UVP Doc-It Life Science User Manual

Doc-It® Life Science Software

Installation and User Instructions

Doc-It®LS Image Acquisition Software
Doc-It®LS Image Analysis Software

UVP, LLC Ultra-Violet Products Ltd

2066 W 11th Street, Upland, CA 91786 Unit 1, Trinity Hall Farm Estate
Tel: [phone] Nuffield Road, Cambridge CB4 1TG UK
Fax: [phone] Tel: [phone] / Fax: [phone]
Email: [e-mail] Email: [e-mail]

Web site: uvp.com

81-0328-01 Rev B

Table of Contents

Introduction.................................................................................................................................................... 1

Welcome .................................................................................................................................................... 1

Minimum System Requirements ................................................................................................................ 2

Registering and Activating the Software .................................................................................................... 2

Single-User License ................................................................................................................................... 4

User Administration .................................................................................................................................... 4

Technical Support ...................................................................................................................................... 7

License Agreement .................................................................................................................................... 8

Navigating the Software .............................................................................................................................. 10

Main Window ........................................................................................................................................... 10

Menus ...................................................................................................................................................... 10

Toolbars ................................................................................................................................................... 11

Image Windows ....................................................................................................................................... 13

Using Plug-In Modules ................................................................................................................................ 15

Overview .................................................................................................................................................. 15

Positioning Plug-in Modules .................................................................................................................... 16

Histogram Controls .................................................................................................................................. 17

Digital Video Player .................................................................................................................................. 17

Image Controls Plug-In ............................................................................................................................ 21

3D Plots ................................................................................................................................................... 23

FTP Transfer ............................................................................................................................................ 24

Log Viewer ............................................................................................................................................... 24

Zoom/Pan ................................................................................................................................................ 24

Camera Plug-In ........................................................................................................................................... 27

Capturing Images ........................................................................................................................................ 30

Creating Templates ..................................................................................................................................... 31

Set-Up Templates .................................................................................................................................... 31

Edit and Delete Templates ...................................................................................................................... 31

Set-Up Canon Capture Templates .......................................................................................................... 31

Creating Colony Templates ..................................................................................................................... 32

Deleting Colony Counting Templates ...................................................................................................... 33

Editing Images ............................................................................................................................................ 34

Overview .................................................................................................................................................. 34

Copy ......................................................................................................................................................... 34

Paste ........................................................................................................................................................ 35

Undo and Redo ........................................................................................................................................ 35

Using the Region of Interest Tools .......................................................................................................... 36

Using Image Filters ..................................................................................................................................... 37

i

Overview .................................................................................................................................................. 37

Filter Navigation ....................................................................................................................................... 37

Filter Menu ............................................................................................................................................... 37

Filter Plugins ............................................................................................................................................ 37

Background Filter ..................................................................................................................................... 38

Burn Changes to a New Image ................................................................................................................ 39

Convert Image ......................................................................................................................................... 39

Duplicating Images .................................................................................................................................. 39

Flip Image ................................................................................................................................................ 39

Image Enhancement Filters ..................................................................................................................... 40

Image History ........................................................................................................................................... 41

Measurement Tools ................................................................................................................................. 42

Merging Two Images ............................................................................................................................... 43

Obtaining Image Information ................................................................................................................... 44

Pseudocolor ............................................................................................................................................. 45

Reduce Image to Mono............................................................................................................................ 46

Resize Image ........................................................................................................................................... 46

Rotate and Align Image ........................................................................................................................... 47

Rulers ....................................................................................................................................................... 48

Scanning Images ..................................................................................................................................... 48

Spatial Calibration .................................................................................................................................... 49

Annotations ................................................................................................................................................. 51

Overview .................................................................................................................................................. 51

Types Of Annotation ................................................................................................................................ 51

Viewing And Hiding Annotations .............................................................................................................. 52

Synchronize Size with Image Zoom ........................................................................................................ 52

New Annotation Window .......................................................................................................................... 52

To Edit the Text of a Text Annotation ...................................................................................................... 52

Selecting Annotations .............................................................................................................................. 53

Moving And Resizing Annotations ........................................................................................................... 53

Formatting Annotations ............................................................................................................................ 55

Deleting Annotations ................................................................................................................................ 55

Creating Annotations ............................................................................................................................... 56

Loading and Saving Images ....................................................................................................................... 57

Loading Images ....................................................................................................................................... 57

Saving Images ......................................................................................................................................... 57

Burn in Changes to a New Image ............................................................................................................ 58

Image File Types ..................................................................................................................................... 58

Performing 1D Analysis ............................................................................................................................... 60

ii

Navigating 1D Analysis ............................................................................................................................ 60

1D Analysis Plugin Module ...................................................................................................................... 60

1D Analysis Context Menu Commands ................................................................................................... 62

Finding Lanes and Bands ........................................................................................................................ 62

1D Analysis Image Window Features ...................................................................................................... 64

1D Analysis Settings ................................................................................................................................ 65

Manually Modifying Lanes and Bands ..................................................................................................... 65

Lane and Band Information ..................................................................................................................... 68

Lane Profile Graph ................................................................................................................................... 69

Viewing and Printing 1D Gel Analysis ..................................................................................................... 71

Viewing Data Explorer Results ................................................................................................................ 72

Printing Data Explorer Tabular Reports ................................................................................................... 75

Performing Concentration Calibrations .................................................................................................... 77

Performing Molecular Weight Calibration ................................................................................................ 82

Retardation factor (Rf) Lines .................................................................................................................... 86

Performing Dendrogram Analysis ............................................................................................................ 87

Performing Colony Counting ....................................................................................................................... 91

Colony Count Module .............................................................................................................................. 91

Preference Settings for Colony Counting ................................................................................................ 92

Automatic Counting .................................................................................................................................. 93

Manual Counting ...................................................................................................................................... 93

Manual Counting Step 1: Select Classes ................................................................................................ 94

Manual Counting Step 2: Finish ............................................................................................................... 94

Edit Colonies ............................................................................................................................................ 95

Add Colonies ............................................................................................................................................ 95

Delete Colonies ........................................................................................................................................ 96

Split Colonies ........................................................................................................................................... 96

Merging Colonies ..................................................................................................................................... 97

User Defined Template Counting ............................................................................................................ 97

Spiral Counting ........................................................................................................................................ 97

Zone Analysis .......................................................................................................................................... 98

Renumbering Colony/Zone Values .......................................................................................................... 99

Reporting Functions ................................................................................................................................. 99

Classes .................................................................................................................................................... 99

Statistics ................................................................................................................................................. 100

Distribution ............................................................................................................................................. 100

Export and Print Colony Results ............................................................................................................ 100

Printing Reports and Images .................................................................................................................... 101

File Print Command ............................................................................................................................... 101

iii

Printing Image History............................................................................................................................ 101

Print ........................................................................................................................................................ 102

Supporting 21 CFR Part 11 Compliance ................................................................................................... 103

Purpose .................................................................................................................................................. 103

Features ................................................................................................................................................. 103

Usage ..................................................................................................................................................... 103

Glossary .................................................................................................................................................... 105

iv

Introduction

Introduction

Welcome

Life Science (LS) software from UVP lets users acquire, enhance, and analyze images in a simple and
efficient way.

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

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

Getting Started

Minimum System Requirements
Registering and Activating the Software

Capturing Images

Cameras

Performing Analysis Functions on Images

1D Analysis
Molecular Weight Calibrations
Concentration Calibrations
Dendrogram Analysis
Counting Colonies

1

Minimum System Requirements

Windows XP Professional with Service Pack-2 or higher (32 bit only), Vista (32 bit only), or

Windows 7 (32 bit only)

Internet Explorer 6.0 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
1 GB of RAM or greater (2 GB recommended)
200 MB of available hard disk space for the program, more for data
To avail the functionality of 21 CFR Part 11, the partition must be formatted with NTFS.
CD-ROM drive
Color monitor, supporting at least 1024 x 768 resolution and 16-bit or better colors; 24-bit or 32-

bit color is strongly recommended

Registering and Activating the Software

Overview

Introduction

Single-User License
User Administration

Overview

Use of LS software requires activation of a security code from UVP. Registration and activation of the
software can be accomplished by phone, email or by the Internet. Two types of licenses are available,
single-user or network-user with a five-user license. Additional licenses are available.

Registering the Software

Activate the software by entering an activation code provided by UVP in order to gain full access rights to
the software.

Once the LS software is installed, it will operate in full-future trial mode for 14 days. Within the 14-day trial
mode, the LS software must be registered with UVP. Otherwise the software will only operate in
demonstration mode after the 14-day trail period. The demonstration mode limits the software to only
open and use the demonstration images provided by UVP.

The License Wizard window will appear. There are three ways to retrieve an activation code: phone,
email or Internet and selecting one of the options from the License Wizard window.

On the Fly Activation: Choose this option to activate the software immediately through the

Internet.
Already Have an Activation ID: This option is useful when reloading (or upgrading) the software

after receiving an initial activation code.
Offline Activation: This option is used if the computer is not connected to the Internet. This

allows the user to obtain the activation code and enter it at another time

2

On the Fly Activation

To immediately activate the software through the Internet:

Choose On the fly activation. If the computer is not connected to the Internet, follow the

instructions for Offline activation or call UVP to register the software.

Introduction

Click Next to continue.
Complete all required information on the form.

Fill out the Serial Number located on the CD. The number should be four sets of six numbers.
Click the Get Activation No. button and then click onto Activate when the Activation Number

appears in the box.

Already Have an Activation ID

Select Already have an activation ID from the buttons. This activation function is useful when

reloading the software after receiving an initial activation code.
Click Next to continue.
Click the link provided and complete the form to obtain instructions. Click Finish.

3

Introduction

Offline Activation

Select Offline Activation if the computer is not connected to the Internet. This allows the user to

obtain the activation code and enter it at another time.
Click Next to continue.
Click the link provided and complete the form to obtain instructions. Click Finish.

Single-User License

Single-user license allows the software to be used on a single computer.
A Welcome to the Licensing Wizard window will appear. Select the Single client access license option,

and select Next.

User Administration

Secure User Accounts
Usernames and Passwords
User Rights

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.

4

This system of usernames and passwords is separate from the one that is used to login to the

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 Tasks >
Set Idle Time. Zero means no idle time.

Password Expiration
Date

Date the password expires.

View

Enables user to view images. To change this setting, click Tasks > Edit
Rights. Click or unclick the View option.

Change

Enables user to change images. To change this setting, click Tasks >
Edit Rights. Click or unclick the Change option.

Has Admin. Rights

Gives user administration permissions. To change this setting, click
Tasks > Edit Rights. Click or unclick the Has Administration Rights
option.

computer.
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.
Navigate to C:\Documents and Settings\All Users
Locate the Application Data folder.
f the Application Data folder is not present in the All Users window, go to the Tools menu and

select Folder Options.
A Folder Options window appears. On the View tab, select Show hidden files and folders.

Select Apply then OK.
Go to the UVPSettings folder inside the Application Data folder.
Have the System Administrator set Read and Write permissions for either the UVPSettings

folder, or for each file within the folder (depending on the Network Security Policy where the LS

software will reside).

Introduction

User Administration History Definitions

The description of the settings for each column of the History section is shown below. To see all of the
columns in History, move the scroll bar to right.

Usernames and Passwords

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

5

Enter a password. On initial installation, a screen will pop up to request a password and

password confirmation. A password is required.
Click Login.

Adding a New User

From the menus, click Tools > User Administration to open the User Administration window.
Click the New User button, type in the user name and password.
Type in the new user name and password. Each time the new user logs in, use that new user

name and password.

Editing a User

Edit the User by highlighting the user name in the User Administration window.
Click the Tasks > Edit Rights 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.

Introduction

Changing a Password or Other Settings

To change a password, from the menu go to Tools > User Administration to open the User

Administration window.

Click on the appropriate user to change.
Select the Tasks > 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.

Deactivating/Reactivating a User

From the menu, select Tools > User Administration to open the User Administration window.
Select that user name and click Tasks > Deactivate. A red X will indicate the user is deactivated.

To reactivate, click Tasks > Activate.
Click OK to close the window.

NOTE: Never disable the Administration Account.

Viewing 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.

6

Introduction

Login Privileges
Rights

Install

Un-Install

Open and
Run

User
Administration

Use the
Camera

Restricted

X* X

Standard/Power

X* X

Admin

X X X X X

X = Supported rights.

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

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:

Technical Support

UVP 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 [phone] or [phone], and ask for Technical Support during regular business

days, between 7:00 am and 5:00 pm, PST.
E-mail your message to: [e-mail] or [e-mail]
Fax Technical Support at [phone]
Write to: UVP, LLC 2066 W. 11th Street, Upland, CA 91786 USA

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

Call [phone], and ask for Customer Service during regular business days between

8:30 am and 5:30 pm.
E-mail your message to: [e-mail]
Fax Customer Service at [phone]
Write to: Ultra-Violet Products Ltd. Unit 1, Trinity Hall Farm Estate, Nuffield Road, Cambridge

CB4 1TG UK

7

Introduction

License Agreement

End User License Agreement

PLEASE READ THE FOLLOWING AGREEMENT CAREFULLY

This Agreement is between UVP, LLC of 2066 West 11th Street, Upland, California 91786 (hereinafter
"Licensor") and the end user of UVP 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"):

Doc-It LS 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 human­perceivable 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
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.

8

Introduction

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.

9

Navigating the Software

Navigating the Software

Main Window - Shows the full software screen
Menus - Discusses the menus available
Toolbars - Discusses the tollbars and the ability to rearrange the tool buttons
Plug-In Modules - Several plug-in modules are provided as user-friendly interfaces for specific

software tasks; this section discusses the various modules and the ability to position the modules

Image Windows - Discusses the use of image windows in the workspace

Main Window

After the LS software is opened for the first time, the screen will look similar to the one shown below. The
LS Main Window contains the application's menu bar, toolbars, image windows, plug-in modules and
status bar. Some parts of the window, such as the toolbars, plug-in modules and status bar, can be
hidden or shown if preferred.

Menus

LS Software offers the following menus:

File Menu: Contains commands to load and to save files, to select profiles, adjust preferences

and to print reports.
Edit Menu: Contains the Undo/Redo commands and the clipboard commands: Cut, Copy,

Paste, Paste Special and Paste Special Options, plus the Crop function.
View Menu: Contains commands that show and hide various main-window features and

commands that affect how the current sub window is displayed.

10

Navigating the Software

NOTE: Although most commands appear on the menus, some features are only available through the
Plug-in Modules. If the Plug-in Modules are hidden, they can be shown by selecting the modules from
View > Plug-ins whenever needed.

Analysis Menu: Contains modules to perform Colony Counting, 1D Analysis and Area Density.
Tools Menu: Contains a list of the tools to enhance the image or software environment including

seeing Loaded Plug-ins, User Configuration, pre-configured image Reports, plus Region of

Interest, Spatial Calibration and Annotation tools.
Macros Menu: Contains commands to work with Macros. A Macro is a collection of commands

that can be saved and replayed with special user-defined keys.
Window Menu: Contains commands to organize Image windows. Shows the arrangement of the

image window and shows the name of the images currently open.
Help Menu: Contains access to the software help, user license wizard and software version.

Toolbars

The toolbars in LS allow the user to select most commands with a single button click. The toolbars are
customizable, so the user can include the commands used most and remove commands rarely used.

Toolbar Buttons

Reduce to Mono: Converts the image to a single-channel (monochrome) image from a multi-

channel (color) image
Align: Aligns the image to a grid
Rotate: Brings up the dialog box to rotate image by a specific degree or by manual rotation
Flip Horizontal: Flips image horizontally
Flip Vertical: Flips image vertically
Despeckle: Applies the despeckle filter to the image
Remove Noise: Applies the remove noise filter to the image
Sharpen: Applies the sharpen filter to the image
Blur: Applies the blur filter to the image
Emboss: Embosses the image with selection of the direction of the emboss filter
Starfield Subtraction: Applies the starfield subtraction filter to the image

Copy: Copies selected text, selected portions of the current image or the entire image to the

clipboard
Paste: Pastes the current clipboard item onto the screen
Paste Special: Pastes an overlay of the current item in the clipboard

11

Navigating the Software

Cut: Cuts a specific area
Undo: Reverses the last command
Redo: Repeats the last command

Arrow: Selects an annotation to edit
Text Tool: Text annotation
Line, Rectangle, Ellipse and Highlighter Tools: Annotation tools
Define Image Scale: Allows users to set the scale for images
Measure Length: Measures the distance between any two points on the image, units depend on

spatial calibration
Measure Angle: Measures an angle
Measure Area: Measures an area on the image

New ROI: Removes the active Area of Interest and prepares for a new one of the current type
Rectangular ROI: Changes the current mouse tool to the select Rectangular Area of Interest and

brings up one if already present on the current image
Elliptical ROI: Changes the current mouse tool to the select Elliptical Area of Interest and brings

up one if already present on the current image
Polygonal ROI: Changes the current mouse tool to the select Polygonal Area of Interest and

brings up one if already present on the current image
Freeform ROI: Changes the current mouse tool to the select a user defined Area of Interest
Magic Wand ROI: Selects a consistently colored area (for example, a red flower) without having

to trace its outline

Open: Opens an image file on disk
Save: Saves the current image to disk
Save As: Saves the current image to a different name
Close: Closes the file
Print: Prints the current image
Preferences: Opens the preferences window to set defaults in the following tabs: Main Settings,

Log Settings, 1D Analysis, Colony Count settings
External Application: Launches a Qwik-Link external application selected in Preferences
Exit: Closes the software program

12

Navigating the Software

Rearranging Toolbars

The order of the individual toolbar sections can be rearranged by placing the mouse arrow over the dotted
line at the edge of each toolbar section and moving the toolbar. The default position of the toolbars is
located horizontally below the menus. The toolbars may be moved to the bottom of the screen or
vertically on the left or right side. Each section can be deleted or added back by clicking View > Toolbars
and select the toolbars to display on the screen.

Image Windows

Each open image in LS 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 (tabbed
interface turned ON in Preferences) for selection of images.

Organizing 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 File > Preferences > Main

Settings and uncheck the Tabbed Interface checkbox.
To bring an Image window to the forefront, either click on the window's title bar or find and select

the image's filename from the list in the Windows menu.
To close an image window, click onto the X next to the image tabs.
To resize a Cascaded Image window, drag the lower right corner (or an edge) to the desired size.

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.

13

Navigating the Software

Showing the Image in Actual Size

To show the image in actual size (no scaling), choose View > Zoom. Set the zoom factor to 100%. Or
click the right mouse button on the image and select View Original Size. Images taken at high resolution
will look large on the screen.

Fitting the Image to the Window

To show the entire image in the window (scaled up or down as required to make it fit), click the right
mouse button and click 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 MENUS OR TOOLBARS. 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:

Copy
Paste
Paste Special
Print Selection
View Best Fit
View Original Size
Image Information

TIP: Both the View Best Fit and View Original Size commands are also available from a shortcut menu on
the Image window itself. The shortcut menu can be displayed by right clicking on the image.

Status Bar

The Status Bar shows the User Name (Profile), current mouse position in an image, the intensity of the
image at that position and status messages during operations. Current date and time is display in the
right corner.

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), date, and time is also reported.

14

Using Plug-In Modules

Using Plug-In Modules

Overview

The plug-in modules in LS allow the user to position modules on the work area for easy access to the
plug-in functions. Position of the modules is customizable, so plug-ins can be organized to include the
plug-ins used most and remove plug-ins rarely used.

To open the plug-in modules, select View > Plugins and select the plug-in to appear in the LS software
workspace.

The plugins automatically loaded on the left side of the screen are Colony Count, Area Density, 1D
Analysis. The plug-ins loaded on the right side of the screen are Histogram, Pseudocolors, Image
controls, Zoom/Pan, Filters, and Player.

Link below for information on using specific plug-in modules:

Cameras
Log Viewer
Digital Video Player
3D Plot
Zoom/Pan
Image Controls
Filters
Pseudocolors
Histogram Controls
File transfer protocol
1D Analysis
Counting Colonies

Using the Plug-in Modules

The LS software plug-in modules are essentially tool boxes for many of the commonly used features.
Plug-in modules open function-specific windows that can be viewed and placed in virtually any position on
the screen. To open the plug-in modules, select View > Plugins and select the plug-in to appear in the
LS software workspace.

The plugins automatically loaded on the left side of the screen are Colony Count and 1D Analysis. The
plugins loaded on the right side of the screen are Histogram, Pseudocolors, Image controls, Zoom/Pan,
Filters, and Player.

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Using Plug-In Modules

Positioning Plug-in Modules

Rearranging Plug-in Modules

Plug-in Modules can positioned anywhere on the screen. Plug-ins can be docked, hidden, and floating.

Dockable: Locks the module in a specific position.
Hide: Closes the module. To reopen, go to View > Plugins and select the plug-in module.
Floating: Allows module to be moved around on the screen. To move a module, click the top bar

of the module and, while holding down the left mouse button, drag the module to the desired

location. Arrows will display. Move the module to one of the arrows to dock the module.
Auto Hide: Automatically hides the module when not in use. These tabs will be displayed in the

same order as they were selected to Auto Hide. To show the full module, roll the mouse over the

tab. To disable the auto hide function, unclick Auto Hide from the module drop down menu or

click the pushpin icon.

Moving a Floating Plug-in Module

When a plug-in module is floating, it can be docked to the top, bottom, left or right on the workspace. A
floating plug-in module can be placed into another plug-in module s window.

To move a floating plug-in module, click on the title bar of the module and drag it to any of the plug-in
module position icons of choice. The following are descriptions of the plug-in module position icons.

Position the plug-in module at the top of the workspace

Position the plug-in module at the bottom of the workspace

Position the plug-in module at the left of the workspace

Position the plug-in module at the right of the workspace

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Using Plug-In Modules

The center arrows console allows positioning of the plug-in module at the top, bottom, left or right of an
empty workspace by using the exterior arrows

The center arrows console middle button allows positioning the plug-in module at the inside of another
plug-in module

Histogram Controls

The Histogram Controls plug-in offers options for viewing tonal and color information about an image. By
default, the histogram displays the tonal range of the entire image.

Go to View > Plugins to load the Histogram Controls plug-in.

Apply a Histogram

If the Histogram plug-in is not showing, choose Plugins > Histogram plug-in.
From the stretch mode drop-down list, select None, Automatic or Manual.
The Options button offers the choice to select the Y-axis, reset zoom or copy graph.

Digital Video Player

Purpose of the Digital Video Player
Using the Player
Player Features
Player Options
Extract or Delete Individual Image Files (Frames)
Create a Sequence (.sqv) File by Merging Images
Saving .AVI Files

Purpose of the Digital Video Player

Digital Video Player (DVP) in LS software clubs multiple images in a single file and shifts through the
images, allowing users to select one (or more) of the clubbed images to analyze later.

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Using Plug-In Modules

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

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, which stops any kind
of playing.

Plays the sequence of images in the reverse order.

This button changes to a Pause/Stop button, which stops any kind
of playing.

Plays the sequence with a number of images to skip. The number
of images to skip can be set in the Options dialog.

If a sample is to be observed over a period of time it is required to snap multiple pictures at regular and
definite time intervals, maybe with progressively higher integration times.

Using the Player

To access the DVP function:

Go to View > Plugins and click on the Digital Video Player plug-in.
The DVP comes up automatically, as soon as the image-capture process for Sequential and

Dynamic Integration is complete.

Player Features

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

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Using Plug-In Modules

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

dialog.

The Options button displays the Options dialog window to set Player
properties.

This option lets the user work with individual frames (images) from a
single .sqv file. Extract a single frame if required. A detailed
description follows in this chapter.

Displays thumbnails of images in a tiled fashion. This can be useful
in extracting specific images. When the player is active, this option
also shows active scrolling and the currently active frame is
highlighted red.

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 minute

This is the number of images that will play during a period of one
minute.

Fast Frame Skip

This is the number of images to be skipped when playing with
{bmc Doci0075.BMP} or {bmc Doci0076.BMP} 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 reverse

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

Player Options

Click the Options button in the player to set individual options for going through frames in a .sqv or .avi
file. Once Options is selected the following window appears:

Extract or Delete individual Image files (frames)

Extracting an image from a .sqv or .avi file creates new images in the workspace and DOES NOT remove
them from the sequence. Deletion deletes the images them from the sequence.

The easiest way to initiate this action is by clicking on Tile View checkbox in the player, which brings up
the following window. Just right click on any image to extract or delete.

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Using Plug-In Modules

The other two ways this action can be initiated is:

If the player is open, click on Extract from the player.
If the player is not open, but the .sqv file is open, click on Images > Extract Frames.

The following window is brought up, that lists all the frames inside the .sqv in question:

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.

Create A Sequence (.sqv) file by Merging images

It is possible to merge existing files (or open images) and create a single .sqv file. This is a good way to
keep all images in one single file. To create a sequence, select Image > Merge files. This feature can be
used to merge images open in the LS workspace.

Controls:

Add: Click on Add button to find files from the hard-disk to merge. Existing files in the workspace

are automatically listed.
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.

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Using Plug-In Modules

Note:

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

Cancel: Closes the window and cancels the process.

Saving .AVI Files

If files need to be shared with another researcher or opened in another place on another computer export
the .sqv files to a standard universal format. (SQV is a custom format used by UVP LLC).

Audio Video Interleaved (AVI) is one such broadly acceptable format. (It is a simplistic Windows format
that caters to the needs of slow animation, audio and video.)

To import an .AVI file, no special steps are required to be taken since it is one of the standard formats
supported by LS Software.

To export a .SQV file to .AVI, use the Save As functionality provided by UVP Software.
Depending on the requirement of the target player, AVI files may need to be compressed/ encoded using

a specific codec. Before exporting, LS software allows users to choose from one of the pre-installed
codecs.

Image Controls Plug-In

The Image Control plug-in offers features to control how an image looks. Changes made to images using
this plug-in will not be permanent changes to the image. All the changes can be reversed with the Reset
button.

Go to View > Plugins to load the Image Controls plug-in.
Specific features 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 the 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: also 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 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

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Using Plug-In Modules

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.

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.

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Using Plug-In Modules

Invert Image

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

Inverted Image

Return to Default Values

After changing any of the Image Control options, click Reset to return all settings to the default settings.

3D Plots

The 3D Plots plug-in 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

LS software 3D plots can be used for static images as well as live preview and integration.

Load an image into LS workspace. (It could be an image captured from the camera or an image

loaded from the disk.)
Click on View > Plugins > 3D Plot Plug-in. This will bring up a separate window that shows the

3D plot.

Controls on the 3D plot window

Viewpoint tab

Controls on this tab let 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.

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Using Plug-In Modules

Y axis: The horizontal axis.
X axis: The axis coming out of the plot, towards you.

The plot can also be rotated by dragging it with the mouse in desired direction.

Zoom Controls:

Zooming in and out of the plot is possible in two ways:

Using the buttons labeled Zoom In and Zoom Out
Using the spin-box and adjusting the percentage.

Output tab

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

New Image: Pressing this button creates a new image in the LS workspace 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.)
Printer: Pressing this button prints the 3D plot on a desired printer. Pressing it brings up the list of

available printers.

FTP Transfer

The FTP Transfer plug-in allows the user to transfer files from one computer to another.

Click on View > Plugins > Ftp Transfer. This will bring up a separate window that shows the Ftp

Transfer plug-in.
Enter the IP address of the system acquiring the image and the TS login and password in the

FTP plug-in preferences window.
Start the software and take pictures.
Press Connect button on the FTP plug-in after starting the software.

Log Viewer

The Log Viewer displays a log of user actions and presents the action list to the user in a log box.

Go to View > Plugins to load the Log Viewer plug-in.

Zoom/Pan

The Zoom/Pan plug-in allows the user to magnify a part of the image. Once the user zooms in on the
image, the entire image will no longer be visible in the window. The user may easily change the portion of
the image that is visible by panning.

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Using Plug-In Modules

Go to View > Plugins to load the Zoom/Pan plug-in.

Using Zoom In or Out

Click on Zoom In or Zoom Out (located below the thumbnail version of the image on the Effects

tab, on either side of the slider).

OR

Slide the zoom slider to the left to zoom out or to the right to zoom in.

OR

Select the desired zoom factor from the drop-down list to the right of the slider and buttons.

TIPS: There is no need to "turn off" the Magnify tool -- it will be turned off automatically by selecting any
other tool (such as a selection tool or an annotation tool).

The image can also be magnified selecting View > Zoom and clicking on the desired zoom percentage.
In the drop-down box, enter a number and press TAB. (The drop down box is particularly useful if a zoom

factor is needed between the pre-defined choices in the list.)

Pan to a Different Part of the Image

In the thumbnail image, drag the Pan rectangle to the desired location.
If the desired location is outside the Pan rectangle, simply click the desired location to "jump" the

pan rectangle there.

Magnify Part of an Image

Click the Magnifying Glass button.
The mouse becomes a magnifying glass. Click anywhere on the image to magnify an area. Adjust

the Magnify factor number to increase or decrease the magnification.
To show annotations under the magnifying glass, click the Magnifying Annotations option.

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