allowing for
detailed focus adjustments.
 Click the minus button to move the platform down.
 Click the plus button to move the platform up.

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Bookmarks
It is possible to temporarily store various platform positions by using the Bookmark tool. This allows the user to
return to a saved bookmark position within an experiment. The Location Map displays the current XYZ position
of platform.

New
 Once the imaging platform is in the desired bookmark location (as indicated by the + on the
Location Map), click the New button. A new location ID will be created.
 To change the name of the bookmark label, click on the label name ("new bookmark") and enter the
new name.
Note: After the imaging platform has been moved, double click on an ID number to return the imaging
platform to a bookmarked position.

Update
It is possible to change the location of an existing bookmark.
 Move the imaging platform to a new position. This is displayed as a + on the Location Map.
 Click the ID number of the bookmark to be updated.
 Click the Update button to modify the bookmark to the new position.

Delete
To delete an existing bookmark:
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 Click the ID number of the bookmark to be deleted.

 Click the Delete button to remove the bookmark from the list.

Clear
To clear all bookmarks, click the Clear button.

Note: Once the software is closed, all bookmarks will be deleted.

Related Topics:
 Set-Up Templates to save and reuse settings for repeat experiments.
 Using the UVP eLITE Multispectral Light Source

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Lighting/Darkroom/Lens

UVP eLITE MultiSpectral Light Source

The automated UVP eLITE MultiSpectral Light Source is an added accessory to some systems. The Automated
TM

eLITE has a fiber optic cable that threads into the darkroom and strictly controls the wavelength of light shining
inside the darkroom.

In the Acquisition Action Tab in the Lighting menu is a list of functions for the UVP eLITE. These are:
 Filter: Drop down list consists of a variety of filters defined by the user.
 Light Engine: Turn the UVP eLITE On and Off.
 Template: A template is a group of UVP eLITE settings, which can be saved under a common name.
Select the Template for the sample, to apply from the drop-down box.
 Intensity: Provides the range for light intensity. The intensity ranges from 0 to 100%.
 Light Table: Turns the light on for the Transillumination light or for the Epi Illumination light.

Using the UVP eLITE Functions

For additional information on using the automated UVP eLITE MultiSpectral Light Source, refer to the user
instruction manual for this unit.
 Turn on the Light Engine in the software.
 Set the Intensity of the UVP eLITE. Select the highest intensity then move to a lower threshold if
desired.
 Turn on the Light Table to Trans or Epi. Use the Trans option if the light source is below the
sample. Use the Epi option if the light source is above and shining down on the sample.

Tip: Changes made to the UVP eLITE through the mechanical buttons on the device will NOT be reflected in
the software. Please double check settings periodically to ensure that the software settings match
with those on the device.

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Related Topics:
 Set-Up Templates to save and reuse settings for repeat experiments.
 Using the UVP eLITE with the UVP iBox® Explorer2 Imaging Microscope
 Set Standard Preferences

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Darkroom Control

The software works with a series of darkrooms offered by Analytik Jena. The software controls the
darkroom lighting and other hardware inside the darkroom. If the system includes a motorized darkroom,
the lift platform height position will be controlled by the software as well. This software controls the
following systems:
 UVP ChemStudio PLUS
 UVP iBox® Scientia Systems

Note: For UVP iBox® Explorer system settings, see separate information.

To access the darkroom controls, click onto the Acquisition Action Tab > Lighting menu button.

Hardware Settings Selection

 Filter: Click the drop down menu to select the user-defined emission filter.
 Reset Wheel: Click on this button to realign the filter wheel after accidental movement of the
darkroom.
 Epi Illumination: Darkroom supplies 365nm, 480nm and white light epi (overhead) illumination.
Click onto the radio button to make a selection.
 Transillumination: Darkroom supplies power to the UV transillumination source and also to the
white light transillumination source. Click onto a radio button to make a selection.
 Open Door Override: Under standard operating conditions, when the darkroom door opens, the UV
Light shuts off in the darkroom. When UV Safety Off is selected as the door opens, the UV Light
stays on.

Tray Height
 Open Door Override: Under normal circumstances when the darkroom door is open, the UV light
shuts down; to override this occurrence, click onto the Open Door Override switch.
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 Tray Location: Slide bar adjusts the height of the automated lift platform. (Manual platform
systems do not have this option). The warning (as shown below) appears when the door is open to
help prevent UV exposure.

Note: If the darkroom door is open, the following message will appear:

Related Topics:
 Set-Up Templates to save and reuse settings for repeat experiments.
 Set Standard Preference Settings

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Lens Control

This section contains information on adjusting lens and darkroom parameters to capture an image. To access
these functions, click on the Acquisition Action Tab > Lighting menu button. These instructions cover a
software-controlled lens included with the system.

Lens Control
 Aperture: Slidebar adjusts the amount of light that enters the lens.
 Zoom: Slidebar controls the object's apparent distance from the observer. Note: Not all systems are
configured with zoom capability. If a system does not have zoom capability, this slider will not
appear.
 Focus: Slidebar adjusts the clarity of the image.

Related Topics:
 Set-Up Templates to save and reuse settings for repeat experiments.

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Camera

Camera Functions

Functions under the Camera menu button include internal camera settings to control the image capture. To
access these functions click onto the Acquisition Action Tab > Camera menu button.

The camera functions are:

Integration
 Manual Integration: When this radio-button is selected before pressing Capture, the software
takes only ONE picture, with the current exposure time set. It lets user adjust all settings.
 Sequential integration: When this button is selected before clicking Capture, multiple pictures are
taken at a uniformly increasing exposure time. There are two options of exposure times: constant
and variable. Software allows for stored preset templates as well.
 Image Integration: With this option selected before capture, multiple pictures are taken at set
uniform intervals. There are two options: continuous, automatic, and total time. In the continuous
option, pictures are added together at a set time. In the automatic option, the picture is taken and
integrated until image is saturated. In total time, user can adjust frames and exposure time to build
consecutive images and see the different exposure times on camera.

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Exposure Time
Adjusts the time for how long the camera should expose the image and collects light from the sample.
Various arrows increment the time in a steady manner.

The Auto Exposure drop down button, located in the menu buttons, can be used for automatic exposure
settings. Select from:
 Best (longer exposure): Exposes the image to the maximum value of the histogram (65,000 gray
levels).
 Better: Exposes to fill the histogram 50% so the brightest portion image is at 32,000 gray levels.
 Good: Exposes to fill the histogram to 25% or 16,000 gray levels.
 Minimum (fast exposure): Exposes to fill the histogram to 10% over background.
Note: Minimum and Good settings are particularly useful for chemiluminescent imaging applications and allow
for quicker image capture overall.

Gain
Available only for some cameras.
 Gain: Set a high value for gain to get increased sensitivity. That also increases background
noise. In preview Gain, as you increase the gain, the image will get brighter.
 Preview ROI%: Set to increase or decrease the zoom onto the region of interest.

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Post Capture
Some cameras may have the post processing functions. Used for longer exposures to produce a high- quality
image by removing the noise floor and filtering out pixels that are substantially brighter than their surroundings.
 Flat Field Adjustment
 Auto-Adjust histogram: Automatically adjusts the image histogram for ideal captured image
results.
 Crop
 Pixels Averaging
 Darkframe Subtraction

Binning
 Preview: Sets the binning mode to be used when Preview is selected.
 Capture: Sets the binning mode to be used when Capture is selected.
 Compensate Exposure for Binning: When the binning mode is changed (above), it automatically
adjusts the exposure time to match the brightness between preview and capture.

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Saturation Preview
Saturation Preview: Click this checkbox during Preview to see if any part of the image is over exposed to light.
Over exposed pixels are shown in Red color.

Preferences
Shows the default camera settings. Click the Preferences button to open a Preferences - Camera window to
modify default settings.

CCD Temperature
For cooled CCD cameras only. Provides the CCD camera's cooling status as a snowflake slide bar. When
completely cooled, the snowflake will be to the far right on READY.

Related Topics:
 Capture an Image
 Set-Up Templates to save and reuse settings for repeat experiments.

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Camera Integration

Integration is the term used to mean the length of time the camera is exposed to incoming light. Integration
time and Exposure time are sometimes used interchangeably. There are various different types of Integration
modes provided by VW software.
 Manual Integration
 Sequential Integration: Constant Time or Variable Time
 Image Integration: Continuous, Automatic, or Total Time

To access the Integration feature go to the Acquisition Action Tab and click onto the Camera Menu button and
find the Integration feature.

Manual Integration
The software takes only ONE picture, with the current exposure time set.

Sequential Integration
Used when the ideal exposure time for the sample is unknown. A low light Chemiluminescence sample may
have an unknown exposure time. This option captures multiple images at either constant or variable time-
intervals. The user may browse through the images taken and select the image that provides the best results.

To use Sequential Integration, click onto the Sequential Integration radio button and click on the
Sequential button.
 Constant Time Intervals: Use this when the number of images and the longest exposure time is
known. VW software will then calculate the integration time to be used for the first image and use
the same as an increment to capture subsequent images. E.g., if five images are to be taken and the
maximum integration time is set at 20s, the exposure times calculated will be as follows:
 First: 4s
 Second: 8s
 Third: 12s
 Fourth: 16s

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 Fifth: 20s

 These five pictures will be placed inside a sequence file, and can be viewed in the Player to select
the perfect image.
 Variable Time Intervals: Use this setting to take multiple images with different exposure times. No
addition of exposures is done as in the ’Constant Time Intervals’ case. A large number of images can
be captured in sequence. Each image needs a separate line of entry in the table shown.

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 New Sequence: Add a new sequence of images.

 Change Name: Enter a new name for the currently displayed sequence.
 Del Sequence: Deletes the currently displayed sequence.
 Add Time: Adds a new entry to the sequence. Enter time in Minutes, seconds and milliseconds.
’Amount’ shows the total time in milliseconds.
 Delete Time: Deletes the currently active entry of the sequence.

Image Integration
Used when the integration time offered by the camera is not enough for a long exposure. In this mode, VW
software does "stacking" of frames, i.e., it adds the corresponding pixel values of first image-frame to the next.
This compensates for a low light limitation, by making dim areas brighter with increasing number of images.
[Stacking replaces the first image after the second is captured and pixel values added to it from the first.]
Analytik Jena’s cameras typically have a long exposure time capability, which would be more than enough for
most samples. If, however, the application’s requirements go beyond what is available, then this feature offers
a software solution.

Switch to the ’Image Integration’ option and select from the drop-down menu options.

 Automatic Exposure: With this box checked, the stacking automatically stops once the image gets
saturated.
 Continuous Exposure: this option allows images to be stacked together in an equal exposure
mode.
 Total Time Exposure: Select this option to have a greater control over how many images to capture,
and for how long each one should be exposed. Interval Time is simply the division of total time by
number of images. Uniformly exposed images are stacked.

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Binning Modes

Binning is an advanced feature provided by most Analytik Jena’s cameras. "Binning" literally means to "bin" or
"combine" pixel values. A camera set to the binning of 4 x 4 (read 4 by 4) means, that it "combines" the values
from 4 pixels across and 4 pixels down (16 pixels in all) into one single pixel on the image. Binning is also
referred to as creating a "Super Pixel".

Higher binning, hence, increases the sensitivity of the images, at the cost of resolution and image-size (due to
combining of pixels). A good strategy is to Focus at higher binning (say 2 X 2) so that the refresh rate is higher
and then to snap at a lower binning, to capture full resolution in the resultant image.

To access the Binning feature go to the Acquisition Action Tab and click onto the Camera Menu button and
find the Binning feature.

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Perform 1D Analysis

1D Analysis Action Tab Overview

The 1D Analysis Action Tab provides the means to perform 1D Analysis on a captured or demo image.

The functions in the 1D Analysis Action Tab includes:

 Find Lanes and Bands Menu
 Find Lanes and Bands
 Define Region of Interest on the image
 Find Lanes and Bands
 Edit Lanes and Bands
 Edit Objects
 Delete Selected Objects
 Add Lane
 Add Band
 Object Properties
 Find Bands in Selected Lanes

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 Straighten Selected Lane

 Auto Curve Selected Lane
 Settings
 Mass Unit
 Background Color
 Force Lanes Straight
 Constant Width for all Lanes
 Lane Volume is Sum of Bands
 Additional Settings
 Lane Profile
 Molecular Weight
 Calibrate Lane
 Uncalibrate Lane
 Concentration
 Lane Profile Graph
 Concentration
 Background Correction
 No Background Correction
 Straight Line
 Rolling Disc
 Joined Valley
 Area Between Lanes
 Show Corrected Image
 Rf (Retardation Factor)
 Edit Objects
 Add Rf Line
 Delete Selected Rf Lines
 Delete All Rf Lines
 Select Standard Lane
 Dendrogram Menu
 Settings Menu - additional settings
 Results Menu
 Print Reports - page set-up, print preview and print options
 Export Report to Excel or CSV
 Report Type (drop down)
 Show Report
 Clear

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Getting Started:
The 1D Analysis topics can be accessed by clicking on the following sections:
 1D Analysis Image Windows Features
 Finding 1D Gel Lanes and Bands
 Edit Lanes and Bands
 1D Analysis Settings and Preferences
 Viewing and Printing 1D Gel Analysis

Related Topics:
 Performing Dendrogram Analysis Calculations
 Performing Molecular Weight Calibration
 Generate Lane Profile Graph
 Performing Concentration Calibrations

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Lanes and Bands

Finding Lanes and Bands

This section identifies the step-by-step processes for automatically finding lanes and bands, identifying
Region of Interest and performing both automatic and manual searches for lanes and bands.

Define Region of Interest (ROI)

By defining a Region of Interest, the software will analyze only the lane and band information within that
area. This typically improves the accuracy of the automatic lane and band finding when the image
background and gel background intensities vary.
 Select Define Region from the Find Lanes and Bands menu. (The ROI tool utilized is
rectangular by default.)
 Outline the lanes of interest with the ROI tool by positioning the mouse at one of the corners to
move that corner of the ROI. Then drag the corner to the desired location. The area defined will
be encapsulated in green.
 Next, go through the Perform Automatic Finding of Lanes and Bands steps below.

Perform Automatic Finding of Lanes and Bands

After defining the region of interest, the software will only analyze the lane and band information within
that area. This typically improves the accuracy of the automatic lane and band finding when the image
background and gel background intensities vary.

 Select Find Lanes and Bands from the Find Lanes and Bands menu. The
Lanes/Bands dialog window appears and a basic search is automatically performed.

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 If the results are not satisfactory, keep the window open and adjust the search parameters
as described in the following Adjust Lanes and Bands Search Parameters section, or click
OK and use the manual Add Lane and Add Band functions to identify all lanes and bands
correctly. Clicking Cancel returns the image to the previous state being opened in the
Lanes/Bands dialog (for instance, if there were no lanes or bands before opening the
window, Cancel will return to an image with no lanes or bands.)

Note: Typically the options for "Constant lane width across all lanes" and "Force all lanes straight" are
turned on for 1D lane/band analysis.

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Adjust Lanes and Bands Search Parameters

If the basic automated search did not find all lanes, the parameters may be adjusted.
Under Search options in the Find lanes and bands dialog window the user may choose from several
options.
 Constant lane width across all lanes: If selected, the width of all the lanes will be consistent. Use
this option if most of the lanes in the image are of the same width
 Force lanes straight: Use this option if the lanes are curved. The software automatically adjusts
the lane values so that they are straight in the analysis.
 Use auto-detected parameter values: If selected, this function returns the find lanes and bands
search options to its default values.
 Under Search Parameters
 Ensure that the Background is correctly set to white or black.
 To add Lanes and Bands change the Lane Sensitivity and/or Band Sensitivity.
 Return to the Automatically Detected Parameters-On the Find Lanes and Bands window click
Use auto-detected parameter values. The original parameters will be restored and the image will
display lanes and bands as originally detected in Basic Search.

Tip: If the search mode is Bands only, the lane sensitivity value will be reset but the system
will not search for lanes with the new value. To search for lanes and bands both, ensure that
the search mode at the top of the window is Lanes and bands.

Next Steps: Perform a Molecular Weight Calibration, Concentration Calibration, or Dendrogram Analysis

Related Topics:
 Add Lanes and Bands
 Delete Lanes and Bands
 Edit Lanes and Bands
 View Lane and Band Information

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Lane and Band Information

First Find Lanes and Bands to view information on lanes and bands. The software allows users to view lane
information in the following formats as listed below:
 Lane and Band Properties
 Lane Profile Graph
 Data Explorer
 Printing Data Explorer Tabular Reports
 1D Analysis Settings (default preference settings)

Lane and Band Properties

View and Use Lane Properties
To select a lane, click a lane of interest outside of a band area. The lane will appear with four white
boxes one in each corner of the selected lane. From 1D Analysis Action Tab > Edit lanes and bands >
select Object properties which allows users to view details for the lane/band including:
 Name
 Current Color
 Current Font
 Geometry
 Molecular Weight Standard
 Mass

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Lane Properties also offers the following information:

 Lane ID
 Unit Name of Mass
 Intensity Maximum
 Intensity Volume
 Concentration Maximum
 Concentration Volume

View and Use Band Properties

To select a band, click on a band of interest. The band will appear with four red boxes one in each
corner of the selected lane. From the 1D Analysis Action Tab > Edit lanes and bands, select Object
properties. In this window, the software allows users to perform various changes to the lane including:
 Name
 Geometry
 Band ID
 Left and Right band positions
 Calculated Peak Values (Rf value and Molecular Weight)
 Intensity of the band, including its Maximum, Volume, % of lane, and Mass; and
 Concentration of the band, including its Maximum, Volume, % of lane, and Mass.

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Information Found in the 1D Analysis Image Window

The Image Window also displays various 1D gel objects and allows editing with the mouse.
 Lane Curve Lines: Vertical lines down the center of each lane that control lane curving.
 Bands: Marked by horizontal lines at the band peak.
 Rf Lines: White lines interrupted by small white circles at each intersection of the Rf line and a
lane.

In addition to the objects above, there are also some 1D gel text labels that help identify data in the image.
The labels cannot be directly manipulated. These labels are:
 Lane IDs: Letter codes at the top of each lane. Calibrated lanes are indicated by showing the lane
ID in brackets (e.g. "[A]" as opposed to "A").
 Lane Names: Names entered in the Lane Information window for each lane, also shown at the top
of the lane.
 Band IDs: Letter-and-number combinations showing the lane (letter) and band position (number)
that uniquely identifies each band.

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Add Lanes and Bands

The software allows the user to add lanes and bands manually.

Add Lanes Method No. 1: From the Find Lanes and Bands Window
 To add lanes, open the 1D Analysis Action Tab > Find Lanes and Bands menu.
 Define region and perform an automated search for lanes and bands.
 While still in the Find Lanes and Bands window (shown below), adjust the Lane sensitivity using the
slider control. In general, to detect more lanes, drag the slider to the right; to detect fewer lanes,
drag it to the left. Sometimes, if the sensitivity is very low, moving the slider to the right may find
more and better-defined lanes. As the sensitivity is changing, the image adjusts automatically.
Values can also be typed into the text box next to the Lane Sensitivity slider.
 Select OK.
 The updated image will display with the new lanes identified in the image window.
Note: The up and down arrows can also be used for incremental adjustment of the lane and band
sensitivity slider bars. The software will automatically search after any adjustments are made.

Add Bands Method No. 1: From the Find Lanes and Bands Dialog
Window
 To add bands, open the 1D Analysis Action Tab > Find Lanes and Bands menu.
 Define region and perform an automated search for lanes and bands.
 While still in the Find Lanes and Bands dialog window (shown above), adjust the Band sensitivity
using the slider control. In general, to detect more bands, drag the slider to the right; to detect fewer
bands, drag it to the left. Sometimes, if the sensitivity is very low, moving the slider to the right may
find more and better-defined bands. As the sensitivity is changing, the image adjusts automatically.
Values can also be typed into the text box next to the Band Sensitivity slider.
 Select OK.
 The updated image will display with the new bands identified in the image window.

Add Lanes Method No. 2: From the Image Window

 To add lanes, open the 1D Analysis Action Tab > Find Lanes and Bands menu.
 Define region and perform an automated search for lanes and bands.
 Click onto the Add Lanes function in the Edit Lanes and Bands menu.
 Move the cursor over the image. A movable box will appear when the cursor is moved. Simply move
the mouse over the image to a specific area to add a lane. If the color of the box is green, a lane can
be placed. If, however, the color is red, there is already a lane at this position and another lane
cannot be placed there. Move the mouse until the box appears green as shown below.

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 Click the left mouse button to place the new lane.

 When finished placing the new lanes, click Edit Objects to disable the Add Lanes tool.

Add Bands Method No. 2: From the Image Window

 To add bands, open the 1D Analysis Action Tab > Find Lanes and Bands menu.
 Define region and perform an automated search for lanes and bands.
 Click onto Add Bands function in the Edit Lanes and Bands menu.
 Move the cursor over the image. A movable horizontal line will appear whenever the cursor is moved
over a lane. Simply move the mouse over the image to the spot where to place the new band. If the
color of the horizontal line is green, a new band can be placed where the cursor is. If, however, the
color is red, there is already a band at this position and a new band cannot placed there. Move the
mouse until the line appears green as shown below.

 Click the left mouse button to place the new band.

 When finished placing band(s), click Edit Objects to disable the Add Bands tool

Next Steps: Perform a Molecular Weight Calibration, Concentration Calibration, or Dendrogram Analysis

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Related Topics:

 Delete Lanes and Bands

 Edit Lanes and Bands
 Clear All Lane and Band Information
 Lane and Band Information
 Viewing and Printing 1D Gel Analysis

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Delete Lanes and Bands

Delete Lanes
 Click 1D Analysis Action Tab > Find Lanes and Bands menu
 Click on the lane to delete. A box will appear around the band with white boxes at the corners.
 Click Delete selected objects.

Delete Bands
 Click 1D Analysis Action Tab > Find Lanes and Bands menu
 Click on the band to delete. A box will appear around the band with red boxes at the corners.
 Click Delete selected objects.

Next Steps: Perform a Molecular Weight Calibration, Concentration Calibration, or Dendrogram Analysis

Related Topics:
 Add Lanes and Bands
 Edit Lanes and Bands
 Clear All Lane and Band Information
 Lane and Band Information
 Viewing and Printing 1D Gel Analysis

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Edit Lanes and Bands

Note: Image analysis must be performed prior to editing the lanes and bands.

Move Lanes and Bands

The software allows the user to move lanes and bands using the Image Window function.
 Click 1D Analysis Action Tab > Find Lanes and Bands menu > Edit objects
 From Find Lanes and Bands menu > Settings, uncheck constant width for all lanes.
 Select the lane or band to move by clicking on it. Control handles will appear at the four corners of
the lane as white boxes and red boxes for bands.
 Drag the box side to side (or up and down) until it is moved to the desired location. Note that lanes
can only be moved between other lanes, not beyond other lanes. Bands can only be moved between
the bands above and below it, not beyond other bands.
Move bands using Lane Profile Graph

Resize Band Extents

The software allows the user to resize bands using the Image Window function.
 To turn on and view the Band Extents, click 1D Analysis Action Tab > Find Lanes and Bands
menu.
 In the Settings module, click onto the Additional Settings function. A new Preference-1D
Analysis window appears.
 Select the 1D Analysis tab and click the Band Extents check box. Click Apply and OK. Close the
Preferences Window.
 Click Edit Objects from the Find Lanes and Bands menu. Place the mouse pointer over the band to
resize, and click on the band. Control handles will appear at the four corners of the band as red
boxes.
 Place the mouse hand over the top or bottom of the band's extents and click and drag the box border
to increase or to decrease the size of the band until the size matches the band seen on the image.
Resize bands using the Lane Profile Graph

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Place Bands Exactly

 Click 1D Analysis Action Tab > Find Lanes and Bands menu.
 Select the band to resize. Control handles will appear at the four corners of the band as red
boxes.
 Right click onto the band of interest. Analysis > 1D Analysis > Bands and then select Band
Properties. The Band Information window appears.
 In the section of the window labeled Geometry, the numerical values of the Top, Peak and
Bottom of the band may be changed.
 Enter the new numbers, click on OK. Now the location and dimensions of the band reflect
precisely the values entered.

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Next Steps: Perform a Molecular Weight Calibration, Concentration Calibration, or Dendrogram Analysis

Related Topics:
 Add Lanes and Bands
 Delete Lanes and Bands
 Clear All Lane and Band Information
 Lane and Band Information
 Viewing and Printing 1D Gel Analysis

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Lane Profile

Lane Profile Overview

The 1D Analysis Action Tab > Lane Profile menu provides the following tools:
.

 Molecular Weight
 Calibrate lane
 Uncalibrate lane
 Concentration
 Lane profile graph
 Concentration
 Background Correction
 No background correction
 Straight line

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 Rolling disc
 Joined valleys
 Area between lanes
 Show corrected image
 Rf (Retardation factor)
 Edit objects
 Add Rf line
 Delete selected Rf line(s)
 Delete all Rf line(s)
 Select standard lane

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Molecular Weight

Perform Molecular Weight Calibrations

Overview
Molecules in an electric field migrate through a gel matrix at rates inversely proportional to the log10 of the
number of base pairs. Large molecules migrate more slowly due to large frictional force from the pore of the
matrix while small molecules migrate faster due to less frictional force.
There are many experimental conditions affecting the migration rate: gel concentration; conformation of the
DNA; applied voltage; direction of electric field; base composition and temperature; presence of intercalating
dyes; and electrophoresis buffer. It is therefore desirable to use a known molecular weight standard as a
reference to unknown samples. This marker is used to calibrate the resulting molecular weight for each
unknown band.

Using a molecular weight (MW) marker results in a band encompassing the whole gel horizontally. This
band can be thought of as the distance traveled of a band relative to its front (Retardation factor - Rf) or
starting position. This Rf line exists for each band in the molecular weight standard. Any bands in the
unknown samples that migrate to any of these Rf lines are then compared to the Rf lines.

Note: Rf line functions are only required if there are less than two calibrated lanes

Next Steps:
 Applying a Molecular Weight Standard to a Lane
 Molecular Weight Calibration: Add, Edit, Remove, Copy Functions
 Retardation factor Rf Lines

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Apply a Molecular Weight Standard to a Lane

 Calibrate a Lane
 Stretch Factor
 Manual Placement of Weights
 Exact Placement of Bands

Calibrate a Lane
 First identify all lanes and bands in the image.
 Select the lane to calibrate. [ Edit Lanes and Bands ]
 From the 1D Analysis Action Tab > Lane Profile Menu select Calibrate Lane.
 A new Molecular Weight window opens. On tab Step 1: Select MW standard click on the
standard to use and then select Next. If the standard is not on the list, click Add to add a
standard to the list (see Adding a Molecular Weight Standard to the Library).

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 A new screen appears Step 2: Calibrate MW standard.

 In the Step 2 screen, the weights can be adjusted to match the bands that actually appear.
Complete instructions for this appear below-see Stretch Factor.
 Click OK to save the calibration.

Stretch Factor
The stretch factor establishes a mathematical relationship between the weights to describe their relative
movement. The larger the stretch factor, the more the lighter weights move in relationship to heavier ones. The
smaller the stretch factor, the less the lighter weights move. A stretch factor of 1.0 indicates linear movement
(weights move in direct proportion to their relative weights).
To adjust the weights to match the bands, use the stretch factor as follows:
 In the Step 2 screen of the Molecular Weight tool, ensure that Proportional calibration mode is selected.

 Drag a known weight up or down with the mouse until it matches the appropriate band. Alternatively,
select the weight with the mouse (or TAB key) and move the weight up and down with the UP and
DOWN arrows on the keyboard (this helps adjust the weight by small amounts). When there is a match of
the weight with the band, the line color changes from blue to yellow (default colors).

 Adjust the stretch factor (scaling) between weights until the other weights match their appropriate
bands. Adjust it using the mouse wheel (rolling up increases the value, rolling down decreases it), or
enter a new value into the text box and click Set.
 Click OK to save the calibration.

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Note: Using the Stretch Factor gives a weight match on the band up to 0.5% of the assigned
weight. To obtain exact placement on the band, use the manual mode, described in the
Using Manual Placement of Weights below.

Manual Placement of Weights

Instead of using the Stretch Factor, the weights can be adjusted individually using manual mode:
 In the Step 2 screen of the Molecular Weight tool, select Independent calibration mode.
 Move each weight separately, with either the mouse or the keyboard arrows, to position them exactly
on the band. Weights cannot pass one another, so it is usually best to start with either the lightest or
heaviest weight and work toward the other end. When there is a match of the weight with the band,
the line color changes from blue to yellow (default colors).
 Click OK to save the calibration.

Exact Placement of Bands

In the Independent calibration mode, as soon as the weight is exactly on the band, the color of the line
changes from blue to yellow (default colors). This means exact placement is achieved-- the weight will be
exactly on the band peak. Exact placement only occurs when the color changes from unmatched to matched;
further movement of the weight may alter the exact positioning. When in doubt, move the weight completely
away from the band and reposition it with the arrow keys until the color changes.

The Independent > Tag All button reduces some manual work by aligning the weights of the ladder starting
with first band in the lane. Stretch factor is not taken into account &endash; only simple matching is done.

Note: After calibration of two or more lanes, Retardation factor lines will be automatically calculated and
will replace any previous Rf line work.
Note: On the second window of the calibration operation (where users adjust weights to bands), the
colors of both the unmatched and the matched lines can be changed by using the controls in the
upper right corner.

Related Topics
 Molecular Weight Calibration

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Changing Molecular Weight Settings

 Add Molecular Weight Standard to a Library

 Edit Molecular Weight Standard to a Library
 Remove Molecular Weight Standard to a Library
 Copy Molecular Weight Standard to a Library

Calibration of molecular weight (MW) involves associating a known standard with one or more lanes in the
image. This allows Rf values to be calibrated to molecular weight values. The software allows the user to
employ several different standards per gel. To help with analysis, a library of molecular weight standards is
provided in the software. Standards can be added, edited, and deleted from the library using the following
instructions.

Add Molecular Weight Standard to the Library

 First identify all lanes and bands in the image.
 Select the lane to calibrate by clicking on it. [ Edit Lanes and Bands ]
 Select 1D Analysis Action Tab > Lane Profile menu and click Calibrate lane.
 In the Step 1: Select MW standard window, click Add. A new MW standard window opens. In this
window, provide the new Name of the standard, Group, and Unit Type.
 Click Add. Now the numerical values of the standard can be entered. After entering the numerical
value, click on Add again for as many values as desired.
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 Click OK on the right side. The first window appears again with the new standard entered.

Edit Molecular Weight Standard in the Library

 First identify all lanes and bands in the image.
 Select the Lane to calibrate by clicking on it. [ Edit Lanes and Bands ]
 Select 1D Analysis Action Tab > Lane Profile menu and click Calibrate lane. A Molecular
Weight window opens.
 In the Step 1: Select MW standard tab select the standard to edit. (NOTE: This applies only to
standards created by users. The MW Standards included with the software cannot be edited or
deleted.)
 Then click on Edit.
 The information previously entered into this window (including group, name, units, or most
commonly, weight) can now be changed.
 Select the value, then click Edit to change the value. Once all changes are made, then click OK.

Remove Molecular Weight Standard in the Library

 First identify all lanes and bands in the image.
 Select the Lane to calibrate by clicking on it. [ Edit Lanes and Bands ]
 Select 1D Analysis Action Tab > Molecular Weight and click Calibrate lane.
 In the Step 1: Select MW standard tab select the standard to delete. (NOTE: This applies only to
standards created by users. The MW Standards included with the software cannot be edited or
deleted.)
 Then click on Remove.

Copy Molecular Weight Standard in the Library

 First identify all lanes and bands in the image.
 Select the Lane to calibrate by clicking on it. [ Edit Lanes and Bands ]
 Select 1D Analysis Action Tab > Molecular Weight and click Calibrate lane. A new window
appears.
 In the Step 1: Select MW standard tab select the standard to copy.
 Then click on Copy.
 The Edit window will appear. Change the Name of the new MW Standard. Click on Add to enter a
new value or click on a value and click Edit to make changes in the copy. Then click on OK.

Related Topics:
 Applying a Molecular Weight Standard

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Background Correction

Background Correction Options

Background correction is necessary to account for possible variable illumination or overexposure during image
capturing, the software offers options to apply mathematical background correction. These options generally
remove background "noise" and elevated levels of pixel intensity due to excess exposure, highlighting data.

Note: Before selecting to correct the background in the image, first find lanes and bands. To use the
background correction options, select 1D Analysis > Lane Profile > Background correction options.

The software offers these background correction options.

 No background correction
 Straight line
 Joined valleys
 Rolling disc
 Area between the lines

No Background Correction
Selecting this option on the menu leaves the image uncorrected for overexposure, "as is."

Straight Line
Selecting this option tells the software to place a straight (but not necessarily horizontal) line under the
lowest points at the beginning and end of each lane. The software removes the area of the graph under
the straight line, so that all remaining values are emphasized. Straight line correction tends to correct
the well for overexposure, and for variable illumination that is focused on an edge or corner of an image.

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Note: Straighten lines by using right-clicking the mouse button to open the shortcut menu.

Joined Valleys
Selecting this option accentuates the data by telling the software to join lines between the lowest point, or
"valley", before the first band, between each pair of bands, and after the last band.
Intensities above the valleys (band data) are emphasized. Joined valleys can perform well in a variable
illumination condition where the "bright spot" is somewhere in the middle of the image, and where
bands are sharply defined and quite distinct. Joined Valleys requires a sensitivity value to be entered. A
higher value of sensitivity starts "eating" into the bands, which may not be accurate.
To Use Joined Valleys:
 Select 1D Analysis > Lane Profile > Background correction options select Joined valleys.
 A pop-up window appears that allows the user to set a sensitivity value from 0 to 100.
 Change the size either by typing in the sensitivity value, or by using the up and down arrow signs. Click
OK after entering the number.

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Rolling Disc
Picture turning the lane profile graph upside and then rolling a ball over the new top. Everything the
ball is able to roll over is eliminated by the software; whatever the ball cannot roll over remains in the
graph for analysis. Rolling disc performs well in all background conditions providing the size of the disc
is carefully chosen. An excessively small disc will "roll into" bands, eliminating the band data almost
entirely. An excessively large disc rolls across the lowest valleys, acting much like Straight Line
correction.
To Use Rolling disk:
 Select 1D Analysis > Lane Profile > Background correction options and select Rolling disk
from the drop down menu.
 A pop-up window appears that allows the user to set a Rolling Disk Radius value from 1 to
1000.
 Change the size either by typing in the sensitivity value, or by using the up and down arrow signs. Click
OK after entering the radius

Area Between Lanes

Part of the image may be overexposed, and there may be patterns of deformity between the lanes. This
correction takes cross-sections between lanes and subtracts those "inter-lane" profiles. Area Between
Lanes performs well in all variable illumination situations, providing lanes are distinct and there are
clear gaps between them. It performs badly if bands in different lanes "bleed together" or touch,
because it will tend to eliminate almost all band data at such a point.

Note: For better concentration calibration accuracy, it is recommended the band

boundaries/extents be reviewed and adjusted if necessary. Related topics: Band
adjustment. See Finding Lanes and Bands.

Related topic:

 Finding Lanes and Bands

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Concentration

Lane Profile Graph

 Use the Lane Profile Graph

 Display Lane(s)
 Axis Options
 Display Options
 Move Bands Using the Lane Profile Graph
 Resize Bands Using the Lane Profile Graph

Use the Lane Profile Graph

The software allows users to view profile graphs (intensity vs. position) of one or more of the lanes in the
image in the Lane Profile Graph.
 To access the Lane Profile Graph, once analysis is performed, select 1D Analysis Action Tab > Lane
Profile > Concentration > Lane Profile Graph.
Underneath the graph, the software displays an image of the graphed lane (or of the lane last selected to be
graphed). In this section, the following topics are presented:
 How to display a single lane
 How to display multiple lanes at one time
 How to change variables for the x-axis and the y-axis
 How to change colors of the graph
 How to display specifics including band extents, band peaks, and background correction

Display Lane(s)
 Perform an automated search for lanes and bands first before continuing to the next steps.
 Click 1D Analysis > Lane Profile > Concentration > Lane Profile Graph and new window
appears.
 From the Lanes section of the Lane Profile Graph window to the right of the graph, click on the
lane to show in the graph. The software automatically displays the graph of that lane.
 To display multiple lanes in the Lane Profile Graph, click the Multiple selection check box and also
click on each lane to display.
 To de-select or re-select a lane to display, click on the desired lane(s) in the Lanes section of the
graph. The lane will be removed from or added to the line graph.

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Axis Options
By default, the x-axis displays Pixels and the y-axis displays Intensity. However, after calibrating molecular
weight, Rf values or Molecular Weights (MW Standard) may be a better naming option for the x-axis.
Similarly, after calibrating concentration, Concentration may be a better naming option for the y- axis.

Change Axis Units

 To change axis units after performing either molecular weight calculations or concentration
calibrations, simply go to the Y Axis and X Axis options under the bottom left of the graph. Use the
drop down menus to select the desired variable.
 If Retardation factor (Rf) or Molecular Weight (MW) is selected to be displayed on the x-axis, then
the graph takes into account Rf effects. This means that other lanes may appear to be stretched or
compressed horizontally relative to the selected lane.
 Once Concentration is selected to be displayed on the y-axis, the curve adjusts the intensities of the
lane, and the relative differences in the graph may change.

Display Options
In the Lane Profile graph, the software allows users to choose what details to show in the graph. The program
also allows users to change the colors of the background, graph, and axes.

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Display Options for Details

Underneath the graph and the lane image the following are available:
 Band Peaks: Selecting this option means VW software will display an arrow labeled with the
band's position at the top of the band on the graph, and a small rectangular control under the
graph that can be used to move the band peak.
 Band Extents: Selecting this option means it will display parentheses showing the width of each
band, and two small rectangular controls under the graph that can be used to adjust the band's
extent.
 Raw or Corrected Values: Selecting this option means it will change the graph to reflect the new
values after the correction.
 Background Correction: Selecting this option means it also will place on the original graph the
graphed line of whatever background correction chosen.

Note: For more information on changing Band Peaks, Band Extents, and Background Correction see
Finding and Modifying Lanes and Bands.
The background correction can be displayed either on the graph with corrected values or the
original graph with the correction line. It is not possible to display both at once.

Selecting Background Color

To change the background color of the graph for easier viewing:
 Underneath the Graph color options in Lane Profile Graph, click on the down arrow of
Background Color.
 Select the color to display. The software automatically changes the color.

Change the Color of the Graph's Axes

 Underneath the Graph color options in Lane Profile Graph, click on the down arrow of Axis
Color.
 Select the color to display. The software automatically changes the color.

Background Correction Options

To change the background correction option from the Lane Profile Graph:
 Underneath the Background Correction options in Lane Profile Graph, click on the down arrow of
No Background Correction.
 Select the correction to display. The software automatically changes the graph. The user may
also select to see a graph that takes into account the corrected values.

Move Bands Using the Lane Profile Graph

 Click 1D Analysis Action Tab > Lane Profile > Concentration > Lane Profile Graph.
 Ensure that Band Peaks is selected. Under the graph find the band markers. Drag the peak marker of

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the band (the large marker in the middle of two smaller markers) to the desired location for that
band. Note that the markers on the graph change position as well. Note that bands can only be
moved between the bands above and below it, not beyond other bands.

 Click on OK. The Lane Profile window closes and bands are now in their new positions.

Resize Bands Using the Lane Profile Graph

 Click 1D Analysis Action Tab > Lane Profile > Concentration > Lane Profile Graph.
 Ensure that Band Extents is turned on. Under the graph, find the band markers. Drag the markers to
the left or the right to the desired location. Note that the markers on the graph change position as
well.
 Click on OK. The Lane Profile Graph closes and the bands are now in their new positions.

Related Topics
Concentration Calibration

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Concentration Calibration

 Graph Options
 Change Unit Type
 Select Unit Type
 Add, Edit or Delete a Unit Type
 Select Data Points
 Select Curve Type
 Remove Concentration Calibrations

With the background of the image corrected, the software is now ready to graph intensity versus
concentration and to fit curves or lines on the graph. It also allows the user to change the Unit Type plotted
on the y-axis. To Show the Concentration Graph:
 From 1D Analysis > Lane Profile click on Concentration. A new window appears with a blank
graph. (The image below includes data points that have been added)

Graph display and units are easily modifiable by the user. The user may change the unit type or the colors of
the background, data points and graph line. The user may also choose to display the anchor lines, point
names and point values.

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Change Unit Type

In the Calibration Graph, the Unit Type plotted along the y-axis is given as Concentration as the default.

Select Unit Type

To plot a different type of unit along the y-axis, do the following:
 Select the Graph Options tab in the Concentration window. Click on the Y-axis unit drop down
menu.
 Select the unit type to display. The y-axis reflects the new unit name.

Note: In the Graph Options tab, click the three dots to the left
of the drop down arrow to add, delete or edit Y-axis unit
descriptions.

Add, Edit or Delete a Unit Type

 To open the Y-axis unit menu, click the "&ldots;" button under the Graph options tab Y-axis unit.
Click a button as appropriate to add, delete, edit or set default.

Add Unit Type

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 To add a unit type, click the Add button.

 A New Unit field will appear and be highlighted. Type in the name of the unit to appear in the Y- axis
unit drop down menu.
 Click OK.

Edit Unit Type

 To edit a unit type, click on the unit name to edit (Concentration cannot be edited).
 Edit the name of the unit to change.
 Click OK.

Delete Unit Type

 To delete the unit type, click on the unit name to delete (Concentration cannot be deleted). Then click
on Delete. The unit name is removed.
 Click OK.

Select Data Points

The software asks the user to select data points to plot on the graph.
In the Concentration Window, note that there are three tabs, Graph, Data Points and Graph Options. Any of
these tabs may be selected when clicking on bands to calibrate to data points on the graph.
 Click on a band in the image that has a known amount to calibrate. The Edit calibrated intensity
window opens. Enter the "known" amount (standard) in the Concentration field.
 Click OK. Continue to select the remainder (individually) of the "known" concentrations and enter the
"known" concentrations in the Concentration Window. The data point entered is now plotted on the
graph under the Graph tab. Under the Data Points tab, the exact position of the data points and
where they will be plotted is shown.
Select as many data points as desired following the steps above. Note that as data points are added, the
software will fit a curve to the points using the curve model selected by the user.

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Edit Data Points

To edit the data points that already selected:
 Click on the Data Points tab of the Concentration window
 Click on the value that to edit.
 Click Edit. The Edit window pops up.
 Change the concentration value to the desired number.
 Click OK.

Delete Data Points

To delete data points from the graph:
 Click on the Data Points tab of the Concentration window.
 Click on the concentration that to delete.
 Click Delete.
 Click OK.

Note: The Concentration window can be accessed from the 1D Analysis Tool bar.

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Select Curve Type

Once the data points are selected to graph, the software allows the user to select the type of curve or line
to fit to the data points.
 In the Graph tab of the Concentration window, select the curve model desired from the drop
down menu.
The software has several possibilities for curve models:
 Least square line: a straight line (polynomial degree 1);
 Least square quadratic: a binomial curve (polynomial degree 2);
 Polynomial 3rd degree: a polynomial curve of degree 3;
 Polynomial 4th degree: a polynomial curve of degree 4;
 Point-to-point: connects the points directly;
 Best Fit: Selects the curve with the highest ’r;Goodness of Fit’ value.

Note: In using polynomial curve types, make sure that there is at least one more data point selected
than the degree of the curve e.g., if a Polynomial 3rd degree is selected, there needed to be at
least four data points.

The software automatically and immediately fits the curve model chosen to the data points as the various
models are selected. In the curve model list, it shows the Best Fit for the curves as they are graphed. The
goodness of fit is found from the coefficient of determination (also known as "r-squared"). The goodness-
of-fit value ranges between 0.0 and 1.0. A value of 1.0 for the goodness of fit indicates a perfect fit.

Remove Concentration Calibration

To remove all calibration information including data points plotted on the graph and curve lines, go to 1D
Analysis Action Tab > Lane Profile and select Concentration. The Concentration Window pops up.
 Select the Data points tab in the Concentration Window then select Delete all. A window will pop
up asking the user to confirm the removal all calibration data.
 Click Yes or No. By clicking on Yes all calibration data is removed and a new analysis can be
started.

Note: Changing the background correction method changes net intensity values and therefore
invalidates concentration calibration. If the user changes the background correction method, the
software will ask the user to confirm deletion of all concentration data. Answering Yes is the same
as selecting Delete all in the Data points tab.
Note: Moving the bands or resizing them also changes their net intensity values. As a result, the user will
see the word "Custom" appear in the data-source column (Concentration Calibration Window),
instead of the name of the specific band. When all lanes and bands information is deleted, the
user will be asked if all corresponding Concentration Curve data should be removed.

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Retardation factor (Rf) Lines

 Automatic Rf Line Determination

 Adjust an Automatic Rf Line
 Add Rf Lines Manually
 Move Rf Lines
 Delete Rf Lines

Automatic Rf Line Determination

When two or more lines are calibrated with molecular weight standards, the software creates Retardation
factor (Rf) Lines automatically. These lines express any differences in horizontal alignment between bands (or
points on a lane) of equal molecular weight. Ideally, there will be one Rf line for each distinct molecular
weight used in a calibration. Since users may utilize more than one standard on a single image, and each
standard may contain several weights, automatic generation can result in a large number of Rf lines.

An automatic RF line can be moved by re-calibrating the lanes. An automatic Rf line can be adjusted by
dragging the lane-intercept marker up or down, but only in lanes that are not calibrated.

Image below shows Rf lines in white drawn manually

Adjust an Automatic Rf Line

 If Rf lines are not visible, turn them on through 1D Analysis Action Tab > Settings > Additional
Settings. When the Preferences window opens, select the 1D Analysis tab and click on the Rf line
box (so that a check appears in the box) in the Visible 1D analysis objects area.
 Any lane that has a white control box without an "X" at the top of the lane is an uncalibrated lane, and
it is possible to move the intercept circle point up or down by dragging it. If a lane has a gray control
handle with an "X," it is calibrated and cannot be moved.
 After adjusting the Rf lines, hide them to view the other 1D objects more easily. To hide the Rf
lines, go to 1D Analysis Action Tab > Settings > Additional Settings. When the Preferences
window opens, select the 1D Analysis Settings and unclick Rf line in the Visible 1D analysis objects
area.
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Add Rf Lines Manually

The Software allows users to add Rf lines to an image with less than two lanes that are calibrated to
molecular weight standards. (On images with two or more calibrated lanes, Rf lines are created
automatically and the software will not allow new lines to be added, although the automatically added lines
can be adjusted as described in the Automatic Rf Line Determination section.)
 On the 1D Analysis Action Tab > Lane Profile menu and click Add Rf Line. Rf lines will be
made visible if they were formerly hidden, and a window will pop up entitled Add Rf Line.
 The cursor will now appear as a square cross. Select the first band that is part of the Rf
relationship in the captured image.
 Click on a second and subsequent bands in other different lanes. Click on as many bands as
preferred to draw the line (up to one per lane), but at least two must be chosen.
 To place an Rf line anchor (circle) on a non-band location, hold down the CONTROL (CTRL) key as
the circle is placed.
 When finished selecting the points that will make up the line, click Confirm Add in the Add Rf
Line dialog window. The green line will now appear white, and a new Rf line will appear.
 The software will require the user to select a standard lane. Identify the standard lane by clicking on
the standard lane in the image. The standard lane will be outlined in green when selected.
 To place more Rf lines, follow the same process. Note, however, that new Rf lines are allowed as
long as they do not cross another Rf line. If the line appears green, the Rf line is allowed. If there
are red marks on the Rf line created, the Rf line will not be created when Confirm Add is selected.
Ensure that the entire line is green before clicking Confirm Add.
 Click Close when finished adding Rf lines.

Move Rf Lines
Existing Rf lines can be adjusted, whether they were created automatically or manually. To move Rf lines to
match bands of the same molecular weight:
 Click 1D Analysis Action Tab > Lane Profile menu and click Edit objects.
 Any lane that has a white control box without an "X" at the top of the lane is an uncalibrated lane,
and it is possible to move the intercept circle point up or down by dragging it. If the lane has a gray
control handle with an "X," it is already calibrated and cannot be moved.
 After Rf lines have been adjusted hide them so other 1D objects can be seen more easily. From the
Analysis menu, select 1D Analysis Settings, then turn off Rf Lines.

Delete Rf Lines
Rf lines that were added manually can also be removed (automatic Rf lines cannot be removed).

Delete One Rf Line

 Click 1D Analysis Action Tab > Lane Profile menu.
 Select the Rf line to delete in the image.
 Click Delete selected Rf line(s).

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Tip: Rf lines can also be deleted by selecting it and pressing the DELETE key.

Remove All Rf Lines

 Click 1D Analysis Action Tab > Lane Profile menu.
 Click Delete all Rf line(s).

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Dendrogram Analysis

Performing Dendrogram Analysis

 Overview
 Generate Dendrogram Graphs
 Modify Dendrogram Graphs
 Dendrogram Standards
 Create Clusters

Overview
Dendrograms are graphical/numerical displays used to show the similarity of bands. The similarity is
grouped into clusters. Each lane in an image has its own cluster. Then, repeatedly, a linkage rule (selected
by the user in the software) is employed to merge smaller groups into larger clusters, until all the clusters
have been combined into a single cluster. The result is a hierarchy of clusters. When moving up the
hierarchy, each cluster contains more but less similar lanes. Lanes that are very similar to each other will
appear together in clusters near the bottom of hierarchy.
This section will explain how to:
 Automatically generate dendrogram information
 Automatically generate multi-image dendrogram information
 Modify dendrogram graphs

Generate Dendrogram Graphs

After finding the lanes and bands in the image the user may begin the process of generating dendrogram
graphs.
 Finding lanes and bands must be performed first. (See: Finding and Modifying Lanes and Bands)
 Go to 1D Analysis > Dendrogram.
 If only one image is open, a Dendrogram View window will appear.
 The user may select from Band Formula: Rf Values or Weight Values, Lane Formula: Dice
Similarity or Jaccard Similarity and the Linkage Formula.
 A Dendrogram View Graph shows the relationships between lanes and bands.

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Generate Multi-Image Dendrogram Graphs

 Finding lanes and bands must be performed first on all images to be used in the graph. Related
topic: Band adjustment. See: Finding and Modifying Lanes and Bands
 Go to 1D Analysis > Dendrogram > Multi-Image dendrogram.
 A Dendrogram Multi-Image window will appear. The names of the currently open images will
display. Click OK to perform dendrogram analysis on the open images, or click Add to add additional
images on which to perform the multi-image dendrogram calculation.
 A Dendrogram View window will appear.
 The user may select from Band Formula: Rf Values or Weight Values, Lane Formula: Dice
Similarity or Jaccard Similarity and the Linkage Formula.

Modify Dendrogram Graphs

The dendrogram graph allows users to change the Background color, Line Color, Node Color, and Text Font.
The user may also select to change the lane identification type to Names or Names and IDs. Use the drop
down menu in each category to select the desired graphical display option.

Dendrogram Standards
Matching bands
Two bands B1 and B2 match when the absolute difference between their values x1 and x2 of a measure is
below the tolerance level:

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Similarity and distance between lanes

Based on band matching, the similarity between two lanes L1 and L2 can be evaluated. Notations:
 B1 is the number of bands in lane L1
 B2 is the number of bands in lane L2

 M is the number of matching bands in each lane, therefore

The similarity between two lanes can be measured using Dice or Jaccard scores. Dice similarity
formula is:

Jaccard similarity formula is:

The opposite to the concept of similarity is the concept of distance:

Distance values will be used to create the dendrogram.

Create Clusters
Initially, each lane has its own cluster. Then, repeatedly, a linkage rule (see below) is used to merge smaller
groups into larger clusters, until all the clusters have been combined into a single cluster. The result is a
hierarchy of clusters. Moving up the hierarchy contains clusters with more but less similar lanes. Lanes that
are very similar to each other will appear together in clusters near the bottom of hierarchy.

The dendrogram shows the links that have been made between the clusters to form larger clusters &endash;
the shorter the distance between items in the dendrogram, the more similar they are.

Related Topics:
 Linkage Rules

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Linkage Rules

A linkage rule offers a method to calculate a measure of the distance between two clusters.
 Single Linkage (nearest neighbor): The distance between two clusters is given by the distance
between the two closest items (lanes) in the different clusters.

Using this method often causes the chaining phenomenon, which is a direct consequence of the single
linkage method tending to force clusters together due to single entities being close to each other
regardless of the positions of other entities in that cluster.
 Complete Linkage (furthest neighbor): The distance between two clusters is given by the greatest
distance between two items in the different clusters.

This method should not be used if there is a lot of noise expected to be present in the dataset,
because outliers are given more weight in the cluster decision. It also produces very compact clusters.
This method is useful if one is expecting entities of the same cluster to be far apart in multi-
dimensional space (provided there is no noise).
 Unweighted pair-group method average (UPGMA): The distance between two clusters is calculated
as the arithmetic mean of the distances between all possible pairs of entities of the two clusters in
question.

This method is a halfway choice between single and complete linkage. The chaining problem is not
observed for this method and outliers are not given any special favor in the cluster decision, which
makes this method the most popular.
 Weighted pair-group method average (WPGMA): This is identical to UPGMA except that the
number of items in a cluster is taken into account &endash; this may be useful when there is a
large variation in the number of items in the clusters.

, where and are the respective sizes of and

 Unweighted pair-group method centroid (UPGMC): The distance between two clusters is the
distance between the centroids of each cluster (the centroid of a cluster is the average point in
the multidimensional space of the cluster).

The resulting trees are not right-aligned and branches can have negative values.

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 Weighted pair-group method centroid (WPGMC): This is identical to UPGMC except that the
number of items in a cluster is taken into account &endash; this may be useful when there is a
large variation in the number of items in the clusters.

 Ward’s method: This method differs from the others in that it uses an analysis of the variance to
calculate distances between clusters. An item is joined to a cluster if the joining results in a
minimum degree of variation within the cluster. This means that items will not get grouped into a
cluster simply because they do not belong anywhere else. As a consequence, Ward’s method can
lead to a large number of small clusters.
 Neighbor joining: At each stage of clustering the total branch length is minimized. The distance
between two items is approximately the sum of the branch lengths between them. The trees are not
right-aligned and branches can have negative values. Details of the method can be found at
http://www.icp.ucl.ac.be/~opperd/private/neighbor.html

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1D Analysis Settings

To access analysis Preference settings, go to the 1D Analysis Action Tab, click on the Settings menu button
and click Additional settings.

Note: Some settings can accessed by clicking on 1D Analysis Action Tab and clicking on the Find Lanes and
Bands menu button.
 Visible 1D analysis objects: Allows users to view specified values in the Image Window such as Lane
ID's, Lane Name, Lane Curve Lines, Band ID's, Band Extents, Band Molecular Weights, and RF Lines.
 Calibration settings: At the request of the user, deletes calibration when changing background
correction.
 Mass Units: This feature is for concentration units. The unit of mass that appears is "ng"
(nanograms). Note that by clicking Customize, users may add additional units. Mass units are
weight numbers, relative units or any relational units defined by the user.
 Font size: By clicking the buttons for Lane Font Size and Band Font Size, font size can be
changed for the Lane ID, Lane Name and Band ID labels. The font range is from 6 - 20.

In the 1D Analysis Action Tab in the Find Lanes and Bands menu under Settings, are the following options:

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 Mass unit: Same as above

 Background color: Allows the user to choose a background for the image. For example, if the image
has white bands with a black background, the software automatically detects the white bands and
black background. If the auto-detection does not occur properly, the user may choose "Black" from the
dropdown menu.
 Force lanes straight: If lanes are curved, the software automatically corrects for the curves.
 Constant width for all lanes: Lanes will automatically be assigned the same width unless
otherwise noted. For example, when one lane is resized, all lanes are resized.
 Lane volume is sum of bands: Software assumes the amount of bands adds up to the amount of
material originally deposited in a lane and enters that information.
 Additional Settings: Same functions as found in the 1D Analysis Action Tab > Settings menu.

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Results

Viewing and Printing 1D Gel Analysis

 Overview
 Lane and Band Information
 Lane Profile Graph
 Results Data Explorer
 Printing Data Explorer Tabular Reports
 Exporting Data
 Fixed Image and Analysis Reports

Overview
The software simplifies viewing and printing information about the image. The linked topics listed above will
describe how to:
 View lane and band information
 Use the Lane Profile Graph, including displaying multiple lanes in a graph, changing the variables on
the axes, and changing the display options
 Manage and print tabular reports
 Use the Data Explorer
 Export data
 View and print fixed reports of analysis settings, analysis lanes, analysis bands and the lane
profile

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Results Data Explorer

Aside from viewing graphs and information windows about the lanes and bands, the software also offers the
option of seeing the data in a spreadsheet format that is user configurable.
 To access this go to 1D Analysis > Results.
 Data Explorer opens a tabular format with the ability to include or exclude certain data fields from the
Data Explorer Report. Predefined report configurations are included to quickly select/deselect data
fields appropriate to certain experiments.
 The Data Explorer window also offers Report Printing and Data Export options.
 The lower right corner (Report Type) of the Data Explorer window offers a drop-down menu for
quickly selecting preconfigured reports rather than having to manually filter report data for
commonly reported analysis data. When selecting these reports, notice the various fields being
selected/deselected from the list of data fields.

Filtering Data
 Accessible when creating tabular reports or export data, the Report Type drop-down menu allows
users to choose what specific data to show in reports and in exported files.
 Users can also check or uncheck fields in the left column (Analysis 1D Report) that are to be
included in the report.

Related Topics:
 Estimate Volume

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Printing Data Explorer Tabular Reports

 Print Reports
 Export Reports
 Report Types
 Fixed Standard Reports

Print Data Explorer Reports

Page Setup
In Tabular Reports, print the data selected about the image. In the bottom left corner of the Data
Explorer Tabular Reports window there are several print options:
 Page header: Displays as the page title on the top of the report
 Page footer: Displays as the page information at the bottom of the report
 Page setup: Displays the page setup options as offered by your specific printer
 Print preview: Displays a preview of what will be print on the report.
 Enter the header and footer information, set the page format, and click Print. When the print
window opens, click OK.

Print Reports
Under the Results menu, select the report needed by clicking into the check box. For example, if the
Analysis Settings report was needed, the user would click onto the Analysis Settings check box.
 Select Print, OK. Click Exit to close the Reports window.

Change General Layout Before Printing

 To change the margins, click on the Page Setup then make the margins larger or smaller by
varying degrees. To view the margin lines, select Show Margins in the Preview Mode in the
Reports window.
 Enter information in Header Text or Footer Text. Note the following abbreviations for header and
footer text:
 %p puts the page number at the top or bottom of the page;
 %c puts the page count at the top or bottom of the page;
 %d puts the date at the top or bottom of the page; and
 %t puts the time at the top or bottom of the page.

Export Data Explorer Reports

The software enables exporting of data to Microsoft Excel® or to other software packages for further
analysis or documentation. To export data:
 Select the data fields you wish to export.
 In the bottom right corner of the Data Explorer Tabular window, select from two options and
select whether to export the data by Comma, Semicolon, Space, Tab (where the delimiting

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character(s) are typed):

VW Software User Guide

 To Excel
 To CSV
 Click the To Excel or To CSV button.
 Name the file and click Save.

Report Types
 All information
 Summary
 Bands
 Lanes
 Molecular Weight
 Calibrated Concentrations

Fixed Image and Analysis Reports

Fixed Standard Reports
The software offers several standard reports that cannot be altered but that provide valuable reference
information:

The Analysis Settings Reports such as:

 Background color
 Background correction
 Disk radius
 Lane width constancy across all lanes
 Lanes forced straight
 Lane volume is sum of all bands

The Analysis Lanes Reports such as:

 Lane ID and name

 Location of lane start and end
 Band count
 Mass
 Unit of mass
 Intensity maximum
 Intensity volume
 Molecular weight information
 Concentration maximum

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 Concentration volume

The Analysis Bands Report such as:

 Band Name and ID

 Calculated peak values (Rf value and molecular weight); Intensity of the band, including its maximum,
volume, percentage of the lane, and mass; and
 Concentration of the band, including its maximum, volume, percentage of the lane, and mass.

The Lane Profile Report:

Gives a graphical representation of lane data.

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Clear

Clear Lane and Band Information

To clear the 1D Analysis information, click onto the Clear button from the 1D Analysis Action Tab and then
click Yes.
To begin a new analysis of your image, save the existing image with its lane and band information. Then
perform a Save As for the new image, filing it under a new name, and proceed as follows:
 Click 1D Analysis Action Tab > Find Lanes and Bands menu.
 All lane and band information will be deleted.
 To restore analysis information in the image, click the Undo button on the Edit Menu. Also Redo
may return to the cleared image. Once the file is saved, however, undo or redo will not work to
restore information.

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Perform Area Density Analysis

Area Density Action Tab Overview

The Area Density Action Tab provides the means to generate Area Density analysis on a captured image.

The functions in the Area Density Action Tab include:

 Define Region of Interest on the image
 Define, Modify, Delete and Edit Region
 Rectangle
 Ellipse
 Polygon
 Freeform
 MagicWand
 Define Background
 Define User Background
 Rectangle
 Ellipse
 Polygon
 Freeform
 MagicWand
 Modify Background Regions
 Delete Background Regions
 Edit an Existing Region
 Calibration Curves
 Measure Tools
 Lines, Areas, Angles
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 Calibration Tools
 Intensity, Amount, Spatial Calibration
 Settings: Display Settings and Preferences
 Results
 Estimate Volume
 Define Image Scale
 Calculate Volume
 Display Results
 Print Results
 Clear - clear analysis settings

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Perform Area Density

 Overview
 Perform Area Density
 Define the Region of Interest (ROI)
 Use MagicWand to Define ROI
 Select Multiple Bands and Regions in the Image
 Modify Regions in the Image

Overview
The Area Density tool can be used to carry out precise quantitative calculations on the regions of interest in
the image. It provides the flexibility to carry out calculations based on Optical Density as well as Grey Levels.
Additionally, users can calibrate the amount of sample loaded in each spot. Calibration curves, spatial
calibration and area density display options can also be selected from the Area Density menu.
To access the Area Density functions, select the Area Density Action Tab. The module will display with the
following functions.
 Define Region: Select the region of interest (ROI) on the active images with the ROI tools.
 Define Background: Defines background intensity on the image for calculations.
 Calibration: Converts pixel information into realized measurements information
 Settings: Select from display options including which colors to use while marking and displaying
areas on the image
 Results: Provides results of Area Density calculations
 Clear: To clear analysis

Perform Area Density Analysis

Define the Region
 Go to Area Density Action Tab > Define region and click on a region of interest (ROI) selection tool.
Select from rectangle, ellipse, polygon, freeform or magicwand tools.
 The Define new region window will open.
 To select a region, left click and drag to define an area on the image. The outline is green. Adjust the
size of the ROI with white bounding boxes.
 When the area is selected, right click within the region to set it (the outline turns red). A number
will appear in each region. Note: Ensure that the number is set inside the box BEFORE clicking
the OK button.
 Then click Keep Changes.

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Green circle turns red

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Use MagicWand to Define ROI

 Click onto Define Region to start the ROI identification process.
 Click onto the MagicWand tool.
 Click onto the shape of interest in the captured image to identify the region. A green shape will appear.
 Adjust the MagicWand Tolerance Slider to outline the entire ROI.
 Right click inside the shape outlined in green. The green shape will turn red and a number will appear
inside the red shape.
Note: Ensure that the number is set inside the box BEFORE clicking the ‘Keep Changes’ button.
 Click Keep Changes to complete the identification process.

Select Multiple Bands and Regions in the Image

Users may want to determine the area density of more than one band or ROI in a single image.
 To identify more than one similarly shaped band in an image, click on a previously defined ROI and
drag that shape to a second or third band.
 When finished, right click onto the area selected to set.
 Once set, a number will display in the ROI and the bounding box will turn red.

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Modify Regions in the Image

To modify regions in the image, select Area Density > Define Region > Modify Regions.

To delete one or more regions, click Delete regions. A list of all regions will be shown in a pop up window.
Select a single region in the left column and click OK to delete the region. To delete all regions, click the
Select All button. Then click OK to delete all regions.

To edit regions, click Edit an existing region and an Edit Objects window will open. Left click on the region to
edit. Left click and drag the white bounding boxes to resize the region.

To move the region, left click and drag inside the region. Once editing is complete, right click on the
edited region. Click Keep Changes in the Edit Objects window.

Related Topics:
 Estimate Region Volume
 Define Area Density Background
 Calibration Curves
 Reporting and Printing Area Density Results
 Define Image Scale

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Area Density Settings

To change Area Density settings go to the Area Density Action Tab > Settings menu button and click onto Set
Display Options.
The Preferences window appears which allows users to change the color of the Label and Outline from the
drop-down list.

The Preferences window also provides check boxes that allow users to Keep Region's Shape, Hide Regions,
and Hide User Background.
 Label color: Select the region’s label color from the drop-down menu.
 Outline color: Select the region’s outline color from the drop-down menu.
 Keep region’s shape: When checked, this saves time by preserving the shape (ROI type) of the
region across new regions. So if most of your regions are of the same shape and size, it is beneficial
to use this option
 Hide Regions: Hides the regions selected by the user
 Hide user background: Hides the regions identified by the user as background

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Define Area Density Background

 Define Background
 Delete Background Region
 Modify and Existing Background Region

Define Background
By default, each area defined using the Define Region of Interest tools in the Area Density Action Tab has a
separate background. It is equal to the sum total of the perimeter around the region marked, three pixels
wide. If a common background for the entire image is needed:
 Once the region is defined, click on the Define Background menu button from the Area Density
Action Tab.
 Click onto a region of interest tool to define the background area.
 Left-click and drag to select a background region of interest. Then right-click on each area to set.
Once set, a number will display in the ROI.
 Click Keep Changes. The bounding box will turn blue.

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Background box turns blue

Delete Background Region

To delete a background region:
 Click onto Delete Background Regions under Area Density Action Tab > Define Background.
 Then highlight the number of the region to delete.
 Click OK.
Tip: Use control and left mouse click to select multiple regions.

Modify an Existing Background Region

 Click onto Edit an existing region in the Area Density Action Tab >Define Background menu.
 Left click on the region.
 Left click and drag on the white bounding box to adjust the region.
 Right click to save the changes.

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Estimate Region Volume

Estimate Region Volume is useful in determining the volume occupied in a cancerous growth in an animal
study, for example. The calculations are based on the linear model in J. of Surgical Research, Vol. 113, No. 1,
July 2003 studies that connect various factors (such as area and pixel intensity) to volume.
 Open an image.
 Go to the Area Density Action Tab > Define region.
 Use an ROI Tool (preferably the MagicWand tool) to define the region(s) and calculate the Area
Density of the area identified by the ROI tool.
 Click inside the region of interest. The outline of the region will change from green to red and will
have an identification number listed inside the ROI.
 Click the Define Background menu button and use the Define User Background tools to define the
background.
 Click inside the background region of interest. The outline of the region will change from green to
blue and will have an identification number listed inside the ROI.
 Click the Results menu button.
 Close the tabular report that opens automatically.
 To calibrate the size of the image, click the Define Image Scale tool from the Results > Estimate
Volume menu.
 Left click on a point in the image. Click again on another point in the image and the Set Scale
window will open.
 Select the appropriate unit of measure and edit the sample width for the defined image scale.
 Click OK.

 Once regions have been defined and calibrated, click Calculate volume in the Results menu to see
the calculated values.

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Calibration Curves

 About Intensity Calibration Curves

 Optical Density
 Grey Levels
 Types of Calibration Curve
 Apply Pre-Defined Calibration Curve
 Add New Intensity Calibration Curve
 Set Amount Calibration Curve
 Change Calibration Curve Graph

About Intensity Calibration Curves

Intensity Calibration is the method of creating a mapping of input intensities to output intensities. The input
and output relationship establishes a curve. Ideally, such a mapping would be linear. However, if finely tuned
results are required, the mapping process may need to change. E.g. a pixel value of 100 might look slightly
brighter, say 120. Or possibly the camera being used has a noise step of 40, which will make all values below
40 look as dark as 0.

Two different metrics can be used in the Area Density tool to carry out analysis:
 Optical Density
 Grey Levels
The software allows users to create curves for both types of calibrations.

Optical Density
Standard Optical Density (OD) is used when the sample of interest is imaged with transmitted light. (i.e. light
going thru the sample, into the camera for imaging.) OD value of an area gives an idea of how much light can
pass through that area. If the area belongs to a sample in question, OD measures how much of sample might
be present in that area. Higher OD means less light can get through, suggesting presence of higher quantity
of sample.

Following Beer’s Law, the Optical Density of a given pixel P (say at position x,y) is calculated by VW software in
the following way:
OD = - Log [ (P(x,y) &endash; Black) / (Incident &endash; Black) ], if P(x,y) < Black
= - Log [ 1/ (Incident - Black) ], otherwise
Where
White = value of brightest white pixel in the imaging environment
Black = value of darkest black pixel in the imaging environment

Total Optical Density of an area is simply the sum total of OD values of all pixels.
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Grey Level

Grey Level calculations are used when the sample is imaged using reflective light. Grey level of an area
is simply the sum of grey levels of all pixels in the area. Changes are reflected on the curve after the
window is closed.

Types of Calibration Curves

Two types of curves options can be defined using the Intensity Calibration Curve button:
 Standard Optical Density - Use this type if the sample is excited through transmitted light (such as
the FirstLight uniform UV Illuminator by Analytik Jena). Also useful when imaging colorimetric
samples.
 Free Form - Use this type when fine-tuning input and output intensity values or when imaging
fluorescent/luminescent samples to produce results in Grey Levels.

Apply Pre-Defined Intensity Calibration Curve

 To apply a pre-defined intensity calibration curve to a previously defined region of interest, click the
Area Density Action Tab > Calibration menu button > Intensity Calibration.
 An Intensity Calibration Curve window opens. To select a previously defined intensity curve, click
the down arrow next to Edit List in the upper right hand corner of the window. A list of intensity
curve options will appear.
 Select the appropriate curve from the list. (For example: choose Black Band Intensity Curve if black
bands are captured in the image)
 Based on the user selection, Free Form or Std. Optical Density will be automatically selected.
 Click OK.

Add New Intensity Calibration Curve

 Click onto Edit List in the Intensity Calibration Curve window.
 A Point List Collection window will appear. Click onto Add to add a new curve. Name the curve, then
select OK.
 The new user-created curve will appear in the drop down menu list. This new curve can be
deleted and edited in the Point List Collection window, if desired.

 With the new curve selected, choose Free Form or Std. Optical Density.

 The scroll-box Number of Samples lets users select the total numbers of samples to display on the X-
axis of the curve. By default, it is set to the highest value of the dynamic range of the image (8
bit=>256, 16bit =>65536).
 If Free Form is selected, new Data Points can be added to increase the accuracy of the curve.
 Click onto the Add button to add points.
 Select OK when finished adding data points.

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Set Amount Calibration Curve

 To set the amount calibration curve, click on Area Density Action Tab > Calibration > Amount
Calibration.
 An Amount Calibration Curve window appears.
 Data points can be added to the amount calibration curve. Select Add to include additional data
points.

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 The Add Graph Point window appears. Area Amount can be added to each Area # defined in the
captured image. Area Volume cannot be changed since the value is automatically calculated from the
given area, and depends on the type of Intensity curve calibrated (Freeform or Standard Optical
Density).

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Change Calibration Curve Graph

 While in the Intensity Calibration Curve window or the Amount Calibration Curve window, click onto
the second tab, Graph options.
 The Y-axis unit can be changed to other user-defined units such as concentration.
 The Calibration always positive check box can be checked in both windows. The Monotonic
calibration can only be checked in the Intensity Calibration Curve window.
 In the Display settings, users may change the appearance of:
 Anchor lines
 Point values
 Background color
 Data point color
 Graph line color
Note: See explanation of Calibration always positive and Monotonic calibration in the Special Cases of
Free Form Curves in this section.

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Reporting and Printing Area Density Results

Area Density Results and Data

Below is a definition of the Area Density Results fields and are found in the Area Density Action Tab >
Results menu button > Display Results. To display specific results, check the desired boxes in the left
column.

Area Density Results Definitions: "Density List" Tab

Region User-defined area of interest for Area Density calculations

Total Sum total of intensities of all pixels within the region, minus the
Density background. Intensity is either in terms of Grey-Levels (GL) or
Optical Density (OD), depending on the Intensity Calibration
curve.
Total Sum total of intensities of all pixels within the region marked as
Background background. Background is calculated in two different ways.
Explanation below.
Mean Average of intensities of all pixels of the region, minus average
Density intensity of background pixels.
Mean Average intensity of background pixels.
Background
Total Raw Sum total of intensities of all pixels within the region. No
Density background is subtracted.
Mean Raw Average intensity of intensities of all pixels within the region.
Density
Area (Px) Total number of pixels in the region.
Minimum Minimum intensity value among all pixels.
Intensity
Maximum Maximum intensity value among all pixels.
Intensity
Calibrated If an Amount Calibration curve exists, this displays the calibrated
Value value based off that curve.

Area Density Results Property Definitions: "Statistics" Tab

Min Minimum value of attribute listed in corresponding columns, among
all regions. Region row below it provides the region for which that
value was recorded.
Max Maximum value of the attribute listed in the corresponding columns,
among all regions. Region row below it provides the region for which
that value was recorded.
Range Difference between Maximum and Minimum values, among all

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regions

Mean Average of the corresponding attribute, among all regions

Std. Standard Deviation of corresponding attribute in columns, among all
Dev. regions
Sum Total of the particular attribute across all regions
Samples Total number of regions

Save the Results

 After performing Area Density analysis, click the Results button. An Area Density Results
window appears.
 From the Area Density Results window > File menu, click Save Outlines to save the file.
Note: This file is readable only in VisionWorks software. To view the results as an Excel or CSV file, see the Export
the Results section below.
 To load a previously saved file, click File > Load Outlines.

Print the Results

 Click the Area Density Results window > File > Print to print analysis data.

Export the Results

 From the Area Density Results window > Data menu, select from multiple options to export analysis
data:
 Copy Data to Clipboard
 Export to CSV
 Export to Excel

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Perform Colony Counting

Colony Count Action Tab Overview

The Colony Counting Action Tab contains information that allows users to count colonies and generate data
on the captured image.

Once a colony image is open, click the Colony Counting tab and the Count menu button as highlighted in the
screen shot above.
The following tools will show in the module bar on the left.

Define Region: Rectangle, Ellipse, Polygon, Freeform and MagicWand Count:

 Click and Add
 Automatic
 Template (user defined templates for automating colony counting)
 Identify by Color

Edit Colonies: Once a colony image is open, click the Colony Counting tab and the Edit menu button. The
following tools will show in the menu bar.
 Add Colonies
 Delete Colonies
 Manually Split Colonies
 Automatically Split Colonies
 Merge Colonies

Settings: Default Analysis Display Settings

Results: Export and Print colony results. Once a colony image is open and counted, click the Colony Counting
tab and the Results menu button. The following tools will show in the menu bar as well as a Colony Count
Results pop up window.
 Spiral Plate: Spiral Plate Analysis, Align Spiral Plate Overlay and Clear Spiral Plate Analysis
 Estimate Area
 Define Image Scale

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Clear: When a colony image is open, click the Colony Counting tab and the Clear menu button to clear all
analysis.

Getting Started:
 Counting Colonies

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Colony Counting Settings

Click the Colony Counting Tab, select the Settings menu button, and then click Analysis Display
Settings. This pop up window allows users to set Preferences for the colony counting display.
 Label Type
 Colony Marking
 Label Color
 Circle Radius

Label Type
To change the Label Type, from the Colony Count Preferences window, click the drop down arrow and select
from:
 None: Assigns no number to the colony or zone counted.
 Class: Assigns the class number to colony or zone counted.
 Number (general): Assigns an increasing value to the colony or zone counted.
 Number (in class): Assigns an increasing value to the colony or zone counted and starts from a value
of one for each class represented.

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Colony Marking
To change the Colony Marking, click the drop down arrow to select from:
 None: Shows no pictorial indication of the count value.
 Outline: Draws a bounding line around the colony or zone.
 Fill: Shows the entire colony or zone filled in with color.

Label Color
 To change the Label Color, click Auto or click the drop down arrow and select from the colors
listed.
Circle Radius
 To change the circle radius, click the drop down arrow and select from the numbers to change the
circle pixel radius.

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Count Colonies

Counting Colonies - Options

The software offers several functions for counting colonies.

 Automatic Counting
 Identify by Color Counting
 Template Counting
 Click and Add Counting
 Spiral Counting

Related topics:
 Creating Templates for Counting
 Colony Counting Action Tab
 Colony Counting Settings (Preferences)

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Automatic Counting

Automatic Counting allows users to generate a colony count for a Petri dish or plate using the Automatic
function.

 To begin automatic counting, click onto the Colony Counting Tab and then the Count menu
button.
 Define the region of interest using the tools provided in the module (Rectangle, Ellipse, Polygon
etc.)
 Select Automatic.

 The colonies will be counted and displayed on the colony image.

 Colonies can be filled in with red or outlined. Colonies can also be identified using multiple colors. Go
to the Colony Counting Settings section for more details concerning changing the appearance of the
image.

 Click the Results menu button to view the results of the analysis.
 If desired, colonies can be added, deleted, split, or merged.

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Related Topics:
____________________________________________________________________________

Identify by Color Counting

 User Defined Template Counting
 Click and Add Counting
 Loading and Saving Images

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Click and Add Counting

The Click and Add counting method allows users to count colonies by clicking onto each colony in the
captured image.
 To begin Click and Add counting, click onto the Colony Counting Tab
 Click onto the Count menu button.
 Select the Click and Add counting method.
 Use the cursor to click onto each colony to be counted in the captured image.

The resulting count total will appear once the Results menu button is clicked in the Colony Counting
Tab.

Note: The result of the Click and Add method is intended to count colonies only and does not provide
individual colony data.

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Related Topics:
 Automatic Counting
 Identify by Color Counting
 User Defined Template Counting

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Set-Up Colony Counting Templates

Templates allow the user to set parameters for colonies most frequently counted in repeat experiments.
Templates provide a quick count of Petri dishes commonly used by the lab.
 Open a captured colony image.
 To set a template for a colony plate, select the Identify by Color count method from the Count
menu button in the Colony Counting Action Tab.
 In the pop up window, click to select the original image or the flattened image.
 A Manual Colony Count Wizard window will open.

Step 1 of 2: Select Classes tab will open.

 Define the region of interest by clicking the Define Counting Region button.
 Use the white corner boxes to adjust the desired region.
 Click the Add Points button in the Points section.

NOTE: Analysis details may be present if manual counting or templates have already been set up. To delete,
click on the color under Analysis Details and click the Remove Point button under the Points section. It is also
possible to remove an entire class by clicking on the class number under Analysis Details and then clicking the
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Remove button under the Classes section.

 Click a colony on the colony plate image. The selected colony and similar colonies will appear in the
Preview window.
 Adjust the point sensitivity slider if necessary to change the number of colonies detected in the
preview window.

To select colonies by color:

 Click Add under the Classes section in the window. On the image, click a colony of a different color.
The selected colony and similar colonies will appear in the Preview window for all classes.

Note: To display only the colonies for a specific class, select the Preview selected item only
check box in the Analysis section.

To save the colony counting template:

 Click the New button in the Template section of the window.
 A new pop-up window will ask for a new Template name.
 Type in the new name and select OK. The Template name window will close.
 Click on the Count button.

The Step 2 of 2: Finish tab will display.

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 The results of the manual colony counts are displayed on the image.
 To adjust the parameters of the colony count by shape or size, adjust the sliders in the Filter colonies
section. Note: If changes are made in this step, then click Save filters button to save the new settings.
 Click Finish to complete the count and save the template.

To delete a Template, from the User Defined Template list:

 Click Identify by Color Count.
 On the Step 1 tab, under the Template section, click the drop-down menu.
 Select the Template name to delete.
 Click Delete.

Related Topics:
 User Defined Template Counting
 Spiral Counting

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Counting Using a Predefined Template

Before proceeding through the next steps, a template must have been set up and saved using the
Manual Count Wizard. If there are no templates, create a template. The template defines a set or
parameters for future colony count analysis.

 Open a colony image.

 Select the Colony Counting Tab, click on the Count menu button.
 Define the region of interest using the tools provided in the menu (Rectangle, Ellipse, Polygon
etc.)
 Click on the Template function under the Count menu.

 A new window appears. Select the desired template from the drop down menu.

 Click OK.
 Click the Results menu button to view the data.

Related topics:
 To learn more about reporting capabilities, go to the Reporting Functions.
 Click and Add Counting

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Edit Colonies

Add Colonies

Users may add colonies by performing the initial count (Automated Count, Identify by Color Count, or
User Defined Template Count), and adding colonies manually.

 To add colonies manually, go to the Edit colonies menu button under the Colony Counting
Action Tab and click on Add Colonies.

 Click on a colony in the image to add.

 The colony selected will now have a circle (filled in or outlined) around the point selected.
 The total colony count will change to include the colonies added.
 If the colony is hard to see, zoom in on the colony by using the zoom/pan functions at the bottom of
the screen. Click on the plus (+) sign to increase the zoom.

 To use a larger circle to highlight the colony, go to the Settings menu button and choose to use a
Circle Radius of 5, 10, 15, or 20.

Related Topics:
 Colony Counting Settings
 Results

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Delete Colonies

Users may delete colonies by performing an initial count (Automated Count, Identify by Color Count, or User
Defined Template Count), and deleting colonies manually.

 To delete colonies, go to the Edit colonies menu button under the Colony Counting Action Tab and
click on Delete Colonies.
 Click on a colony in the image to delete.

 The colony circle (filled in or outlined) will now disappear. The total colony count will change to
remove the colonies indicated.
 If the colony is hard to see, zoom in on the colony by using the zoom/pan functions at the bottom of
the screen. Click on the plus (+) sign to increase the zoom.

Related Topics:
 View Counting Results

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Split Colonies

Manual Split Colonies

Users may split colonies by performing an initial count (Automated Count, Identify by Color Count, or
User Defined Template Count), and splitting colonies manually. Colonies should be split when two or
more colonies are very close together and are counted as one colony by the software.

 To split colonies manually, go to the Edit colonies menu button under the Colony Counting
Action Tab and click on Manually Split Colonies.

 A new window will ask the user to "Draw lines through the colonies you want to split then
release".

 Draw lines through two or more colonies that are close together and treated as one. Use the
pointer and, while holding the left mouse button down, move from one edge of the colony to the
other.

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 The total colony count will change to add new colonies identified by the split.
 If the colony is hard to see, zoom in on the colony by using the zoom/pan functions at the bottom of
the screen. Click on the plus (+) sign to increase the zoom.

Auto Split Colonies

Users may split colonies by performing the initial count (Automated Count, Identify by Color Count, or
User Defined Template Count), and splitting colonies by clicking on the colony to split. Colonies should be
split when two or more colonies are very close together and are counted as one colony by the software.

 To split colonies automatically, go to the Edit colonies menu button under the Colony Counting
Action Tab and click on Automatically Split Colonies.

 Click onto the colony in the image to split.

 If the colony is hard to see, zoom in on the colony by using the zoom/pan functions at the bottom of
the screen. Click on the plus (+) sign to increase the zoom.

Related topics:
 View Counting Results

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Merging Colonies

Users may merge colonies by performing an initial count (Automated Count, Identify by Color Count, or
User Defined Template Count), and merging colonies manually. Colonies should be merged when one
colony is treated as two separate colonies by the software. Colonies will only be merged if they are less than
4 pixels apart.

 To merge colonies, go to the Edit colonies menu button under the Colony Counting Action Tab and
click on Merge Colonies.

 A new window will ask the user to "Select the desired colonies and then press the Merge
button to join them."
 Click onto the colonies to be merged.

 The total colony count will change to reflect the changes due to using the merge function.
 If the colony is hard to see, zoom in on the colony by using the zoom/pan functions at the bottom of
the screen. Click on the plus (+) sign to increase the zoom.

Related Topics:
 Split Colonies
 View Counting Results

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Identify by Color Counting

Identify by Color Counting

Frequently colonies are identified by their color. The software allows users to differentiate colonies by color and
generate a total count based on the color properties.
 Open a colony image.
 Open the Colony Counting Action Tab and then select Count.
 Define the region of interest using the tools provided in the module (Rectangle, Ellipse, Polygon etc.)
 Select Identify by Color.

 Click on the Original Image or Flattened Image to continue. (The flattened image will
sometimes produce improved counting results)

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 The Manual Colony Count Wizard window will open.

Next Steps:
 Manual Counting Step 1: Select Classes
 Manual Counting Step 2: Finish

Related Topics:
 Loading and Saving Images

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Identify by Color Counting Step 1: Select

Classes

Please refer to the Identify by Color Count page before proceeding.

Define the Counting Region

 In Step 1 of 2: Select Classes, define the region of interest. The region of interest is identified by a
green circle that should include all the colonies (or zones) of interest in the Petri dish. The software
automatically selects a region of interest but by clicking the Define Counting Region button, the
user can increase or decrease the circle size. Hold and drag the pointer over one of the corners of the
circle to change the size.

Select Classes
 To select the desired colonies (or zones), click the Add Points button and click on a colony (or zone)
in the main image. (Not the image shown in Step 1 of 2: Select classes preview window.)
 Classes can be defined as different types of bacteria, yeast, or mold present on the same Petri dish
sample. The software can detect various types of classes in one dish. To add a class, click onto the
Add button in the Classes section of the window.

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Click Here

 Once the first desired colony (or zone) is selected, the new image in the Step 1 of 2: Select
classes window will show a black background along with all of the colonies that contain the
same color as the point selected.

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 The color of the point selected will also appear in the Analysis Details box (for example: rgb (93, 93,
93).
 Select the Preview selected point only.
 Continue adding points and classes as necessary until the black and white image shows all the
colonies of interest in white.
 To remove a class or a point, highlight the class or point in the Analysis Details box and click the
Remove Point button. Note: To display only the colonies for a specific class, select the Preview
selected item only check box in the Analysis section.
 Click the Count button to go to Step 2 of 2: Finish.

NOTE: The Step 1 of 2: Select classes tab allows the settings created in this window to be saved in a user
defined template. If there are no templates created, the drop down menu will list Default as the only
template option.

Next Steps: Manual Counting Step 2: Finish

Related topics:
 Templates: Create template for automating colony counting

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Identify by Color Counting Step 2: Finish

After completing Identify by Color Count Step 1: Select Classes the software brings up the Identify by
Color Step 2 of 2: Finish tab. This tab allows users to filter the colonies (or zones) by adjusting the shape
or colony size (or add and subtract zones) selected.

 Change slider buttons for shape (from circular to irregular) and size (1 pixel to 200 pixels) to
capture additional colonies or eliminate colonies (or until all of the zones of interest are
highlighted).

Note: This window allows users to save settings as templates. To save a template, click onto Create Template
and assign a name to the template to be used in a future counting session.
 Click Finish to exit.

The software will redirect to the counted image. To view the analysis data, click onto the Results menu button.

Related Topics:

 To learn more about reporting capabilities, go to the Reporting Functions.

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Spiral Counting

 Perform Spiral Count

 Adjust Grid Size and Volume
 View, Save and Print Spiral Plate Results
 User Tips

Perform Spiral Count

To perform a spiral plate count:
 Open or capture an image.
 Use the Automated, Identify by Color, or Template counting function to generate an initial count of
the spiral plate.
NOTE: If using the software for the first time, no templates are created and the User Defined Template Count
option appears grey. To create a template, first proceed through the Manual Count Wizard functions (in
Identify by Color count) to store template settings.
 Click on the Results menu button. A colony count results window will appear. Either minimize or
close the window.
 Click onto the Spiral Plate Analysis menu button. A green grid will appear over the counted
image. A spiral plate analysis window will appear.

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Adjust Grid Size and Volume

To change the overlay grid size:
 In the Spiral Plate Analysis window move the Overlay Size slider bar to the left (to decrease the
grid size) or to the right (to increase the grid size).
To calculate the SPLC/mL:
 Type in or use the up or down arrows in the Total volume deposited box. Click the Calculate
SPLC/mL button. The calculated amount will appear immediately below the Calculate SPLC/mL
button.

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View, Save and Print Spiral Plate Results

To view the resulting Data Table analysis for the spiral plate count:
 Click onto the + sign for Data Table (expanded report will be displayed after clicking the + sign). The
values listed will provide the number of colonies found in each quadrant and section of the counted
plate.

To save the spiral plate settings in a template:

 Click onto Save As and provide a name for the template. To
print or export the data into Excel:
 Click onto the Print or Export to Excel button.
 Note: The analysis can only be saved by printing or exporting to Excel.

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User Tips
While in the Spiral Plate Analysis window, the user may choose to move the green overlay grid.
To move the grid click and drag the green grid until the center of the grid is aligned with the center of the
captured image. Another way to do this is to click on the Align spiral plate overlay under Spiral Plate while
having Spiral plate analysis open.

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Colony Counting Results

Colony Counting Reports

The results of the colony count can be displayed in the results window. To show the results:

 In the Colony Counting Action Tab click the Results menu button to bring up the colony count results.
 The colony count results for the Petri dish are displayed with tabs on the upper left hand side of the
screen.
 The tabs are: Classes, Colonies, Statistics and Distribution

Related Topics:
 Export Reports to Excel Export
 Supporting 21 CFR Part-11 Compliance

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Export and Print Colony Results

Exporting to Excel
 To export data, click on the Results menu button from the Colony Counting Tab. A Colony
count results window will appear.
 In the pop up window, click File > Send results to Excel. Save the file in Excel format to later open
the file.
 The first tab shows Classes. The second tab shows Colonies. The third tab shows Statistics.
The fourth tab shows Distribution.

Printing Colony Results

To print these reports, use Excel to open and print the data.

Related Topics:
 Reporting Functions

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Reporting Colony Class Information

Colony class types can be displayed in the Colony Count Results window. To access the window click onto
the Results menu button from the Colony Counting Action Tab. A Colony count results window will
appear. Then click onto the Classes tab after the new window appears. The Classes tab displays:

 Number of classes in the sample

 Number of colonies in that class
 Percent of colonies of that colony classification in the sample
 Total area of the class on the sample (in pixels)
 Percentage of area of the class on the sample
 Mean area of the class (in pixels)
 Standard deviation of the area
 Minimum area (in pixels)
 Maximum area (in pixels)

All dimensional values are reported in pixels unless the calibration process is performed on the image.

Related Topics:
 Reporting Functions

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Reporting General Colony Information

Colony information can be displayed in the Colony Count Results window. To access the window click onto
the Results menu button from the Colony Counting Action Tab. A Colony count results window will
appear. Then click the Colonies tab after the new window appears. The Colonies tab displays:

 Class number
 Total area of that colony
 Perimeter of the colony
 Average diameter of the colony
 Circularity of the colony (numerically depicts roundness of the colony)

All dimensional values are reported in pixels unless the calibration process is performed on the image.

Related Topics:
 Reporting Functions

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Reporting Colony Statistical Information

Statistical colony information can be displayed in the Colony Count Results window. To access the window
click onto the Results menu button from the Colony Counting Action Tab. A Colony count results window
will appear. Then click onto the Statistics tab after the new window appears. The Statistical tab displays:

 Area of the sample (in pixels) of the colony

In the second window, the property is listed alongside the area. Several numerical values are listed which
include:

 Minimum area
 Colony with the minimal area
 Maximum area
 Colony with the maximum area
 Range of area values
 Mean of area values
 Standard deviation of values
 Sum of all values
 Number of colonies

All dimensional values are reported in pixels unless the calibration process is performed on the image.

Related Topics:
 Reporting Functions

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Reporting Colony Distribution Information

Distribution information can be displayed in the Colony Count Results window. To access the window click
onto the Results menu button from the Colony Counting Action Tab. A Colony count results window will
appear. Then click onto the Distribution tab after the new window appears. The Distribution tab displays
graphical information.

 The drop-down menu allows users to report graphical information about the average diameter,
area, perimeter, and circularity of the colonies counted in the Petri dish.
 Users may also change the number of bins that are set to display in the graph.
All dimensional values are reported in pixels unless the calibration process is performed on the image.

Related Topics:
 Reporting Functions

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Modify Images

Image Action Tab Overview

The Image Action Tab provides functions to enhance and edit images captured with the Analytik Jena system.

The Image Action Tab contains the following functions:

Display Control
 Corrections (Brightness, Contrast, Gamma, Invert)
 Histogram
 Pseudocolor
 3D Plot
 Annotations (Create, Edit, Types of Annotation)
 Measure (Line, Area and Angle)
 Options
 View Annotations
 Synchronize Annotations with Image Zoom
 Layer Actions
 Flatten Layers
 Multi-Image Actions
 Background Filters (Background Correction and Subtraction)
 Compositing: Multiple Color Channels and Composite Images
 Sequences (slideshow of captured images)

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Display Control

Image Corrections

The image Display Control offers features to control how an image looks. Changes made to images using this
module will not be made permanent by default. All the changes can be reversed with the Reset button.
Note: If an image is modified in the VW Software and then opened in a different software program, the
changes will not be displayed. To make changes viewable in other programs, use the Flatten Layers
tool. This tool creates a new image with the modifications permanently integrated.
To access the Corrections functions, click on the Image Action Tab and then select the Display Control
menu button.

Corrections
 Brightness
 Contrast
 Gamma
 Invert

The specific functions available on the Image Control module are:

 Brightness: affects the overall brightness or dimness of the image. Brightness level of 50 means the
image is displayed in its original brightness (i.e. unchanged). Changing the brightness level can make
features near the top or bottom of the intensity scale easier to see.
 Contrast: affects the difference between light and dark parts of the image. A contrast level of 50
means that the image is displayed in its original contrast. A level higher than 50 means that
contrast has been increased (lights are lighter, darks are darker). A level lower than 50 means that
contrast has been decreased (lights and darks are both closer to middle values). Increasing the
contrast tends to highlight differences in intensity level; decreasing it can make patterns that cross
intensities more clear.
 Gamma: affects the difference between light and dark parts of the image, but it does so by using a
"gamma correction curve." The gamma correction curve affects middle values more quickly than
values at either the darkest or the lightest ends of the spectrum. Gamma contrast values range from
0.1 to 5.0. A value of 1.0 means that no gamma correction curve is in effect (the

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image is displayed at its original levels). Gamma contrast changes have similar results to regular
contrast changes.
 Invert: reverses all intensities, light for dark and dark for light. This also will have the effect of
complementing colors (e.g. red to turquoise, yellow to blue). Inverting the image can make certain
features easier to see.

Change Brightness, Contrast, Gamma Or Invert

Change Brightness
 Slide the Brightness control either left or right, or type a desired brightness value into the
Brightness text box to the right of the slider.

Image Before Effects Applied

Brightness Applied

Change Contrast
 Slide the Contrast control either left or right, or type a desired contrast value into the Contrast text
box to the right of the slider.

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Contrast Enhanced

Change Gamma
 Slide the Gamma control either left or right, or type a desired Gamma value into the Gamma text
box to the right of the slider.

Invert Image
 Select the Invert check box. To stop inverting the image: clear the Invert check box.

Inverted Image

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Histogram Controls

The Histogram Controls offer options for viewing tonal and color information about an image. By default, the
histogram displays the tonal range of the entire image. To display histogram data for a portion of the image,
first select that portion.

Note: If an image is modified and opened in a program other than this software, the changes will not
be displayed in that program. To make changes viewable in other programs, use the Flatten Layers
tool. This tool creates a new image with the modifications permanently integrated.

To access the Histogram functions, click on the Image Action Tab and then select the Display Control
menu button.

Apply a Histogram
 From the top options, select No adjust, Auto or Manual.
 Use the sliders or arrows to adjust the histogram values. Adjusting these values will change the
stretch mode to Manual.

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Options

 In the Options button select: Identical Y-scales, reset zoom or copy graph.

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Pseudocolor

The Pseudocolor applies a false-color spectrum to a monochrome or colored image.

Note: If an image is modified and opened in a software other than the VW Software, the changes will
not be displayed in that program. To make changes viewable in other programs, use the Flatten
Layers tool. This tool creates a new image with the modifications permanently integrated.
This process is sometimes called "colorizing." There are two primary reasons for using pseudocolor:
 To make the image look more like what might be seen in an actual color image with various kinds of
lighting, primarily for comparison purposes.
 To highlight specific intensities for analysis purposes. For example, the Over Saturation option
indicates white (maximum intensity 255) pixels with red, identifying the oversaturated parts of the
image.
To access the Pseudocolor functions, click on the Image Action Tab and then select the Display
Control menu button.

Pseudocolor Spectrums
Each pixel within a range of intensities is assigned a specific color across the entire histogram. The
software includes the following pseudocolor options:
 In Vivo: Red denotes the most intense signal and blue the least intense signal. This provides a
color-coded representation of intensity rather than just one color (where intensity would be
difficult to distinguish).
 Inverted Over Saturation: Colors pixels in bottom 5% of dynamic range red and next 5% as
yellow. There is no indication for oversaturated pixels.
 Ethidium Bromide: Mimics the colors used in Ethidium Bromide gel preparation.

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 Fluorescein: Mimics the colors used in the Fluorescein process.

 Texas Red: Mimics the colors that appear with a Texas Red stain.
 SYBR Gold: Mimics the colors that appear with a SYBR Gold stain.
 SYBR Green: Mimics the colors that appear with a SYBR Green stain.
 SYPRO Orange: Mimics the colors that appear with a SYPRO Orange stain.
 SYPRO Red: Mimics the colors that appear with a SYPRO Red stain.
 Coomassie Blue: Mimics the colors that appear with a Coomassie Blue stain.
 Silver: Mimics the colors that appear with a Silver stain.
 Blue to Red: Colors all intensities from blue at the low end to red at the high end using a natural
light spectrum.
 Red to Blue: Colors all intensities from red at the low end to blue at the high end using a natural
light spectrum.
 Blue: Colors all intensities from black to bright blue.
 Cyan: Colors all intensities from black to bright cyan.
 Green: Colors all intensities from black to bright green.
 Magenta: Colors all intensities from black to bright magenta.
 Red: Colors all intensities from black to bright red.
 Yellow: Colors all intensities from black to bright yellow.
 Black Background Blue to Red: Colors all intensities from blue at the low end to red at the high end
using a natural light spectrum.
 Black Background Red to Blue: Colors all intensities from red at the low end to blue at the high end
using a natural light spectrum.

Apply or Remove a Pseudocolor

 From the Pseudocolor drop-down list, select the desired pseudocolor. The image will be
colorized.
 To remove a Pseudocolor, from the Pseudocolor drop-down list, select None.

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3D Plots

 Using the 3D Plot Function

 Viewpoint Tab
 Output Tab

The 3D Plots function allows the user to see a three dimensional view of the sample. For example, if two
bands look equally bright in an image, or with naked eye, a 3D plot can actually show if there is a quantitative
difference in intensity. A 3D plot can also be used as a great presentation tool.
The uniformity of the light source in conjunction with the camera response can be checked using 3D plots.

Using the 3D Plot Function

The 3D plots can be used for static images as well as live preview and integration.
 Open an image.
 To access the 3D Plot function, click on the Image Action Tab and then select the Display
Control menu button.

 This will bring up a separate window that shows the 3D plot.

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Viewpoint Tab
Controls on this tab lets the user set the correct angle of view.

Rotation Controls
One can rotate the image in Y as well as Z axes, using the ’Y’ rotation and ’Z’ rotation handles. The axes
are as follows:
 Z axis: The vertical axis.
 Y axis: The horizontal axis.
The plot can also be rotated by dragging the spin-box preview image on the Image 3D Plot tab with the
mouse in a desired direction.

Zoom Controls
Zooming in and out of the plot is possible in two ways:
 Adjusting the Zoom Value using the up and down arrows or typing in the appropriate value.
 Using the buttons labeled ’Zoom In’ and ’Zoom Out’

Output Tab
Three controls in this tab let you export the 3D plot information for various uses:

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 New Image: Pressing this button creates a new image in the software with what is visible on the
surface plot. This new image must be saved.
 Clipboard: Pressing this button copies the 3D plot onto clipboard, so that it can be pasted to any
other software (eg. MSWord, Excel, Paint, Photoshop etc.)
 Print: Pressing this button prints the 3D plot on a desired printer. Pressing it brings up the list of
available printers.

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Annotations

Annotations

 Overview
 Annotation Navigation
 Types of Annotation
 Creating Annotations
 Viewing and Hiding Annotations
 Modify Annotations
 Synchronize Annotation with Image Zoom
 Spatial Calibration
 Rulers

Overview
Annotations allow users to rotate areas of an image without changing the image itself. This means that areas in
the image that need more study, are particularly interesting or that support a particular scientific interpretation
can be identified. At any time, annotations can be viewed or hidden to see the image with or without
annotations.

Annotation Navigation
Users may add and edit annotations through the Image Action Tab > Annotation menu button.

Types Of Annotation
The software offers five different types of annotation:
 Text: Text annotations consist of written information. Use them to label a particular part of an
image. Users have the ability to change the font size, color and formatting (bold, italic or
underline) of a Text annotation.
Note: Users can increase/decrease the size of annotations while zooming in or out. See section
Synchronize Annotations with image zoom.
 Line: Line annotations permit users to draw lines with optional arrowheads at one or both ends. Use
them to associate other annotations such as text with a particular image feature or to draw attention
to an image feature. Select the color, line thickness, line style (solid, dotted or dashed) and
arrowheads (none, at start, at end, or both) of a Line annotation.
 Rectangle: Rectangle annotations allow users to draw a rectangular frame around part of the image.
Use them to show the boundaries of an image feature. Select the color, line thickness and line style
(solid, dotted or dashed) of a Rectangle annotation.
 Ellipse: Ellipse annotations are very similar to Rectangle annotations except that they are oval
rather than rectangular. Select the color, line thickness and line style (solid, dotted or dashed) of an
Ellipse annotation.
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 Highlighter: Highlighter annotations work like a highlighting pen by altering the color of the
underlying image to draw attention to an area. Select the color of a Highlighter annotation.

Annotation Tools
Other tools located in the Annotations Action Tab include the following:
 Measure
 Import/Export
 Options
 Layer Actions

Next Steps
 Draw, Edit and Delete Text Annotations
 Draw, Edit and Delete Line Annotations
 Draw, Edit and Delete Shape and Highlight Annotation

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Draw Annotations

Draw a Text Annotation

Text annotations allow users to place labels on an image to describe or to name a feature of the image.
To draw a text annotations, click Annotations Action Tab and select Text annotation from the menu.
 A cursor will appear on the image. Position the cursor in the desired location on the image where the
annotation should be placed. Click the mouse button.
 The New Annotation window appears.
 Type the desired text in the New Annotation window.
 Use the format text drop down menu to adjust font size and style (bold, italic, underline) or to
indicate word wrap. Click OK.

To edit annotations:
 Click the Select and Edit from the Edit Annotations
 Right click on the annotation to be edited.
 Select options from the pop up menu. Depending on the type of annotation, these options can
include copy, edit, color, line formatting, font size, bold, italic or underline.

To delete an annotation:
 Click the Select and Edit from the Edit Annotations.
 Right click on the annotation to be deleted.
 Select delete.
Note: Annotations can be deleted anytime simply by right-clicking with mouse.

Related Topics
 View and hide annotations
 Synchronize annotation with image zoom

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Draw Line Annotations

 Select Image Action Tab > Annotations menu > Draw new line
annotation.
 Click and release a position on the image to begin the line annotation. A line
will follow the mouse as it is dragged. To cancel adding a line, simply press the
ESC key.
 Click a position on the image to end the line. The new line will be drawn.

To edit annotations:
 Click the Select and Edit from the Edit Annotations.
 Right click on the annotation to be edited.
 Select options from the pop up menu. Depending on the type of annotation,
these options can include copy, edit, color, line formatting, font size, bold,
italic or underline.
To delete an annotation:
 Click the Select and Edit from the Edit Annotations.
 Right click on the annotation to be deleted.
 Select Delete Annotation from the pop up menu.

Note: Also refer to the Modify Annotations section for more information.

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Draw Shape and Highlight Annotations

Draw a Rectangle, Ellipse, Highlighter Annotation

 Select Image Action Tab > Annotations menu and choose the appropriate tool (Rectangle,
Ellipse, Highlighter).
 Click a position on the image to place a corner of the annotation. Release the mouse button.
 A view of the new annotation will follow the mouse as it is dragged. To stop the process of adding an
annotation, simply press the ESC key.
 Click a different position on the image to place the opposite corner of the annotation. The
annotation will be drawn.

NOTE: The Highlighter annotation is only available as a rectangle, not an ellipse.

Note: To edit an annotation, ensure that the edit annotations tool is selected.
To edit annotations:

 Click the Select and Edit from the Edit Annotations.

 Right click on the annotation to be edited.
 Select options from the pop up menu. Depending on the type of annotation, these options can
include copy, edit, color, line formatting, font size, bold, italic or underline.
To delete an annotation:
 Click the Select and Edit from the Edit Annotations.
 Right click on the annotation to be deleted.
 Select Delete Annotation from the pop up menu.

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View or Hide Annotations

The software allows annotations to be viewed or hidden on an image with a single command.
 To view annotations, click Image Action Tab > Annotations menu > Options: View Annotations. A
green check mark indicates that annotations are viewable. If this menu option is checked but no
annotations appear, no annotations exist for this image.

 To hide annotations, click Image Action Tab > Annotations menu > Options: View Annotations. A
red X indicates that annotations are hidden.
 It is possible to toggle between viewing and hiding by clicking the View Annotations button
repeatedly.

Note: To edit an annotation, ensure that the edit annotations tool is turned on. Select the annotation in the
image, right mouse click on the annotation, then select from the menu options to change the
annotation. Also refer to the Modify Annotations section for more information.

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Modify Annotations

 Select Annotations
 Edit Text Annotations
 Move and Resize Annotations
 Rotate Text Annotations
 Format Annotations
 Delete Annotations

Select Annotations
After creating an annotation, select the annotation to change the formatting properties or to
graphically move, stretch or resize it.

 To edit an annotation, select Image Action Tab > Edit Annotations .

 Click on any part of the annotation. Control handles will appear to mark the selected annotation.
Note: The cursor will change from an arrow to a hand when the cursor is over an annotation.

Edit Text Annotation

 To edit an annotation, select Image Action Tab > Edit Annotations .
 Right click on the text to be edited.
 Select options from the pop up menu including copy, edit, color, font size, bold, italic and
underline.
Note: It is possible to edit the text by double clicking the annotation and making text changes in the
Annotation Text Edit window or select formatting options from the Format Text drop down menu.

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Move and Resize Annotations

Once an annotation is selected, the annotation can be moved and resized with the mouse.

Move an Annotation
 To move an annotation, select Edit Annotations Tool if not already selected.
 Click on any part of the annotation. Control handles will appear.
 Drag the annotation to move it to the new position.

Change the Points of an Existing Line, Length Measure or Angle Measure

Annotation
 Select the annotation as described above.
 Drag the control handle to the new position. The annotation will stretch or move appropriately as it
is dragged.

Resize an Existing Rectangle, Ellipse, Highlighter or Area Measure Annotation

 Select the annotation as described above.
 Drag a control handle inward or outward to define the new size. The point on the opposite corner
will remain fixed and the annotation will resize as it is moved.

Rotate Text Annotations

 Select the annotation as described above.
 Drag any control handle and rotate to the desired amount of rotation.

Format Annotations
The annotation formatting contains options to format a selected annotation. Change the formatting of an
annotation by selecting the Edit Annotations Tool and then right clicking on the desired annotation. On the
appearance tab there will be various options to format and change the selected annotation.

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The Annotation Formatting menu contains the following formatting options:

 Color: Pick a color from the list or choose Custom Color at the bottom of the menu. All annotation
types support color options.
 Line Style: Choose from solid, dashed or dotted lines. Only the following line annotations support line
style: Line, Rectangle, Ellipse, Length Measure, Angle Measure and Area Measure.
 Line Thickness: Choose a line thickness from the choices. Only select Line Thickness if the line style
is Solid. Otherwise the line thickness will be 1 and the Line Thickness menu will be unavailable. The
same annotation types that support Line Style support Line Thickness.
 Arrow Style: Choose whether a Line annotation (only) has:
 No arrowheads.
 An arrow at the start (first point) of the line.
 An arrow at the end (second point) of the line.
 Arrows at both ends of the line.
 Font Size: Choose the font size of Text, Measure Length, Measure Angle and Measure Area
annotations from among the listed values.
 Bold: Choose whether Text, Measure Length, Measure Angle and Area Measure annotations
should be boldfaced.
 Italic: Choose whether Text, Measure Length, Measure Angle and Measure Area annotations
should be italicized.
 Underline: Choose whether Text, Measure Length, Measure Angle and Measure Area
annotations should be underlined.

Delete Annotations
Deleting an annotation removes it permanently from the image.
 Select the Edit Annotations.
 Right click on any part of the annotation.
 Select Delete Annotation from the pop up menu.

Note: If an image is modified in the VW Software and then opened in a different software program, the
changes will not be displayed. To make changes viewable in other programs, use the Flatten Layers tool. This
tool creates a new image with the modifications permanently integrated.

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Synchronize Annotations

Annotations can either grow or shrink in size depending on image zoom level, or can remain the same size
regardless of zoom. The default setting is Synchronize annotations with image zoom which will maintain
annotation scale compared to the image. To keep the annotations the same size regardless of the size of the
image (not to scale), uncheck the Synchronize annotations with image zoom.

 To change this setting, go to Image Action Tab > Annotations menu > Options: Synchronize
annotations with image zoom.
 Click on Synchronize annotations with image zoom to uncheck or check this function.

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Measurement Tools

The measure tools allows users to measure a portion of the image with regard to length, area or angle.
 Line Measure
 Area Measure
 Angle Measure

NOTE: Length Measure and Area Measure annotations use the image's pixel scale in calculations. If these
annotations display information in pixels ("px"), no custom scale has been set. See the Spatial Calibration
tool "Changing Sample Width" for instructions on changing the image's scale.

Line Measure
 Choose Image Action Tab > Annotation > Line Measure or choose the Area Density Action Tab
> Calibration > Line Measure.
 Click a position on the image to begin the line measure. A line will follow the mouse as it is
dragged. To cancel adding a line, simply press the ESC key.
 As the mouse is moved, the scale tool will show how many pixels (unless the calibration process has
been performed) are contained in the line drawn.
 Click a position on the image to end the line. The annotation will now display the total length
measurement value.

Area Measure
 To use the Area Measure tool, click Image Action Tab > Annotation > Area Measure or Area
Density Action Tab > Calibration > Area Measure.
 Click a position on the image to place a corner of the area measure annotation. Release the
mouse button.
 A view of the area measure annotation will follow the mouse as it is dragged. To stop the process of
adding an annotation, simply press the ESC key.
 Click a different position on the image to place the opposite corner of the area measure
annotation. The annotation will be drawn.
 The new area measurement annotation now appears in pixels (unless the calibration process has
been performed).

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Angle Measure
The measure angle tool requires three points to be placed on the image to define an angle.

 Choose Image Action Tab > Annotation > Angle Measure or choose the Area Density Action Tab >
Calibration > Angle Measure.
 To create an angle measurement annotation to define a specific degree, three points will be
marked as shown.

 Click a position on the image to place the first point of the angle measure annotation. Release the
mouse button.
 Drag the mouse to second position to create the angle point and click and release the mouse to set
the angle position.
 Drag the mouse to a third position. A view of the angle measure annotation will follow the mouse as
it is dragged.
 Click and release the mouse to set the third position.
 The angle measure tool shows the degree measurement for the angle drawn .

Note: To edit a measurement annotation, ensure that the edit annotations tool is turned on. Refer to
the Modify Annotations section for more information.
Note: If an image is modified in software and then opened in a different software program, the changes will
not be displayed. To make changes viewable in other programs, use the Flatten Layers tool. This tool creates a
new image with the modifications permanently integrated.

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Layer Actions

The Flatten Layer function embeds annotations and analysis markings in an image. This feature is useful when
users want to open and see analysis and annotations in a program other than the VW Software. If layers are
not "flattened", markings will not appear after opening the image in another program.

To access the Flatten Layers function go to the Image Action Tab and click on the Flatten Layers button.

This function creates a new untitled image with annotations and/or analysis permanently embedded.
Save the image as a new file which can be opened in other programs to view the image with annotations and
analysis. Note: The flattened image markings cannot be edited.
Note: The original image will continue to display annotation and analysis information if it is saved and
reopened in VW Software. The annotations and analysis can be modified in the original image only.

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Multi Image Actions

Multi-Image Actions

Background Filters
Background correction and subtraction tools are filters available through the Multi-Image Actions Tab.

Background Correction
This command allows users to subtract a flat level of intensity off the current image.
 To access this function go to the Image Action Tab > Multi-Image Actions menu, click on
Background Correction.
 Select a Background image and the Black Level.

Background Subtraction
This command allows users to subtract one image from another.
 To access this function go to the Image Action Tab > Multi-Image Actions menu, click on
Background Subtraction.
 Select a Background image.

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Image Compositing

The Compositing function allows the user to take two or more images and create a composite of the two
images. For example, the user may take a white light image of a mouse and a fluorescent image of a mouse.
These two images can be used to combine into one composite image that outlines the location of the
fluorescence inside the mouse body.

Create a Composite Image

 Open the images that will be used in the composite image. Use the Pseudocolor function to
colorize the fluorescent image, if desired and as shown below.
 Go to the Image Action Tab > Multi-Image Actions menu and select the Composite feature.

 Select the desired number of images by using the drop-down menus at the top of the Image
Compositing window.
 Change the Threshold, if necessary, to optimize the image shown in the Resulting image
preview window.
 When finished, select OK.

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Player (Image Sequences)

 Purpose of the Player

 Using the Player
 Merge Functions
 Player Features
 Player Options
 Extract or Delete Individual Image Files (Frames)
 Saving_.AVI_Files

Purpose of the Player

The player combines multiple images in a single file and scrolls through the images. If a sample is to be
observed over a period of time, (e.g. Chemiluminescence blots), it may be required to capture multiple
images at specific time intervals. Depending on the camera used, the software provides two features -
Sequential Integration and Image Integration. These integration functions produce a series of images
which the software combines into a single file. The file is saved with a .sqv extension that the
Sequences player can run.

Using the Player

To access the Image sequences player function:
 Go to Image Action Tab, Multi-Image Actions button. The following Sequences menu
will display.

Tip: Use the SQV whenever possible. AVI file types reduce the image to 8-bit.

To play a sequence of images:

 Open images.
 Click Merge.
 In the Merge Images window, click Merge Files .

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 A new file is generated which includes all open images (file name is untitled).
 Save the file as .sqv with a desired name.

 Click Play button or select other Play Options from the Sequences menu.

Note: If images are larger than the screen area, right click on any image in the sqv file and select View Best
Fit.

Merge Functions
These functions can be used to modify the merged images.

 Add: Click the Add button to find files to merge.

 Remove: Select a file and click on Remove to remove it from the list.
 Merge Files: Merges files in the list into a single .sqv.
 Cancel: Closes the window and cancels the process.

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Player Features

Below is the description for each of the Player’s buttons:

BUTTON FUNCTIONALITY
Views the next image.

Views the previous image.

Plays the sequence of images. Playing will show the images one after
another.

This button changes to a Pause/Stop button when clicked.

Plays the sequence of images in the reverse order.

Plays the sequence with a number of images to skip. The number of

images to skip can be set in the Player Options dialog. See Player
Options below.
Plays the sequence with a number of images to skip in reverse order. The
number of images to skip can be set in the Player Options dialog. See
Player Options below.

Player Options
Click the Play Options button to set individual options for going through frames in a .sqv or .avi file. The
following window appears:

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Frame Rate This is the interval (in milliseconds) between two consecutive images that are
displayed. For example, a value of 500 means that a new image will be
displayed a half second after the previous image. ’Frames per minute’ is
automatically calculated based on this value.
Frames per This is the number of images that will play during a period of one minute.
minute
Fast Frame
Skip
This is the number of images to be skipped when playing with or

button.
Repeat When the Player reaches the end of the sequence of images, it starts again
with the first image.

Play to end When this option is selected, the player will stop when it reaches the end of
the sequence of images.

Auto When this option is selected, the player goes back in reverse order after it
reverse reaches the end of the sequence of images.

Extract or Delete individual Image files (frames)

Extracting an image from a .sqv or .avi file creates a new image in the workspace and DOES NOT
remove it from the sequence. Delete removes the image from the sequence.

The easiest way to initiate this action is by clicking on Enable Tile View from the Multi-Image Actions under
the Image Action Tab, which brings up the following window. Right click on any image to extract or delete.

Click Extract from the Multi-Image Actions menu. The following window opens which lists all the frames
inside the .sqv:

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All the images contained in the active sequence are in the list. The user can Extract (open the specified
image in a new window) images or Delete (remove) images from the active sequence.

Saving .AVI Files

SQV is a custom format used by the Analytik Jena software. If files are to be opened in another
program, export the .sqv files to Audio Video Interleaved (AVI) which is standard file format.
 To save a .SQV file as an .AVI, use the Save As function and select AVI files from the Save as
type drop down.
Depending on the requirement of the target player, AVI files may need to be compressed/encoded using
a specific compressor format. When saving as an AVI file, the Video Compression window will appear.
Select the appropriate compressor from the drop down menu.

Note: Use the SQV whenever possible. AVI file types reduce the image to 8-bit.

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Create Templates

Set-Up Hardware Master Templates

Master Templates (also called Presets) enable users to configure specific camera, darkroom and other
settings and save them with user-defined names. Templates allow users to select the saved settings for
repeat experiments.

Prior to creating a new template, it is recommended to adjust the camera, lens, lighting, UVP eLITE (if
included) and darkroom settings in the main VW Software window.

Create a New Template

To create a new template:
 Click the Acquisition Action Tab > Manage Templates button. A Master Template window will
pop up.
 The screen shot below shows a sample template with the "Camera" tab selected (tab text may
be different depending on the connected hardware).
 Click the appropriate hardware tab to see the template setting options for other
connected hardware such as the UVP ChemStudio PLUS or Automated UVP eLITE.

 Name the template in the Template drop down box.

 Click the Sync button to synchronize hardware settings that were selected in the main software
window. Modifications to the settings can also be made in the Master Template pop up
window. Note: Syncing settings applies to all hardware shown.
 Click Save & Close to save the settings and close the New Template window.

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Note: Once a template is created, it can be selected from the Acquisition Action Tab > drop down menu
to the left of the New Preset button. The template settings will automatically be applied to the
applicable hardware and will show in the hardware control modules on the main screen.
Note: Use the Preferences - Miscellaneous - Template Settings menu (access via Advanced Menu >
Configure Applications) to define template saving options when closing the software by selecting: Ask,
Always or Never.

Related Topics:
 Editing and Deleting Templates Edit or synchronize changes to a template or delete templates.

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Edit, Synchronize and Delete Templates

Edit a Template
To edit a template:
 From the Acquisition Action Tab, click the Manage Templates button. The Master Template
window will pop up.
 Select an existing template from the Template drop down menu.
 Click on a hardware tab and adjust the settings. Any changes made will be highlighted in yellow.
Note: To remove hardware from the Template, click the Edit button. In the new pop up
window, select the hardware in the right column to be removed. Click the single left
arrow button. Click OK.
 When all modified settings have been made, click Save and Close.

Synchronize a Template
If changes are made in the hardware control modules (lighting, camera, eLITE, etc.), these changes can
be synchronized to an existing template.
To synchronize a template to new settings:
 Select a template from the Acquisition Action Tab > template drop down menu to the left of
the New Preset button.
 Make changes in the main screen hardware control modules (lighting, camera, eLITE, etc.).
The changes will be highlighted in orange.
 To synchronize the changes to the template, click on the Acquisition Action Tab > Manage
Templates button. The Master Template window will open. The currently selected template
name and settings will be displayed.
 Click the Sync button.
 Click the Save & Close button to save the synchronized settings.

Delete a Template
To delete a template:
 From the Acquisition Action Tab, click the Manage Templates button. The Master
Template window will pop up.
 Select an existing template from the Template drop down menu.
 Click the Delete button. The selected Template will automatically be deleted.
 Click Save & Close to confirm deletion of the template. Or click Cancel to reinstate the template.

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Open and Save Images

Open and Save Images

 Open Images
 Save Images
 Image File Types

Open Images
The software will open images in standard file formats including JPEG, TIFF, GIF, PNG, TGA and BMP.
Video files can be saved as AVI and SQV. If the image was previously saved using this software, then
other image details such as the image's scale, history and annotations will be loaded as well. Many demo
images are included with this software to increase user familiarity with the software.

Open a Previously Saved Image

 From the File menu, choose Open image from file.
 Select the type of file to open. If unsure of the file type, select "All Supported Formats."
 Navigate through the drives to the file folder in which the image is stored.
 Select the desired image file.
 Click Open. An Image window containing the desired image will appear.

Open a Demo Image

 Go to File menu and click on Open Demo Image. The software keeps a folder "Images" that
shows by default where the demo images are stored.
 Select the desired demo image file from the list of available files.
 Click Open.

Save Images
Save images acquired in the software so they can be used in later sessions. To save a new image:

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 Click on the File menu and select Save or Save As. The Save window will appear.
 Select the file type to use from the drop-down list. TIFF is the default file type. It is ideal to
save images in the TIFF format to maintain the most image data for analysis purposes.
 Navigate through the drive, folder or network structure to the desired location to save the image.
 Enter a filename for the image.
 Click Save.

NOTE: If analysis, annotation, etc. is performed on an original image, the file must be opened with
VW software to view or modify this information. To view the analysis/annotation in a different
program, use the Flatten Layer tool and save the image as a NEW file. Once the flatten layer tool is
applied, the analysis cannot be modified in the new image.

Save Using a Different File Folder, Name or Type

 From the File menu choose Save As. The Save window will appear.
 Select the file type to use from the drop-down list near the bottom of the window.
 Navigate through the drive, folder and network structure to the location to save the image.
 Enter a file name for the image.
 Click Save.

NOTE: Analytik Jena imaging systems and software support network connectivity for saving and
sharing image files.

Image File Types

The software supports the following formats:
 TIFF: Tagged Image File Format, a common image format. Depending on settings, TIFF can be
either a lossy or a lossless compression format. In the software, it is used in the lossless mode to
reduce image file size without losing integrity. TIFF files generally have TIF or TIFF extensions.
 JPEG: Joint Photographic Experts Group. A common lossy compression image format used to
store images on disk. JPEG files generally have JPG or JPEG extensions.
 TGA: Truevision Targa image format. TGA is a lossless compression format that reduces file size
somewhat. TGA files generally have a TGA extension.
 BMP: Microsoft Bitmap image file format. BMP is a lossless format which provides
some compression to reduce file size. BMP files generally have a BMP extension.
 PNG: Portable Network Graphics, a common image format. PNG is a lossy compression format
that results in very small files. Files stored in PNG usually have a PNG extension.
 GIF: Graphic Interchange Format, a proprietary Xerox image compression format. GIF is a lossy
compression format that results in very small files. Files stored in GIF usually have a GIF
extension.

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JPEG, PNG and GIF are lossy compression formats. TIFF, TGA and BMP are lossless compression
formats (at least, as used by this software; TIFF can actually be either lossy or lossless). Lossy
compression makes small, usually non-visible changes to an image in order to make the file size
smaller. Typically, formats that use lossy compression store in much less space than lossless
compression formats. By comparison, a lossless format does not store as compactly, but also does not
change the image in any way.

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Print Reports

Print

 Printing Image History

 File Print Command
 Printing Colony Count Results
 Viewing and Printing 1D Gel Analysis
 Reporting and Printing Area Density Results

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File Print Command

 Go to File > Print and select a printer to print from.

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Print Image History

Reports
The software provides several types of reports:
 Image Report: Prints the image, using as much of the page as possible while preserving the
image's aspect ratio.
 Image History: Prints the image history, as reported in the Image Information window.
 Image Notes: Prints the image notes, as entered in the Image Information window.
 Image Properties: Prints the image's resolution (width and height), depth, scale and file
information.
 Other Reports: Print additional reports based on image analysis including Analysis Settings,
Analysis Lanes, Analysis Bands and Lane Profile Report.
All reports include a header and footer that are user defined. The Report Preview window shows the layout of
the data on each page.

Preview and Print a Report

 Choose File > Print a Report and then choose the desired report from the Reports window.
 To change the target printer, paper, paper source (tray) or page layout, click Page Setup and
make the desired changes.

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 To enter the header or footer text, type new text in the text box and click Preview the pages.
There are some special character combinations in the header and footer:
 "%p" is the current page number.
 "%d" is the current date.
 "%t" is the current time.
 "%c" is the total count of pages for printing
 To change the margins, choose an alternate margin setting in the Page Setup window, click OK
after selection.
 In the Reports > Preview Options, click Show Margins in Preview Mode to see the margins
graphically.
 When the preview looks correct, click Print.

Print an Image
Images can be printed to any Windows-supported printer, regardless of it being a file-printer, local printer or a
network printer.
 Open an Image.
 Choose File > Print.
 If necessary, choose the target printer, paper size, paper source (tray) and page layout.
 Click OK.

Note: The Print command (File > Print) uses exactly the same format as the Image Report in Reports.
Note: The Print command is also available on the Files module, but does not show the Page Setup
dialog window. Instead, it prints an Image Report directly to the default printer.

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Support 21 CFR Part 11 Compliance

Supporting 21 CFR Part 11 Compliance

 Purpose
 Features
 Usage

Purpose
US - Food and Drug Administration (US-FDA) created and released Part 11 of Title 21 of Code of Federal
Regulations (CFR) in August 1997. The rules delineate the conditions under which the US-FDA considers
electronic records and electronic signatures equivalent to paper records and paper signatures. The
instructions for compliance span the entire organization and its practices. The software supports
organizations with their 21 CFR Part 11 compliance.

NOTE: While software from Analytik Jena is an essential tool for assisting an organization to maintain CFR
compliance, Analytik Jena cannot claim that this is the only tool needed to achieve overall CFR compliance.
The organization must establish policies and procedures that work in conjunction with such efficient tools,
to ensure total compliance with 21 CFR Part 11 regulations.

Features
Analytik Jena provides software support for the following two sections of CFR regulations:
 Section 11.10 (e) &endash; For electronic records, this section requires the use of computer
generated, time-stamped audit-trails to track changes.
 The software keeps track of all changes that affect image-data. Any action in the software that
modifies the original data of an image open in the VW workspace, is logged. The log of such
changes is individually maintained for each image and is referred to as ’r;History’ in the software.
 Section 11.3 (b) (4) &endash; This section mandates that the system be controlled by users
responsible overall for contents of electronic records required to track.
The software provides an elaborate system of maintaining secure user accounts. Assign unique usernames
and passwords to all the users who will be using the software. Each account can also be configured to
provide read or modify access to other users’ data. Events generated in the audit trail (above) are logged
with the user name.

Usage
View an Image History Audit Trail
 Open the image in question.
 Right click on the image and select Image Information. Open the History tab.
 Events are listed in the left column. Click on each event to view the entry details on the right.
 Add notes to each event if required.
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Print an Audit Trail (History)

 Open the image for which to print the Audit Trail.
 Go to File > Print a Report. (This option is disabled, if no printer is available.) A window opens
with various types of reports available.
 To print the Audit Trail, check the Image History item. To print the image along with the trail,
check the Image Report and Image History options. Adjust the header and footer settings or
page settings if necessary.
 Click Print to print report.

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Related links:
 For information on user accounts and passwords, go to: User Administration

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Image History

Each material change to an image is tracked in the software’s Image History feature. Material changes include
use of any filters applied and use of the Paste Special feature. Changes to Effects and Annotations are not
tracked in the Image History.

View Image History

 Right click onto the image. A shortcut menu will appear.
 Click onto Image Information at the bottom of the shortcut menu. The Image Information
window will appear and the image properties are shown by default.
 Click the History tab to view the image history.

Entries in the Image History may be of three types:

 Creation: Describes how an image was created (captured or scanned) and provides some
details.
 Change: Describes use of image filters or Paste Special.
 Error: Describes an error that occurred while reloading the image from a saved file. The main use of
an Error entry is to track the times when the image was changed in another software package, which
is important for some kinds of laboratory practice.

The Image History includes information on:

 What type of entry it is, from among the types described above.
 When the change occurred.
 What the change was and details about it.
 Any notes that the user added to explain the entry.

Add Notes in the Image History

 Right click on the image, choose Image Information. The Image Information window will be
displayed.
 Click the History tab at the top of the window.
 Click on any history entry in the list on the left side to display details about the entry.
 Type the notes in the Notes field.
 Repeat steps for any other history entries.
 Click OK.

Note: Image History is useful in Supporting 21 CFR Part-11 Compliance.

Related Topics:
 Printing Image History
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Glossary

Glossary

 Artifact: In imaging, a flaw caused either by the imaging process or by the hardware itself. For
example, dust on the camera lens could cause small bright or dark spots in an image.
 Aspect Ratio: The ratio between an image's width and its height. If the aspect ratio is not
preserved, the image will appear stretched or squashed.
 Bits: The smallest units of computer measurement. A bit is a single binary value (i.e. it can be "on" or
"off" only). Bits typically are combined into units of eight, called "bytes." Modern computer processors
work with groups of 4 ("32-bit processor") or 8 ("64-bit processor") bytes at a time.
 BMP: Microsoft Bitmap image file format. BMP is a lossless format which provides some
compression to reduce file size. BMP files generally have a BMP extension.
 Control Handle: A small square at the corner (or similar point) of a graphical object that marks its
extent and indicates that the object is selected. Usually the object can be resized by dragging the
control handle; in some cases, different behavior results.
 Electrophoresis: The movement of suspended particles through a fluid or gel through the
application of electrical current to the suspension medium.
 Fidelity: The degree to which an image is true (i.e. accurate and uncorrupted) to the original
scene it represents. Also used in audio technology with the same meaning.
 GIF: Graphic Interchange Format, a proprietary Xerox image compression format. GIF is a lossy
compression format that results in very small files. Files stored in GIF usually have a GIF extension.
 Image Depth: The size (and thus range) of intensity numbers supported per pixel in an image.
 Intensity: The measure of brightness of a pixel. In a monochrome image, each pixel has a single
intensity. In a colored image, each pixel has three intensities: one for red; one for green; and one for
blue. The actual intensity values depend on an image's depth.
 JPEG: A common lossy compression image format used to store images on disk. JPEG files
generally have JPG or JPEG extensions.
 Lossless Compression: Compression schemes that preserve the image's integrity in full. Generally,
lossless compression results in much larger files than lossy compression on the same image.
 Lossy Compression: Compression schemes that tolerate some pixel value changes to make the image
compress to a smaller size. Because the changes are irreversible, the image has "lost" some of its
original detail after such an operation.
 Macro Mode: Close-up mode for a digital camera or web-camera. Macro mode is usually
appropriate for imaging microbiology slides.
 Microbiology: The branch of biology dealing with microscopic forms of life.
 Microscopy: The use of or investigation with a microscope.
 Monochrome: Black-and-white, with shades of gray.
 Pixel: Short for "picture element." A pixel is a single dot in a computer image. The dot has a
certain color (for a color image) or an intensity (for a monochrome image). For a more detailed
explanation, see Inside a Pixel.

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 PNG: Portable Network Graphics, a common image format. PNG is a lossy compression format that
results in very small files. Files stored in PNG usually have a PNG extension.
 Pseudocolor: Artificial application of color to a non-color (monochrome) image, or artificial re-
tinting of a colored image. VW Software provides several built-in pseudocolor sets that mimic
certain lighting conditions and reveal specific information in the image.
 Resolution: The number of total pixels (width of the image in pixels multiplied by height of the
image in pixels). Higher resolution produces a smoother image (especially when zoomed in) but
requires more RAM and disk space.
 TGA: Truevision Targa image format. TGA is a lossless compression format that reduces file size
somewhat. TGA files generally have a TGA extension.
 Thumbnail: A reduced-size version of an image. From "thumbnail sketch."
 TIFF: Tagged Image File Format, a common image format. Depending on settings, TIFF can be either
a lossy or a lossless compression format. In VW Software, it is used in the lossless mode to reduce
image file size without losing integrity. TIFF files generally have TIF or TIFF extensions.
 Zoom Factor: The percentage by which the image is scaled. A zoom factor of 100% (1.0) means that
each pixel is not scaled; it is its original size. Zoom factors greater than 100% indicate that the image
has been scaled up (meaning that several screen pixels are used to show one actual pixel). This
generally makes detail easier to see. Zoom factors less than 100% mean that the image has been
scaled down. This makes it possible to see more of the image in the Image window.

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Index
1 Colony Counting Reports .................................... 198
1D Analysis Preference Settings ........................ 141 Concentration Calibration .................................. 127
1D Analysis Settings ........................................... 141 Contrast ............................................................... 207
3 Convert Image ........................................................ 58
3D Plots ............................................................... 214 Convert color depth ............................................ 58
Three dimensional .......................................... 214 Convert image bit depth .................................... 58
A Copy ........................................................................ 39
Acquisition............................................................. 75 Counting Colonies ............................................... 171
Action Tabs ........................................................... 30 Capture ............................................................ 171
Add Colonies ....................................................... 181 Preview .............................................................171
Analysis Display Settings ................................ 181 Create Line Annotations .....................................221
Circle Radius .................................................... 181 Creating Annotations ........................................... 219
Add lanes............................................................. 104 Text Annotation ............................................... 219
Annotation .......................................................... 219 Creating Colony Templates.................................. 176
Annotations ........................................................ 217 Manual count ...................................................176
Area Density ........................................................ 151 Save Filters .......................................................176
Auto Split Colonies.............................................. 183 User Defined Template....................................176
Automated BioLite ............................................... 82 Creating Macros ..................................................... 68
Automatic Counting ............................................ 172 Create Macro ...................................................... 68
B Record Macro ..................................................... 68
Background Correction ....................................... 119 D
Joined Valleys .................................................. 119 Darkroom and Lens Plugin.................................... 84
Rolling Disc ...................................................... 119 Darkroom Functions .............................................. 84
Straight Line .................................................... 119 Darkroom Templates ............................................. 84
Background Filter ............................................... 231 Delete Colonies ................................................... 182
Background correction ................................... 231 Delete Templates ................................................ 240
Background subtraction ................................. 231 Digital Video Player.............................................. 233
Binning Modes ...................................................... 94 Distribution........................................................... 205
Blur ........................................................................ 46 E
Bookmark .............................................................. 78 East ......................................................................... 48
Brightness ........................................................... 207 Edit Bands ........................................................... 108
C Edit lanes .....................................................104, 108
Calibrating Image Scale ........................................ 28 Edit Menu ............................................................... 38
Calibration Curves ............................................... 160 Edit Templages ................................................... 240
Capture an Image ................................................. 75 Editing and Deleting Templates ........................ 240
Capturing Images .................................................. 75 Editing Images ....................................................... 38
Classes ................................................................. 200 Emboss Direction ................................................... 48
Colony Classes ..................................................... 200 Estimate Region Volume ..................................... 158
Colony Count Module ......................................... 167 Export .................................................................. 199

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Export Area Density Results………………………..165 L

Export Data Explorer Reports………………………145 Lane and Band Information ................................ 101
Band Properties ............................................... 101
Lane Properties ................................................ 101
F
Lane Profile Graph ............................................... 123
License Agreement ................................................ 22
File Menu……………………………………………………..32 Line Annotations ................................................. 221
Linkage Rules ....................................................... 139
File Print Command............................................. 245 Loading and Saving Images ....................33, 241
File Type...................................................33, 241 Log Viewer.............................................................. 60
Login History View........................................................
Finding Lanes and Bands ...................................... 98
17, 61
Fine focus ............................................................... 78
M
Flip Image .............................................................. 54
Magnification......................................................... 78
Flip Horizontally ................................................ 54
Manual Counting ................................................. 186
Flip Vertically ..................................................... 54
Add class .......................................................... 186
FTP Transfer…………………………………………………36
Add points .................................................... 186
G
Count ............................................................ 186
Gamma ................................................................. 207
Filter colonies............................................... 186
Glossary ................................................................ 252
Manual Count Colony Wizard ..................... 186
H
No. of classes ............................................... 186
Histogram Controls………………………………………210
Remove class................................................ 186
I
Remove point............................................... 186
iBox Explorer………………………………………………..78
Shape ............................................................ 186
Image Acquisition………………………………………….75
Size ............................................................... 186
Image Compositing……………………………………...232
Manual Counting Step 1 Select the Classes . 188
Image Display Controls…………………………………207
Manual Counting Step 2 Finish ........................ 191
Image Enhancement Filters……………………………45
Blur………………………………………………………………45 Manual Split Colonies.......................................... 183

Emboss....................................................................45 Measurement Tools ............................................ 228

Remove Noise .................................................... 45 Menus .................................................................... 30

Sharpen…………………………………………………….45 Merging Colonies................................................. 185

Image History....................................................... 251 Microscope ............................................................. 78

Image Information ................................................. 28 Minimum System Requirements ............................ 3

Image Properties ................................................. 246 Molecular Weight Calibration ............................. 117

Image Report ....................................................... 246 Molecular Weights .............................................. 113

Image Sequences ................................................. 233 Move Bands ......................................................... 108

Image Windows ..................................................... 26 Move Lanes .......................................................... 108

Integration ............................................................. 91 Multi-Image Actions............................................ 231

Image integration .............................................. 91 Multiple-Image Player ........................................ 233

Manual integration…………………………………….91 N
Sequential integration………………………………91 Navigating the Software ....................................... 24

Invert .................................................................... 207 Main Window..................................................... 24

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New User button ........................................ 17, 61 Obtaining Image Information ............................... 28

North ...................................................................... 48 OK........................................................17, 48, 61
Northeast, East ...................................................... 48 Open Demo Image................................... 33, 241
Northwest .............................................................. 48 Open Image ............................................. 33, 241
NOTE.........................................................17, 61 Operating System Requirements............................ 3
O
Other Settings ............................................17, 61 Results for 1D Analysis ........................................ 144
P Retardation factor Rf Lines ................................. 132
Paste…………………………………………………………….40 Rotate ..................................................................... 51
Blend .......................................................................40 Rulers ..........................................................................67
Merging Images ................................................. 40 S
Paste Special……………………………………………...40 Save Area Density Results ................................... 165
Pasting an Image……………………………………….40
Performing Dendrogram Analysis………………….135
Select ......................................................... 17, 61
Dendrogram Calculations………………………….135
Set-Up Templates ................................................ 238
Performing Molecular Weight Calibrations…….113
Sharpen .................................................................. 47
Retardation factor lines…………………………….113
Show Results ........................................................ 202
Preferences Settings for Colony Counting………169
Single-User License ................................................. 7
Circle radius…………………………………………….169
Southeast, South ................................................... 48
Colony Marking……………………………………….169
Spiral Counting .................................................... 193
Label Color………………………………………………169
Split Colonies ........................................................ 183
Label Type………………………………………………169
Statistics ............................................................... 203
Logging………………………………………………….169
Supporting 21 CFR Part-11 Compliance ............ 248
Preview…………………………………………………………48
Audit trail ......................................................... 248
Print ..........................................................35, 244
Image history ................................................... 248
Print Area Density Results................................... 165
Print Audit trail ................................................ 248
Print Data Explorer Reports ................................ 145
Synchronize Templages ....................................... 240
Print Image History.............................................. 246
T
Printing .....................................................35, 244
Technical Support .................................................. 21
Printing Data Explorer Tabular Reports ............. 145
UVP offices ......................................................... 21
Printing Image History ........................................ 246
Text Annotation ................................................... 219
Pseudocolor .......................................................... 212
U
R
Undo and Redo ...................................................... 42
Reduce Image to Mono ......................................... 57
User Administration............................................... 14
Monochrome ..........................................................57
Passwords........................................................... 14
Registering the Software......................................... 4
User Accounts..................................................... 14
Remove Noise ........................................................ 49
User names......................................................... 14
Reporting and Printing Area Density Results.165
User Rights ......................................................... 14
Reporting Functions ............................................ 198
User Defined Template Counting ........................ 180
Reset ..........................................................17, 61
Using the Region of Interest Tools ....................... 43
Resize Bands ........................................................ 108
Copy ROI ............................................................. 43
Resize Image .......................................................... 56
Crop ROI ............................................................. 43
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Elliptical ROI ....................................................... 43 Viewing and Printing 1D Gel Analysis ................ 143
FreeForm ROI..................................................... 43 Viewing Data Explorer Results ............................ 144
MagicWand ROI ................................................. 43 W
Polygonal ROI .................................................... 43 Welcome ....................................................................... 1
Rectangular ROI ................................................. 43 Z
ROI .......................................................................... 43 Zone Analysis ....................................................... 197
V

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