Cleaver Scientific Chemiluminescence documentation system chemiLITE User guide

ChemiLite

Instruction Manual

Version 1
Issued: 08/2018

ChemiLite Safety-1

SAFETY INSTRUCTIONS

Safety Practices

This document describes the general safety practices and precautions that must be observed when
operating a ChemiLite system.

This advice is intended to supplement, not supersede, the normal safety codes in the user’s country.

The information provided does not cover every safety procedure that should be followed.
Ultimately, maintenance of a safe laboratory environment is the responsibility of the user and the
user’s organisation.

Please consult all documentation supplied with the ChemiLite System before starting to work with
the instrument. Carefully read the safety information in this document and in the other
documentation supplied. When setting up the instrument or performing analysis or maintenance
procedures, strictly follow the instructions provided.

Warning Notices

Within this User Guide WARNINGS are used to highlight information or instructions that must be
followed in order to avoid personal injury to yourself or other people in the vicinity, e.g. switch off
the mains voltage and remove the mains cord before cleaning.
WARNINGS appear as below:

WARNING

Switch off the mains voltage and remove the mains cord before cleaning.

WARNING

Ensure that all instrument users read and understand the precautions listed below.

WARNING

You are advised to post a copy of the precautions near to or on the instrument
itself.

Precautions

The following precautions must be observed when using a ChemiLite:

• Be sure that the voltage of the ChemiLite corresponds to the voltage available where it is

to be installed.

• Never remove the side or back panels of the ChemiLite System without first shutting down

the instrument and disconnecting the mains cord.

ChemiLite Safety-2

General Operating Conditions

ChemiLite Systems have been designed and tested in accordance with the safety requirements of
the International Electrotechnical Commission (IEC). ChemiLite Systems conform to IEC61010-1:2010
(Safety Requirements for electrical equipment for measurement, control and laboratory use) as it
applies to IEC Class 1 (earthed) appliances, and therefore meet the requirements of EC directive
2006/95/EC.
If possible, avoid any adjustment, maintenance or repair to the instrument while it is open and
operative. However, if any adjustment, maintenance or repair is necessary while the instrument is
open, this must be done by a skilled person who is aware of the hazards involved.
Whenever circumstances arise that mean a ChemiLite System may be unsafe, make it inoperative. In
particular, a ChemiLite System may be unsafe if it:

• Shows visible damage.

• Fails to perform the intended measurement.

• Has been subjected to severe transport stresses.

• Has been subjected to prolonged storage in unfavorable conditions.

Environmental Conditions

ChemiLite Systems should only be used under the following conditions:

• Indoors.

• At altitudes below 2000m.

• In ambient temperatures between 5°C and 40°C.

• With relative humidity below 80% for temperatures up to 31°C, decreasing linearly to 50%

relative humidity at 40°C.

• Electrical supply fluctuations not exceeding +10% of the nominal voltage.

WARNING

The protection provided by the equipment may be impaired if the environmental
conditions do not lie within these parameters.

ChemiLite Safety-3

Electrical Safety

ChemiLite Systems are designed to protect the user from potential electrical hazards. This section
describes some recommended electrical safety practices.

WARNING

Lethal voltages are present at certain points within the instrument.
When the instrument is connected to mains power, removing the instrument

covers is likely to expose live parts.
Even when the power switch is off, high voltages can still be present – capacitors

within the instrument may still be charged even if the instrument has been
disconnected from all live voltage sources.

The ChemiLite System must be correctly connected to a suitable electrical supply. The supply must
have a correctly installed protective conductor (earth or ground) and must be installed and checked
by a qualified electrician before connecting the instrument.

WARNING

Any interruption of the protective conductor inside or outside the ChemiLite, or
disconnection of the protective conductor terminal is likely to make the
instrument dangerous.

Intentional interruption of the protective conductor is prohibited.

WARNING

Ensure that the mains supply socket on the instrument is not obstructed, i.e. leave
a gap to allow easy disconnection of the mains cord.

WARNING

If the mains power cord has to be replaced, ensure that the replacement cord is
appropriately rated and approved for the intended use.

When working with the ChemiLite System:

• Connect the instrument to a correctly installed mains power outlet that has a protective

conductor connection.

• Do not operate the instrument with any covers or internal parts removed.

• Do not attempt to make internal adjustments or replacements except as directed in the

ChemiLite System documentation.

• Disconnect the instrument from all live voltage sources before opening it to make any

adjustments, replacements, maintenance or repair. If the opened instrument must be
operated for further adjustment, maintenance or repair, this must only be done by a
supplier’s Service Engineer.

• If it is possible that the instrument is no longer electrically safe for use, make the

instrument inoperative and secure it against any unauthorised or unintentional operation.
The electrical safety of the instrument is likely to be impaired if:

• It has any signs of visible damage.

• If it has been subjected to prolonged storage in unfavourable conditions.

ChemiLite Safety-4

• If it has been subjected to severe stress during transportation.

Electrical Protection

• Insulation: Class I rating for external circuits. Only connect equipment that meets the

requirements of IEC 61010-1:2010, IEC 60950-1:2005 (including AMD1:2009 AND
AMD2:2013 CSV) or equivalent standards.

• Installation Category: The instruments are able to withstand transient overvoltages

typically present on the mains supply. The normal level of transient overvoltages is impulse
withstand (overvoltage) category II of IEC 60664-1:2007.

• Pollution Degree 2: Normally only non-conductive pollution occurs. Occasionally, however,

temporary conductivity caused by condensation must be expected.

EMC Compliance

EC Directive

The ChemiLite System is designed and tested to meet the requirements of the EC directive
2004/108/EC and 93/68/EC. The instrument complies with the EMC standard EN61326-1:2013 (EMC
standard for electrical equipment for measurement, control and laboratory use) and EN55011:2009
AND A1:2010 (ISM) class A (rf emissions).

FCC Rules and Regulations

The ChemiLite System is classified as a digital device used exclusively as industrial, commercial or
medical test equipment. It is exempt from the technical standards specified in Part 15 of the FCC
Rules and Regulations based on Section 15.103 (c).

Warning Labels

Warning labels attached to the instrument draw attention to specific hazards - refer to this User
Guide and other documentation provided with the instrument for more details concerning potential
hazards and any precautions or other actions that must be taken.

WARNING

To prevent potential personal injury and damage to the instrument, switch OFF all
components in the system and disconnect them from the mains power supply
before altering, or making any new electrical connections.

ChemiLite Contents-1

Table of Contents

UNPACKING ChemiLite system 1

Removing from the Packaging ....................................................................................... 1

Visual Inspection ............................................................................................................... 1

Unpacking the Main Box .................................................................................................. 1

OVERVIEW 3

ChemiLite ..................................................................................................................... 3

GenePIX Software ......................................................................................................... 4

SOFTWARE INSTALLATION 5

Minimum System Requirements ................................................................................... 5

Software Installation ..................................................................................................... 5

Run the Set-up Program ................................................................................................... 5

Select the Instrument Hardware Information .................................................................. 6

Select the Installation Folder Destination Location ......................................................... 7

Select the Start Menu Folder ........................................................................................... 7

Install Device Drivers using the Device Driver Installation Wizard .................................. 8

OPERATING 10

Operator Controls ....................................................................................................... 10

Rear Panel ....................................................................................................................... 10

Connected PC ................................................................................................................. 10

Instrument Set-up - Standard Darkroom ...................................................................... 10

Entering Personal Preferences ..................................................................................... 16

Adjusting Basic Screen Viewing Size ............................................................................ 18

Loading Test Samples .................................................................................................. 19

Sample Drawer ............................................................................................................... 19

Automatic Image Capture Mode .................................................................................. 19

Automatic Image Capture Using Standard View ............................................................ 19

Manual Image Capture Using Standard View ................................................................ 19

Automatic Image Capture Using Classic View ................................................................ 19

Automatic Image Capture Basic Workflow .................................................................... 20

Automatic Image Capture - Blot / Chemi Selected ........................................................ 20

ChemiLite Contents-2

Automatic Image Capture - Capturing the Image .......................................................... 24

Automatic Image Capture - Image Actions Following Capture ...................................... 25

Manual Image Capture Mode ...................................................................................... 28

Manual Image Capture - Start ........................................................................................ 29

Manual Image Capture - Single Image ........................................................................... 30

Manual Image Capture - Series ...................................................................................... 35

Manual Image Capture - Additive Series ........................................................................ 40

Manual Image Capture - Multiplex ................................................................................ 44

Manual Image Capture - Image Actions Following Capture........................................... 48

CONFIGURATIONS - SAVING, OPENING AND EDITING 49

Introduction ................................................................................................................ 49

Creating and Saving a Configuration ............................................................................ 49

From the Standard View Home Screen .......................................................................... 49

In Auto Image Capture Mode ......................................................................................... 50

In Manual Image Capture Mode .................................................................................... 51

Using Configurations ................................................................................................... 53

Opening a Configuration ................................................................................................ 53

Deleting a Configuration................................................................................................. 54

Editing a Saved Configuration ...................................................................................... 54

IMAGE FUNCTIONS 56

Load Images Screen ..................................................................................................... 56

Image Actions from Load Images Screen ....................................................................... 57

View Images Screen .................................................................................................... 58

View Images Screen - Single Images............................................................................... 59

View Images Screen - Multiplexed Images ..................................................................... 59

View Images Screen - Image Display Options ................................................................ 59

View Images Screen - Combining Single Images into a New Multiplexed Image .......... 63

Image Edit Screen ....................................................................................................... 64

Image Edit Screen - Image Editing Main Options ........................................................... 64

Image Edit Screen - General Option ............................................................................... 65

Image Edit Screen - Annote Option ................................................................................ 67

Image Edit Screen - Enhance Option .............................................................................. 70

Image Edit Screen - General / Annotate / Enhance Options Common Controls ........... 73

ChemiLite Contents-3

Image Edit Screen - 3D View Option .............................................................................. 75

Image Edit Screen - All Options Common Controls ........................................................ 77

Common Screen Functions and Tools .......................................................................... 79

Saving Images ................................................................................................................. 79

Export for publication…………………………………………………………………………………………………84

Printing ........................................................................................................................... 84

OPERATOR MAINTENANCE 91

Looking After a ChemiLite Instrument ......................................................................... 90

Cleaning a ChemiLite Instrument..................................................................................... 91

Contacting Cleaver Scientific ....................................................................................... 91

ChemiLite .................................................................................................................... 92

DISPOSAL 94

Disposing of a ChemiLite ............................................................................................ 94

The Waste Electrical and Electronic Equipment (WEEE) Directive ................................ 94

ChemiLite system 1

UNPACKING A CHEMILITE SYSTEM

Removing from the Packaging

Visual Inspection

Upon taking delivery of a new ChemiLite Instrument:

• Check the contents of the cartons as they are unpacked against the contents listed on the

packing list

• Check each item on the packing list for damage and document any damage carefully

• If any items are missing or damaged, contact your local distributor immediately

Unpacking the Main Box

The ChemiLite Instrument is packaged in a large carton which is securely strapped. Some
Instruments may be shipped as a carton only, others may be shipped with the carton strapped onto
a wooden pallet. Accessories are shipped in one or more separate cartons.
To unpack a typical ChemiLite Instrument:

WARNING

ChemiLite Instrument requires two people to lift it safely. A ChemiLite Instrument
complete weighs approximately 20Kg.

ChemiLite system 2

ChemiLite Unpacking Guide

A. Original packing of ChemiLite

B. Open the box and remove the

drawer and accessories bag

C. Remove the cardboard surrounding

the ChemiLite and gently lift out of
box

D. Remove the foam and plastic

surrounding the ChemiLite

E. Slide in the ChemiLite drawer and the

system is now ready to use

ChemiLite system 3

TYPICAL ACCESSORIES

Mains power cord - suitable for country of use
Camera to PC lead (USB Type A)
Darkroom to PC USB lead

OVERVIEW

The ChemiLite system is dedicated to Chemiluminescence imaging. The system is built for high

performance, automation and features a next generation high quantum efficiency CCD camera
for even greater sensitivity.

Western blot imaging has never been so easy than with the ChemiLite. The system
automatically selects the right imaging conditions for any blot irrespective of the
chemiluminescent reagents being used.

Darkroom - this provides a completely black environment into which the sample to be
imaged is enclosed.
White LED lights are provided on each side of the Darkroom to provide general illumination
when positioning and setting up samples.

ChemiLite system

The ChemiLite system is to be used with your own monitor and computer.

Specifications

Image resolution (pixels M)

4

Effective resolution (pixels M)

16

A/D

16 Bit

Greyscales

65536

Quantum efficiency @425nm

73%

Cooling regulated

Peltier cooled

Lens (motor driven)

Fixed f0.95

Epi LED white lights

Yes

Maximum blot size

11x8cm

Use with external PC

Yes

Software

GenePix Image capture software and

GeneQUANT software

ChemiLite system 4

GenePix Image Capture Software

The GenePix software runs in a standard Windows environment and provides an application driven
and time-saving workflow for running a variety of life-science applications.

The ChemiLite Instrument is controlled and operated by the GenePix software running on an
external PC operating a standard Microsoft Windows environment. Two cable connections are
required between the PC and the ChemiLite Instrument; one for the Darkroom, and one for the
Camera.
The raw data recorded by the digital camera is processed by the GenePix software to generate the
images and technical files which are the ChemiLite Instrument's basic outputs.
The GenePix software provides both automatic and manual modes of control of the ChemiLite
hardware and has an inbuilt database of application specific data which it uses in automatic capture
mode to optimise the hardware configuration in order to obtain the optimal sample image. The
database contains information relating to:

• Sample format; Blot

• Blot type; Chemiluminescence

• Sample type; Protein

• Substrate types

TYPICAL CHEMILITE- FRONT

Darkroom

Sample Drawer

ChemiLite system 5

SOFTWARE INSTALLATION

Minimum System Requirements

The GenePix software can operate on the following Microsoft Windows Operating Systems:

Windows 7 Professional SP3 (32 bit and 64 bit versions)
or
Windows 8 and Windows 10 Professional

Note: Home versions of the Windows Operating Systems are not supported.

Software Installation

A ChemiLite Instrument needs to have the ChemiLite software (GenePIX) installed on the associated
PC from which the instrument is to be controlled.
The GenePix Image Capture software can only be installed from a Windows account that has
Administrator rights. Installation is performed in the following order:

1. Run the Set-up Program

2. Select the Instrument Hardware Information

3. Select the Installation Folder Destination Location

4. Select the Start Menu Folder

5. Install Device Drivers using the Device Driver Installation Wizard

Run the Set-up Program

6. Insert the Cleaver Scientific USB stick/CD ROM and run the Set-Up Program. The

following screen will appear:

SETUP - GenePix WELCOME TO THE GenePix SETUP WIZARD SCREEN

7. Click on the Next > button. The first Hardware Information screen will appear.

ChemiLite system 6

Select the instrument Hardware Information

SET-UP -GenePIX - HARDWARE INFORMATION SCREEN-INSTRUMENT TYPE

8. Select the instrument type that you have by selecting the appropriate radio button, i.e.

ChemiLite.

9. Click on the Next > button. The CFR compliance screen will appear

Select if running GenePIX software in a CFR21 part 11 compliance environment

` SET-UP- GenePix-CFR COMPLIANCE

10. Click on the Next > button. The setup-Select Destination Location screen will appear

ChemiLite system 7

Select the Installation Folder Destination Location

SET-UP GenePix-SELECT DESINATION LOCATION SCREEN

Select the folder in which you would like the GenePix to be installed:

• To accept the displayed default folder click on the Next > button.

• To choose a different folder click on the Browse... button and navigate to the desired

folder or create a new folder. Then click on the Next > button.

Note: The GenePix Image Capture software installation requires free space of at least 80.7MB.

11. The Setup-GenePix Select Start Menu Folder screen will appear.

Select the Start Menu Folder

SET-UP-GenePix-SELECT START MENU FOLDER SCREEN

12. Select the folder in which you would like GenePix program start shortcut to be installed:

• To accept the displayed default folder click on Next > button.

• To choose a different folder click on the Browse... button and navigate to the

desired folder or create a new folder. Then click on the Next > button.

13. The Ready to Install screen will appear. Click on the install button to start the

installation process.

ChemiLite system 8

SETUP- GenePix –READY TO INSTALL SCREEN

14. The Device Driver Installation Wizard screen will appear

Install device drivers using the Device Driver Installation Wizard

This part of the installation process installs the software drivers that some computers need in
order to complete the installation.

DEVICE DRIVER INSTALLATION WIZARD WELCOME SCREEN

15. Click on the Next > button. The Wizard (a sub-program, part of the GenePix Image

Capture software) will automatically install the necessary device drivers on the PC that
the hardware device you selected previously needs in order to operate.

Once the device drivers have been installed, the screen will change to the second Device Driver
Installation Wizard screen. This displays details of the device drivers that have been installed.

ChemiLite system 9

DEVICE DRIVER INSTALLATION WIZARD FINISH SCREEN

16. Click on the Finish button.

17. The setup-GenePix software completing the GenePix Setup Wizard screen will appear.

This indicates that the installation process has finished successfully.

SETUP-GenePix Image Capture- COMPLETING THE Image GenePix Capture SETUP WIZARD
SCREEN

18. Click on the Finish button to complete the set-up process.

19. Remove the Cleaver Scientific USB Stick

ChemiLite system 10

OPERATING

Operator Controls

Rear Panel

The rear panel of the ChemiLite Instrument contains two User controls:

• An ON/OFF rocker switch, used for energising/de-energising the instrument.

Connected PC

The keyboard and mouse of an external PC connected to a ChemiLite Instrument function as normal.

Instrument Set-up - Standard Darkroom

Make sure that the Laboratory bench is strong enough to support the ChemiLite Instrument and is
stable and level.

Caution

Do not energise any of the components until instructed to.

Make the following cable connections:

20. Connect the mains power cord between a power supply socket and the Instrument. DO

NOT switch on.

WARNING

Ensure that the mains supply socket on the Instrument is not obstructed, i.e. leave
a gap to allow easy disconnection of the mains cord.

21. Connect Darkroom to the PC using the USB lead.

22. Connect the camera USB cable to the back of the darkroom to connect the camera to

the PC.

23. Energise the Darkroom - ON/OFF switch on the back of the Darkroom.

24. Startup the PC and install the GenePix Image Capture software.

25. The GeneQUANT software will install automatically.

26. Double click the (

) icon to start the GenePix software.

ChemiLite system 11

GenePix STANDARD VIEW HOME SCREEN

GenePix Standard View Home Screen Layout

TITLE BAR

Displays an icon to show where you are in the GenePix program,

e.g. here it shows the icon to show that you are on the
Home Screen. On other screens within the GenePix program this
button is used to return you to the Home screen.

Displays the camera resolution, the connected hardware and the

program title , for this particular installation it
shows that a with a with a 4MP image resolution system is
installed and the GenePix program is running.

Displays the icon, for accessing System data - camera
hardware and program version information, as shown below:

WORKFLOW
STATUS BAR

INFORMATION
PANES

USER

SELECTABLE

ACTIONS

TITLE

NAVIGATION ICONS

ChemiLite system 12

Also displays the standard Windows program buttons

, for minimise, maximise, and close.

At various points through the image capture process the top left
hand corner of the title bar is used to display icons which indicate
the stage in the process that has been reached/is being actioned,
e.g. when the system is in the ChemiLite process of making an

automatic exposure the icon is displayed,
and when a manual exposure is being made the

icon is displayed.

USER SELECTABLE
ACTIONS

Buttons for selecting the various main actions or functions that are
available to the User from the current screen, in this case:

Quick access into the automatic image capture process for a Blot

sample, .

Accessing manual image capture .

INFORMATION PANES

Displays information or images. May be presented in a number of
configurations depending on the User's location within the
program.

The Standard View Home screen displays Saved Protocols (also
referred to as User Configurations) and sort/select options for the
Protocols.

WORKFLOW STATUS BAR

Displays various items of information:

Home icon (when not on the Home screen).
Workflow icons - illustrate the User's position within a

series of steps that form a sequence of actions necessary
to complete an activity, e.g. Manual Capture. Clicking on
an icon takes the User to screen associated with the icon.

When multiple steps are displayed a grey arrow appears

ChemiLite system 13

in between each icon. This indicates each step back in
sequence.

Instrument status, e.g. here it shows the icon,
indicating that the Camera is establishing connection with
the program. This icon changes depending on status:

indicates that the Camera and Darkroom are

OK and ready for use

indicates that the Camera is overheated or

otherwise not ready

indicates that the Darkroom is establishing

connection with the program

indicates that the Darkroom is not connected

Indicates that neither the Camera nor the

Darkroom are connected

Navigation icons - enable a User to navigate to various
Settings or System Tools screens. The icons displayed
depend on the activity being undertaken within the
program.

NAVIGATION ICONS

Shown here, with icon labels displayed:

Load Images icon, to navigate to Load Images

screen

View Images icon, to navigate to View Images

screen

Settings icon, to navigate to User Preferences

screen

ChemiLite system 14

GenePix Image Capture CLASSIC VIEW HOME SCREEN

GenePix Image Capture Classic View Home Screen Layout

WORKFLOW
STATUS BAR

INFORMATION
PANES

USER

SELECTABLE

ACTIONS

TITLE

NAVIGATION ICONS

ChemiLite system 15

TITLE BAR

Same as the Standard View Home screen.

USER SELECTABLE
ACTIONS

Buttons for selecting the various main actions or functions that are
available to the User from the current screen, in this case:

Access to the automatic image capture process, from

.

Access to the manual image capture process, from

.

Access to the browse images process, from

.

Access to the view images process, from .

INFORMATION PANES

Displays information or images. May be presented in a number of
configurations depending on the User's location within the
program.

The Home screen is split into two panes:

User Configurations (also referred to as Protocols) - saved
sets of specific setting combinations that form repeatable
workflows.

System data - camera hardware and program version
information.

WORKFLOW STATUS BAR

Displays various items of information:

Home icon (when not on the Home screen).
Workflow icons - illustrate the User's position within a

series of steps that form a sequence of actions necessary
to complete an activity, e.g. Manual Capture. Clicking on
an icon takes the User to the screen associated with the
icon.

When multiple steps are displayed a grey arrow appears in
between each icon. This indicates each step back in
sequence.

Instrument status, e.g. here it shows the icon,
indicating that the Camera is establishing connection with
the program. This icon changes depending on status:

indicates that the Camera and Darkroom are

ChemiLite system 16

Entering Personal Preferences

Every individual who logs on to a ChemiLite a customised set of Instrument settings, i.e. a profile,
which reflects the nature of the work the individual normally undertakes and what they do with the
test results is available.

27. Select the Settings icon on the Home screen. This displays the User Preferences

screen.

OK and ready for use

indicates that the Camera is overheated or

otherwise not ready

indicates that the Darkroom is establishing

connection with the program

indicates that the Darkroom is not connected

Indicates that neither the Camera nor the

Darkroom are connected

Navigation icons - enable a User to navigate to various
Settings or System Tools screens. The icons displayed
depend on the activity being undertaken within the
program.

NAVIGATION ICONS

Shown here, with icon labels not displayed:

Settings icon, to navigate to User Preferences

screen

Hardware icon, to navigate to Hardware screen

ChemiLite system 17

USER PREFERENCES SCREENS

27. Set your preferences:

REPORT SETTINGS
Report Settings enables you to preset some report defaults, this is useful where you are
doing repetitive tests and want the same type of report for each test. The settable options
are:

• Full Report - checking this checkbox sets the Instrument to generate a Full Report

for each test. The Full Report content can be controlled using the additional
checkboxes, check to include the feature:

o Image
o File Description
o Capture Properties

• Basic Report - checking this checkbox sets the Instrument to generate a Basic

Report for each test. Additional features are:
o Basic Report Image Only - if the checkbox is checked, the printed report

contains only the captured image for the test. If not checked, the report
contains the image plus some basic information, e.g. filename / username
/ date / time / sample / filter, etc.

o Preview Before Printing - if the checkbox is checked, the screen displays a

preview of the report before it is printed. If not checked, the report is
printed without a preview being displayed.

SAVING DEFAULTS

• Saving Defaults - enables you to select and set as a preset default the file format

that the GenePix Image Capture Software saves your images in. If you do not set
a preference here, the GenePix Image Capture Software will use the *.sgd format
by default. To set a preference for a different file format uncheck the Use Default
File Type checkbox and select your preferred file format from the drop-down
menu.

AVAILABLE FILE FORMATS

ChemiLite system 18

PRINTER SETTINGS

• Printer Settings - enables you to select a printer and set printer preferences for

your selected printer, generally these will only be settable for the current session.
The options available to you in Printer Settings will vary based on your operating
system and printer make/model.

GENERAL SETTINGS

• Show labels on navigation buttons - checking this checkbox turns on the labels

on the Navigation buttons, i.e.:

with labels

without labels

• Classic View - checking this checkbox changes the display from Standard View,

the default setting, to Classic View.

28. To save any changes you make, select the Save icon . If you attempt to navigate

away from the User Preferences screen without first saving the changes, the following
pop-up message is displayed:

SAVE CHANGES MESSAGE POP-UP

29. Select the icon to return to the Home screen.

Adjusting Basic Screen Viewing Size

By default GenePix Image Capture starts up with the display at full screen size. The size of the screen
display can be adjusted by selecting the Maximise/Restore GenePix Image Capture button in the

Title Bar and then resizing the display by dragging the dotted arrow icon in the bottom right
hand corner.

STANDARD VIEW HOME STANDARD VIEW HOME

SCREEN – DEFAULT SCREEN-ADJUSTED

ChemiLite system 19

Loading Test Samples

Sample Drawer

Place the test sample centrally into the drawer so that the sample fits within the indentations. It is
recommended that the sample is placed horizontally to ensure maximum image resolution.

Automatic Image Capture Mode

Automatic image capture can be carried out from either Home screen. In Standard View the sample
defining process has been simplified but once you have specified your sample type the remainder of
the process is the same as in Classic View

Automatic Image Capture Using Standard View

30. Open the Darkroom Drawer and position the sample.

A Blot sample

(i) Select the Blots icon on the Home screen. This displays the Blots drop-

down list.

BLOTS DROP-DOWN LIST

(ii) Select your Blot type from the drop-down list.
(iii) Select Chemi Blot (Single Image) from the drop-down list.
(iv) This displays the Dye Selection screen. Proceed to Automatic Image Capture - Blot

/ Chemi Selected at Select Single Image.
(v) Select Chemi Blot (Series) from the drop-down list.
(vi) This displays the Chemi Series Capture screen. Proceed to Automatic Image

Capture - Blot / Chemi Selected at Select Series.

Manual Image Capture Using Standard View

Manual image capture from the Standard View Home screen follows the same process as manual
image capture from the Classic View Home screen. Proceed to Manual Image Capture Mode.

Automatic Image Capture Using Classic View

The basis of the Auto Capture mode is a series of steps that form a structured workflow. The
workflow takes the User through a series of steps which define the sample and how it is to be
imaged, enabling the software to determine the optimum hardware setup using the pre-specified
lighting types installed. The workflow is navigated through using the green 'bouncing' arrow in the

ChemiLite system 20

bottom right hand corner of the screen to move forward to the next screen. The grey status bar
shows the progress of the workflow. Selecting any of the icons allows the user to move between any
of the stages that make up the workflow.

Automatic Image Capture Basic Workflow

The following image represents the Automatic Image Capture workflow, with each of the icons
representing a stage in the process.

AUTOMATIC IMAGE CAPTURE WORKFLOW

AUTOMATIC IMAGE CAPTURE

WORKFLOW STEPS

Automatic Image Capture - Blot / Chemi Selected

The following instructions apply if you have made the following selections in Automatic Image
Capture - Step 1 Sample Selection:

Sample Format pane select Blot
Blot Type pane select Chemi

SAMPLE SELECTION - BLOT - CHEMI - CAPTURE METHOD SCREEN

1. In the Capture Method pane select Auto (Single) or Series.

1a. Select Auto (Single).

(i) Select the bouncing green arrow . This displays the Dye Selection screen.

Step 1 Sample selection

(Gel / Blot / Other)

Step 2 Dye selection

(Single / Multiplex)

Step 3 Protocol selection

Step 4 Sample positioning
(Single / Multiplex)

ChemiLite system 21

BLOT - CHEMI - AUTO (SINGLE) - DYE SELECTION SCREEN

Note: The Samples icon has been added to the Workflow.

The Blot - Chemi - Auto (Single) - Dye Selection screen contains a range of options, as
outlined below:

UPPER PANE

By default the upper pane displays all chemiluminescent substrates in the database.
Scroll vertically to view the entire selection. A selected substrate turns red.

CENTRE PANES

Selected substrates appear in the Selected Items pane. Select the Clear All button to
remove selected substrates and restart substrate selection.
Check the Visible marker checkbox if you have used a colorimetric marker on the sample.
The GeneSys program will automatically take two separate image captures; one for your
sample, one for the marker (with white light), and combine the two images together.

LOWER PANE

The lower pane displays the total number of chemiluminescent substrates found in the
database.
To limit the chemiluminescent substrate selections displayed in the upper pane check the
Recent selections only checkbox. Only recently used chemiluminescent substrates will be
displayed.
Use the Search for dye here... box to search for a chemiluminescent substrate by name.
Enter the chemiluminescent substrate's name in the box.
(ii) Select your substrate, direct or by searching.
(iii) Check the Visible Marker checkbox if you have used a colorimetric marker.

(iv) Select the bouncing green arrow . This displays the Sample Positioning
screen. See Automatic Image Capture - Step 4 Sample Positioning.

2. Select the bouncing green arrow . This displays the Automatic Capture screen.

ChemiLite system 22

AUTOMATIC CAPTURE SCREEN

Note: The Positioning icon has been added to the Workflow.

The Automatic Capture screen contains a range of information display and User
selectable actions, as outlined below.

CONTROLLING THE IMAGE SATURATION

Select the Show Saturation button . The Saturation function can be
used to check if areas of the image are going to be over-exposed; over-exposed white
bands will be highlighted in red on the image, over-exposed black bands will be
highlighted in blue on the image. This function is useful if the Select AutoExpose Area
function has been used. Please note that saturated bands are not quantifiable.

Select the Histogram button . This displays a histogram or graphical representation of
the distribution of grey scales recorded by the camera sensor; with black to the extreme
left, white to the extreme right.

HISTOGRAM DISPLAY

The Histogram button turns red to indicate that the function has been selected.
Selecting the button again cancels the Histogram function.
The histogram is a graph showing the number of pixels in the image at each different
intensity value found in that image. For a 16-bit image there are a possible 65535
different intensities so the histogram will graphically display 256 numbers showing the
distribution of pixels amongst those grayscale values. If the graph is bunched up to the
left it indicates that not many grayscale levels have been captured and the red lines on
the histogram graph may need to be adjusted to see bands. If the graph reaches to the
far right (65535 grayscales) this indicates that the image may be saturated.

ChemiLite system 23

IMAGE SLIDER CONTROLS

The following controls are available to adjust the way a captured image looks.

IMAGE SLIDER CONTROLS

The Digital Zoom slider allows you to zoom in or out of the displayed image. Dragging the
slider towards the + sign zooms in, dragging the slider towards the - sign zooms out.
The Gamma slider changes the tone of the overall image. With reference to the
histogram mentioned previously, the Gamma function changes the relative brightness of
the recorded midrange tones by shifting them either towards the dark end or the white
end of the graph, without changing the extreme dark or extreme white values. This gives
the recorded image an overall darker or lighter appearance.
Contrast is a measure of how bright highlights are in an image. Brightness is a measure of
how bright shadows are in an image. Use the Contrast slider to control how bright the
lightest objects in an image are displayed. Use the Brightness slider to control how bright
dark objects in an image are displayed.
If you make changes using the sliders you can undo the changes by selecting the Reset
icon.
Use the Image Inversion button to invert the image, i.e. white appears black, black
appears white. This can help when making changes with the slider controls. Selecting the
Image Inversion button a second time changes the image back to normal.

CAPTURED IMAGE INFORMATION

Select the Image Information icon . This displays a pop-up window displaying
captured image information. The information displayed is as follows:

• Dye

• Image capture date / time

• Filter

• Light

• Exposure time

• Iris f number

• Image size

• Range (range of grey scales captured)

Digital Zoom slider

Image Inversion button

Contrast / Brightness
sliders

Gamma slider

Reset button

ChemiLite system 24

IMAGE INFORMATION POP-UP WINDOW

The Image Information icon turns red. Selecting the Image Information icon a second
time closes the pop-up window.

Selecting the Save Protocol icon saves the displayed settings as a configuration (or
protocol) or repeatable workflow. Refer to CONFIGURATIONS - SAVING, OPENING AND

EDITING.

Automatic Image Capture - Capturing the Image

3. To capture an image using the entered selections, select the Capture button .

4. The following pop-up message is displayed as the Instrument makes an image capture:

AUTO EXPOSING MESSAGE POP-UP

The Exposure Timing icon appears at the bottom of the screen. This changes to
display the progress of the exposure as a coloured bar progressing around the icon. If
capturing multiple exposures, the icon displays multiple coloured bars.
While the exposure is progressing, and this may take several minutes, it is possible to
navigate away from the Automatic Capture screen and browse, view and edit previously

captured images. The Exposure Timing icon remains displayed at the bottom of the
screen. Selecting this icon at any time returns you to the Automatic Capture screen.
Once the image is captured, it appears in the left hand pane and also as a thumbnail in
the central Image Pool pane. As more images are captured, these also appear in the
Image Pool. When initially captured, images in the Image Pool are unsaved and are
outlined in red.

UNSAVED IMAGE POOL IMAGE

5. To save the captured image, select the image in the Image Pool and select the Save icon

.

Once saved, images in the Image Pool are outlined in green and their filename appears
below the image.

ChemiLite system 25

SAVED IMAGE POOL IMAGE

If further images are captured, additional images appear in the Image Pool, stacked
vertically.
Images can be dismissed from the Image Pool by selecting them and then selecting the

Close button . If an image has not been saved you will see a Save
prompt.

SAVE PROMPT

6. If multiple images are captured without any images being saved, multiple images can be

selected and saved in a single operation. Check the Multi Select Mode checkbox in the
Image Pool and select multiple images.

7. To save the selected images, select the Save icon .

Automatic Image Capture - Image Actions Following Capture

Further actions can be performed on captured images by selecting Image Action icons. The function
of these is explained in other parts of this User Guide.

IMAGE ACTION ICONS

Save icon

Print icon

Edit icon

Save Protocol

Analyse icon

View Images

ChemiLite system 26

1b. Select Series.

(i) Select the bouncing green arrow . This displays the Chemi Series Capture

screen.

CHEMI SERIES CAPTURE SCREEN

Note: The Samples icon has been added to the Workflow. If you arrive at this screen from

the Standard View Home screen, the Samples icon does not get added to the Workflow.

The Chemi Series Capture screen contains a range of options, as outlined below:

UPPER LEFT HAND PANE
The upper left hand pane contains options for choosing your reagent/substrate type and
an option for indicating whether or not you have used a colorimetric marker.
Select the Reagent button and select your substrate from the drop-down list.

REAGENT/SUBSTRATE LIST

Check the Visible marker checkbox if you have used a colorimetric marker on the sample.
The GeneSys Image Capture program will automatically take two separate image
captures; one for the sample, one for the marker (with white light), and combine the two
images together.

LOWER LEFT HAND PANE

The lower left hand pane contains options for; choosing how many images you want to
capture, the level of binning that you want to use, and whether you want to add all the
images in a multiple image capture process together.

Use the plus and minus buttons of the Number of images selector to set how
many images of your sample that you want to capture. Select plus to increase the
number, select minus to decrease the number.

ChemiLite system 27

The Binning function is a way of improving image capture times. By combining the
outputs from adjacent pixels on the image sensor, in square groups, e.g. 2 x 2, 3 x 3, 4 x 4,
etc, the pixels are effectively enlarged while being reduced in number. This provides
faster image capture, due to the reduced number of data reading operations required,
improved signal to noise ratios, but reduced spatial resolution, i.e. 2 x 2 binning on an 8
MP sensor effectively results in a 2 MP sensor with pixels four times the size of the 8 MP
sensor pixels.
Select the Binning button and select the binning ratio you want to use from the drop­down list.

BINNING RATIO DROP-DOWN LIST

The lower left hand pane also contains two buttons; a Reset button and a Proceed
button.
(ii) Select your substrate.
(iii) Check the Visible Marker checkbox if you have used a colorimetric marker.
(iv) In the Number of images box select the number of images you want to capture.
(v) In the Binning box select the binning option you require.
(vi) Check the Add contents of previous image checkbox if you want to capture

multiple images and combine them together into a single composite image.

(vii) Select the Next button to display the available options in the right hand pane.

Once selected the Next button changes to . At the same time the Reset

button changes from to .

RIGHT HAND PANE

The right hand pane contains simple controls for setting exposure times for your image
capture or series of captures. If you are taking multiple captures, checking the Use the
same exposure for all images checkbox will use the exposure time that you set for each
of the image captures in the series. These options are only displayed after you have
selected the Proceed button in the left hand pane.
The Exposure controls are simple plus/minus buttons for adjusting the following time
periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .

EXPOSURE CONTROLS - SINGLE IMAGE OR SAME FOR ALL IMAGES SELECTED

(viii) Check the Use the same exposure for all images checkbox if you want all images in

a series to have the same exposure time.
(ix) If you want to set different exposure times for each image, leave the Use the same

exposure for all images checkbox unchecked.

ChemiLite system 28

(x) Using the Exposure plus/minus buttons enter exposure times for each image in the

series in turn. Use the arrows below the Exposure timer to select an image number

and set an exposure time for each image.

EXPOSURE CONTROLS - MULTI IMAGES WITH DIFFERING TIMES

(xi) To cancel any settings made in the right hand pane select the Reset button .

Once selected the Reset button changes to . At the same time the Next button

changes from to and the options in the right hand pane are hidden and

you can make changes to the options in the left hand pane.
(xii) Once you have finished making settings in both panes, select the bouncing green

arrow . This displays the Sample Positioning screen. See Automatic Image

Capture - Step 4 Sample Positioning.

Manual Image Capture Mode

Manual Capture mode allows the User to take complete control of every function of a ChemiLite
Instrument. Manual image capture is particularly useful for the more unusual imaging applications or
if a User has known imaging parameters that they want to use.
Within the Manual Capture mode, the following options are possible:

• Single Image - used to capture a single image of your sample.

• Series Images - used to capture a series (variable number) of separate images of

your sample, using the same or different exposure/filter/lighting settings for each
capture. For example, capture a series of images using different exposure
settings, compare the resulting captured images, save the best captured image
and delete the unwanted captured images.

• Multiplex - used to capture an image of Chemi blot and a visible marker, with

different exposure/filter/lighting settings for each capture, which are then
displayed as separate images and as a combined image.

• Additive Series - used to capture a series (variable number) of separate images of

your sample, with the same or different exposure/filter/lighting settings for each
capture, which are then combined into a single combined (additive) image.

ChemiLite system 29

Manual Image Capture - Start

1. Open the Darkroom Drawer and position the sample in the Drawer within the

guidelines, as noted previously.

2. Select the Manual Capture icon on the Home screen. This displays the

basic Manual Capture screen.

MANUAL CAPTURE - BASIC SCREEN - DEFAULT

Note: By default the Manual Capture screen opens in Single Image mode.

3. Select the type of image capture you want to make by selecting from the options in the

right hand pane.

IMAGE CAPTURE OPTIONS

• To capture a single image press the Single Image button. See Manual Image Capture -

Single Image.

• To capture a series of images, with different settings for each, press the Series button. See

Manual Image Capture - Series.

• To capture a single image press the Single Image button. See Manual Image Capture -

Single Image.

• To capture a series of images, with different settings for each, press the Series button. See

Manual Image Capture - Series.

ChemiLite system 30

• To capture a series of images, with the same or different settings for each, which will then

be combined into a single combined image press the Additive Series button. See Manual
Image Capture - Additive Series.

• To capture a series of images, with different settings for each, which will then be displayed

as separate images plus a combined image press the Multiplex button. See Manual Image

Capture - Multiplex.

Manual Image Capture - Single Image

Note: A single image can be captured directly from the basic Manual Capture screen without

accessing the Image Capture options.

4. Make Single Image settings directly on the basic Manual Capture screen or by selecting

the Single Image button from the Image Capture options.

MANUAL CAPTURE - SINGLE IMAGE SELECTED

5. Using the Lighting and Filters functions in the right hand pane to make your lighting and

filter selections.

LIGHTING AND FILTERS FUNCTIONS

(i) Select the Lighting button and select your preferred light from the drop-down

menu.

LIGHTING DROP-DOWN MENU

LIGHTING TO IMPROVE SAMPLE PREVIEW IMAGING

ChemiLite system 31

The Lighting function provides light inside the Darkroom for better aligning of the

sample. Selecting the icon turns the interior white lights on, giving greater visibility

of the sample in the Darkroom. Re-select the icon to turn the white lights off again.

SAMPLE IMAGE ZOOMING

• The Digital Zoom slider allows you to zoom in or out of the displayed image.

Dragging the slider towards the + sign zooms in, dragging the slider towards the ­sign zooms out. Zooming in or magnifying an area of the image allows you to
align the sample more accurately, using the grid overlay.

SAMPLE ALIGNMENT USING THE GRID

• The Grid button lets you overlay a grid on the image, enabling you to better

align the sample. Use the Door Open button on the right hand side of the
Darkroom to open the Darkroom Door slightly to enable you to move the sample
around to align it with the grid projection. Pressing the Grid button calls up the
grid menu.

o No Grid option removes the grid projection.
o Show Grid option displays the default grid projection, 2 rows x 2 columns.

GRID MENU SHOW GRID OPTION

USING A SELECTED AREA TO IMPROVE SAMPLE IMAGE QUALITY

The Select AutoExpose Area function allows you to define an area of interest to set the
Camera exposure. This can be used to improve an area of the image where the bands are
very faint. The software determines the correct exposure settings for the defined area,
resulting in a good image of the defined area. However, although this procedure may
result in faint bands becoming more visible, more prominent bands may be overexposed
(saturated).

Select the Select AutoExpose Area button . This introduces a
yellow selector box onto the sample image. The yellow box can be dragged around and
resized.

ChemiLite system 32

AUTOEXPOSE AREA SELECTOR BOX

You also have the option to use the area outside of the yellow box to set the exposure.
This is useful if the bulk of the image is faint and only a small area contains prominent
bands. The yellow box can be positioned to contain the prominent bands and then the
Use Area Outside ROI checkbox can be checked. Exposure will then be based on the area
outside the yellow box.

6. Select the Camera resolution that you want to use to capture your sample image.

The Binning function is a way of improving image capture times. By combining the
outputs from adjacent pixels on the image sensor, in square groups, e.g. 2 x 2, 3 x 3, 4 x 4,
etc, the pixels are effectively enlarged while being reduced in number. This provides
faster image capture, due to the reduced number of data reading operations required,
improved signal to noise ratios, but reduced spatial resolution, i.e. 2 x 2 binning on an 8
MP sensor effectively results in a 2 MP sensor with pixels four times the size of the 8 MP
sensor pixels.
Select the Binning button and select the binning ratio you want to use from the drop­down list.

BINNING RATIO DROP-DOWN LIST

7. You are now ready to capture your sample image. You have two options; to let the

GenePix Image Capture program set the exposure time automatically, or, you set the
exposure time manually.

8. Select the Auto Capture button .

9. The GenePix Image Capture program will decide the best exposure time for the settings

you have entered. This time will appear in the Exposure function in the right hand pane.
The Auto Capture function is designed to capture the maximum available number of
grey scales without allowing image saturation. This function is useful for quantifying
data.

10. The following pop-up message is displayed as the Instrument makes an image capture:

ChemiLite system 33

AUTO EXPOSING MESSAGE POP-UP

11. The Exposure Timing icon appears at the bottom of the screen. This changes to

display the progress of the exposure as a coloured bar progressing around the icon.

12. While the exposure is progressing, and this may take several minutes, it is possible to

navigate away from the Manual Capture screen and browse, view and edit previously
captured images.

13. Once the image is captured, it appears in the left hand pane and also as a thumbnail in

the central Image Pool pane. If more images are captured, these also appear in the
Image Pool. When initially captured, images in the Image Pool are unsaved and are
outlined in red.

UNSAVED IMAGE POOL IMAGE

14. To save a captured image, select the image in the Image Pool and select the Save icon

.

15. Once saved, images in the Image Pool are outlined in green and their filename appears

below the image.

16. To save a captured image, select the image in the Image Pool and select the Save icon

.

17. Once saved, images in the Image Pool are outlined in green and their filename appears

below the image.

SAVED IMAGE POOL IMAGE

ChemiLite system 34

18. If further images are captured, additional images appear in the Image Pool, stacked

vertically.

19. Images can be dismissed from the Image Pool by selecting them and then selecting the

Close button . If an image has not been saved you will see a Save
prompt.

SAVE PROMPT

20. (i) If multiple images are captured without any images being saved, multiple images

can be selected and saved in a single operation. Check the Multi Select Mode checkbox
in the Image Pool and select multiple images.

21. (ii) To save the selected images, select the Save icon .

MANUAL CAPTURE - SINGLE IMAGE WITH MANUAL EXPOSURE

22. Set an exposure time:

23. The Exposure controls are simple plus/minus buttons for adjusting the following time

periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .

MANUAL EXPOSURE CONTROLS

24. Using the Exposure plus/minus buttons enter an exposure time for the image.

25. Select the Capture button .

The following pop-up message is displayed as the Instrument makes an image capture:

AUTO EXPOSING MESSAGE POP-UP

The Exposure Timing icon appears at the bottom of the screen. This changes to
display the progress of the exposure as a coloured bar progressing around the icon.

ChemiLite system 35

While the exposure is progressing, and this may take several minutes, it is possible to
navigate away from the Manual Capture screen and browse, view and edit previously
captured images.
Once the image is captured, it appears in the left hand pane and also as a thumbnail in
the central Image Pool pane. If more images are captured, these also appear in the Image
Pool. When initially captured, images in the Image Pool are unsaved and are outlined in
red.

UNSAVED IMAGE POOL IMAGE

To save a captured image, select the image in the Image Pool and select the Save icon
Once saved, images in the Image Pool are outlined in green and their filename
appears below the image.

SAVED IMAGE POOL IMAGE

If further images are captured, additional images appear in the Image Pool, stacked
vertically.
Images can be dismissed from the Image Pool by selecting them and then selecting the

Close button . If an image has not been saved you will see a Save
prompt.

SAVE PROMPT

(i) If multiple images are captured without any images being saved, multiple images

can be selected and saved in a single operation. Check the Multi Select Mode
checkbox in the Image Pool and select multiple images.

(ii) To save the selected images, select the Save icon .

Manual Image Capture - Series

26. Select the Series button from the Image Capture options.

ChemiLite system 36

You must now define the number of images you want in your series. In the right hand
pane the Number of images selector is displayed.

NUMBER OF IMAGES SELECTION

27. Use the + / - buttons to select the number of images you want to capture, then select

the Next arrow . For this example, set to 3 by selecting the + button.

You must now define a Camera resolution for your series of images. In the right hand
pane the Binning selector is displayed.

BINNING SELECTOR

28. Select the No Binning (4.03MP) button and select the binning ratio you want to use

from the drop-down list, then select the Next arrow , or if you want to use the full
resolution just select the Next arrow .

BINNING RATIO DROP-DOWN LIST

29. You must now set the interval time (time between captures in the series), the exposure

times for each image in your series of images, and the lighting/filter sets for your
images. The controls for these are displayed in the right hand pane.

ChemiLite system 37

SERIES EXPOSURE CONTROLS - FIRST IMAGE SERIES EXPOSURE CONTROLS - SECOND IMAGE

SAME AS PREVIOUS UNSET

SERIES EXPOSURE CONTROLS - THIRD IMAGE

SAME AS PREVIOUS UNSET

The display is almost the same for each image in the series and by default starts at image

1.
The Capture Interval controls are simple + / - buttons for adjusting the following time
periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .
Using the Capture Interval + / - buttons enter an interval time for the series of images.
The manual Exposure controls are simple + / - buttons for adjusting the following time
periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .
To set a manual exposure time select the Manual button and use the Exposure + / ­buttons enter an exposure time for the first image. Alternatively, selecting the Auto
button after you have selected the lighting and filters allows the system to automatically
select the most appropriate exposure time for the image 1.
Use the Lighting and Filters functions in the right hand pane to make your lighting and
filter selections as described previously.

ChemiLite system 38

30. Select the Next arrow to make the settings for image 2. Select the Last arrow

to apply the settings you have entered for image 1 to all of the remaining images in
your series. Go to Step 14.

31. By default the Same as previous checkbox is checked, making the settings for the

second image the same as the settings for first image, and the setting boxes are greyed
out meaning that no manual changes can be made. To make changes for the second
and subsequent images, uncheck the Same as previous checkbox.

32. Enter the settings for all the images in your series.

33. Select the Next arrow .

34. The exposure/interval/lighting/filter choices that you have selected are now displayed

as a set of Current Protocols in the right hand pane.

SERIES PROTOCOLS

35. Position the sample and improve the the preview sample image as much as possible

using the Light / Digital Zoom / Grid / Select Autoexpose Area / Lens Controls, as
described previously.

36. Select the Capture button .

The Exposure Timing icon appears at the bottom of the screen.
This changes to display the progress of the exposures as concentric coloured bars

progressing around the icon .
While the exposures are progressing, and this may take several minutes, it is possible to
navigate away from the Manual Capture screen and browse, view and edit previously
captured images.
The Current Protocol display changes as the series of captures is made. As a capture is
made using a protocol, the protocol box is highlighted yellow. When the capture is
complete a green tick appears inside the protocol box and the yellow highlight is
removed. The yellow highlight then appears on the next protocol box in the series, once
that capture has commenced.

ChemiLite system 39

SERIES EXPOSURE - FIRST IMAGE SERIES EXPOSURE - ALL FIVE

BEING CAPTURED CAPTURES COMPLETE

As the first image is captured, it appears as the main image in the left hand Image pane,
as a thumbnail in the Image pane, and as a thumbnail in the central Image Pool pane. As
subsequent images in the series are captured, these also appear as thumbnails in the
Image pane, the images being stacked vertically. The main image in the Image pane
changes as each image is captured, displaying the current image. The thumbnail image in
the Image Pool also changes as each capture is made, displaying a combined image.

UNSAVED IMAGE POOL IMAGE

37. The series of images captured can be viewed individually as a large image in the left

hand pane by selecting the desired image from the series of thumbnail images.

The thumbnail images in the Image pane overlay and partially obscure the main image.
To view the entire main image, select the minimise icon in the top right hand corner
above the first thumbnail image. This hides the thumbnails, leaving just a banner
containing a minimise icon. Selecting the minimise icon in the banner displays the
thumbnail images again.
The best image or images can then be saved, and the unwanted images can be deleted.

38. To save a captured image, select the image in the Image pane or the Image Pool and

select the Save icon .

Once saved, images in the Image Pool are outlined in green and their filename appears
below the image.

SAVED IMAGE POOL IMAGE

ChemiLite system 40

Images can be dismissed from the Image Pool by selecting them and then selecting the
Close button . If an image has not been saved you will see a Save

prompt.

SAVE PROMPT

(i) If multiple images are captured without any images being saved, multiple images

can be selected and saved in a single operation. Check the Multi Select Mode
checkbox in the Image Pool and select multiple images.

(ii) To save the selected images, select the Save icon .
For more information on saving refer to Common Screen Functions and Tools.

Manual Image Capture - Additive Series

39. Select the Additive Series button from the Image Capture options.

You must now define the number of images you want in your series. In the right hand
pane the Number of images selector is displayed.

NUMBER OF IMAGES SELECTION

40. Use the + / - buttons to select the number of images you want to capture, then select

the Next arrow . For this example, set to 3 by selecting the + button.

You must now define a Camera resolution for your series of images. In the right hand
pane the Binning selector is displayed.

BINNING SELECTOR

41. Select the No Binning (4.03MP) button and select the binning ratio you want to use

from the drop-down list, then select the Next arrow , or if you want to use the full
resolution just select the Next arrow .

ChemiLite system 41

BINNING RATIO DROP-DOWN LIST

42. You must now set the exposure time, capture intervals, and select lighting and filter

options for image 1. This process is the same as that for Manual Image Capture - Series.

43. The display is almost the same for each image in the series and by default starts at

image 1.

44. The Capture Interval controls are simple + / - buttons for adjusting the following time

periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .

45. Using the Capture Interval + / - buttons enter an interval time for the series of images.

46. The manual Exposure controls are simple + / - buttons for adjusting the following time

periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .

47. To set a manual exposure time select the Manual button and use the Exposure + / -

buttons enter an exposure time for the first image. Alternatively, selecting the Auto
button after you have selected the lighting and filters allows the system to
automatically select the most appropriate exposure time for the image 1.

48. Use the Lighting and Filters functions in the right hand pane to make your lighting and

filter selections as described previously.

49. Select the Next arrow to make the settings for image 2. Select the Last arrow

to apply the settings you have entered for image 1 to all of the remaining images in
your series.

50. By default the Same as previous checkbox is checked, making the settings for the

second image the same as the settings for first image. To make changes for the second
and subsequent images, uncheck the Same as previous checkbox.

51. Enter the settings for all the images in your series.

52. Select the Next arrow .

53. If the Dynamic Fielding option is available, determined by your lighting/filter selections,

you now have to decide whether or not to apply Neutral Fielding.

The Dynamic Fielding option allows you to correct the image for uneven lighting. This can
cause problems when quantifying bands or spots across a large sample. The image of the
dynamic field is normalised for light illumination. This normalisation is then applied to the
gel image, such that uneven light illumination generated by the light source is addressed.

ChemiLite system 42

The exposure/lighting/filter choices that you have selected are now displayed as a set of
Current Protocols in the right hand pane.

ADDITIVE SERIES PROTOCOLS

54. Position the sample and improve the preview sample image as much as possible using

the Light / Digital Zoom / Grid / Select Autoexpose Area / Lens Controls, as described
previously.

55. Select the Capture button .

The Exposure Timing icon appears at the bottom of the screen.
This changes to display the progress of the exposures as concentric coloured bars

progressing around the icon .
While the exposures are progressing, and this may take several minutes, it is possible to
navigate away from the Manual Capture screen and browse, view and edit previously
captured images.

ADDITIVE SERIES PROTOCOLS - WITH CAPTURES TAKEN

The Current Protocol display changes as the series of captures is made. As a capture is
made using a protocol, the protocol box is highlighted yellow. When the capture is
complete a green tick appears inside the protocol box and the yellow highlight is
removed. The yellow highlight then appears on the next protocol box in the series, once
that capture has commenced.

ChemiLite system 43

ADDITIVE SERIES EXPOSURE - READY TO ADDITIVE SERIES EXPOSURE - ALL THREE

START CAPTURES CAPTURES COMPLETE

As the first image is captured, it appears as the main image in the left hand Image pane
and also as a thumbnail in the left hand pane. As subsequent images in the series are
captured, these also appear as thumbnails in the Image pane, the images being stacked
vertically. The main image in the Image pane changes as each image is captured, as each
of the newly made captures is added to the main image to produce a combined or
additive image.
Once the series of captures is complete, the combined image appears as the main image
in the Image pane, along with the stack of series captured images, and also as a
thumbnail in the central Image Pool pane. When initially captured, images in the Image
Pool are unsaved and are outlined in red.

UNSAVED IMAGE POOL IMAGE

56. To save a captured image, select the image in the Image Pool and select the Save icon

.

Once saved, images in the Image Pool are outlined in green and their filename appears
below the image.

SAVED IMAGE POOL IMAGE

Images can be dismissed from the Image Pool by selecting them and then selecting the
Close button . If an image has not been saved you will see a Save

Images prompt.

ChemiLite system 44

SAVE PROMPT

(i) If multiple images are captured without any images being saved, multiple images

can be selected and saved in a single operation. Check the Multi Select Mode
checkbox in the Image Pool and select multiple images.

(ii) To save the selected images, select the Save icon .
For more information on saving refer to Common Screen Functions and Tools.

Manual Image Capture - Multiplex

57. Select the Multiplex button from the Image Capture options.

You must now define the number of images you want in your series. In the right hand
pane the Number of images selector is displayed.

NUMBER OF IMAGES SELECTION

58. Use the + / - buttons to select the number of images you want to capture, then select

the Next arrow . For this example, set to 3 by selecting the + button.

You must now define a Camera resolution for your series of images. In the right hand
pane the Binning selector is displayed.

BINNING SELECTOR

59. Select the No Binning (4.03MP) button and select the binning ratio you want to use

from the drop-down list, then select the Next arrow , or if you want to use the full
resolution just select the Next arrow .

BINNING RATIO DROP-DOWN LIST

ChemiLite system 45

60. You must now set the exposure time, and select lighting and filter options for image 1.

The display is almost the same for each image in the series and by default starts at image

1.
The Capture Interval controls are simple + / - buttons for adjusting the following time
periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .
Using the Capture Interval + / - buttons enter an interval time for the series of images.
The manual Exposure controls are simple + / - buttons for adjusting the following time
periods; hours (h) , minutes (m) , seconds (s) , and milliseconds (ms) .
To set a manual exposure time select the Manual button and use the Exposure + / ­buttons enter an exposure time for the first image. Alternatively, selecting the Auto
button after you have selected the lighting and filters allows the system to automatically
select the most appropriate exposure time for the image.
Use the Lighting and Filters functions in the right hand pane to make your lighting and
filter selections as described previously.

61. Select the Next arrow to make the settings for image 2. Select the Last arrow

to apply the settings you have entered for image 1 to all of the remaining images in
your series.

62. Enter the settings for all the images in your series.

63. Select the Next arrow .

64. The exposure/lighting/filter choices that you have selected are now displayed as a set of

Current Protocols in the right hand pane.

MULTIPLEX PROTOCOLS

65. Position the sample and improve the the preview sample image as much as possible

using the Light / Digital Zoom / Grid / Select Autoexpose Area / Lens Controls, as
described previously.

66. Select the Capture button .

The Exposure Timing icon appears at the bottom of the screen.
This changes to display the progress of the exposures as concentric coloured bars

progressing around the icon .
While the exposures are progressing, and this may take several minutes, it is possible to
navigate away from the Manual Capture screen and browse, view and edit previously
captured images.

ChemiLite system 46

The Current Protocol display changes as the series of captures is made. As a capture is
made using a protocol, the protocol box is highlighted yellow. When the capture is
complete a green tick appears inside the protocol box and the yellow highlight is
removed. The yellow highlight then appears on the next protocol box in the series, once
that capture has commenced.
As the first image is captured, it appears as the main image in the left hand Image pane,
as two vertically stacked thumbnails in the Image pane, and as a thumbnail in the central
Image Pool pane.
As subsequent images in the series are captured, the main image in the Image pane and
the top image in the thumbnail stack change, becoming combined images. Also the newly
captured image is added to the bottom of the thumbnail stack. The thumbnail stack of
images represents the combined image and the separate images that make it up. By
default the main image is the selected image from the thumbnail stack, this is indicated
by a yellow highlight around the top image in the stack.
Once the series of captures is complete, the combined image appears as the main image
in the Image pane along with the stack of series captured images, and also as a thumbnail
in the central Image Pool pane. The thumbnail stack in the Image pane will consist of one
more image than the number of images selected on the Number of images selector since
it displays the individual capture images and the combined image.

MULTIPLEX EXPOSURE - READY TO MULTIPLEX EXPOSURE - ALL TWO
START CAPTURES CAPTURES COMPLETE

In the left hand pane the main image displayed is the image in the thumbnail stack that is
selected, this is indicated by a yellow highlight around the thumbnail. By default this is
the combined image.
(i) To make one of the individual capture images in the stack the main image, select

the drawing side of the thumbnail. The yellow highlight will move from the default
thumbnail to the selected thumbnail.

MINIMISE BUTTON

(ii) To view the complete main image in the left hand pane, select the Minimise

button above the thumbnail stack.

(iii) To view the thumbnail stack once more, select the Minimise button again.

Minimise Button

ChemiLite system 47

The appearance of the individual captured images can be manipulated if desired to
improve the appearance of the overall combined image, e.g. by changing the colour of
the coloured bands to produce a greater colour contrast.
(iv) Select the right arrow at the side of the thumbnail image you want to change and

select a new colour from the drop down menu. To reject a colour and return to the
original setting select Default from the drop down menu.

When initially captured, images in the Image Pool are unsaved and are outlined in red.

UNSAVED IMAGE POOL IMAGE

67. To save a captured image, select the image in the Image Pool and select the Save icon

.

Once saved, images in the Image Pool are outlined in green and their filename appears
below the image.

SAVED IMAGE POOL IMAGE

Images can be dismissed from the Image Pool by selecting them and then selecting the
Close button . If an image has not been saved you will see a Save

prompt.

SAVE PROMPT

(i) If multiple images are captured without any images being saved, multiple images

can be selected and saved in a single operation. Check the Multi Select Mode
checkbox in the Image Pool and select multiple images.

(ii) To save the selected images, select the Save icon .
For more information on saving refer to Common Screen Functions and Tools.

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Manual Image Capture - Image Actions Following Capture

Further actions can be performed on captured images by selecting Image Action icons. The function
of these is explained in other parts of this User Guide.

IMAGE ACTION ICONS

Save icon

Print icon

Edit icon

Save Protocol

Analyse icon

View Images

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CONFIGURATIONS - SAVING, OPENING AND EDITING

Introduction

The GenePix Image Capture software can make the running of repeated workflows easier by storing
a workflow as a Configuration (or Protocol). Configurations/Protocols can be:

• Easily created

• Have a wide variety of settings

• Easily re-used

• Easily modified

Creating and Saving a Configuration

From the Standard View Home Screen

To create a Configuration for a Blot from the Standard View Home screen:

1. Work through the following process; select the Blot icon , select your

sample type, select your dye, position your sample, and capture an image.

2. Once the image has been captured the Saved Protocols pop-up appears.

SAVED PROTOCOLS POP-UP

(i) Select the Yes button.
The Save Configuration pop-up appears.

SAVE CONFIGURATION POP-UP

(ii) Follow the prompt in the pop-up and either select an existing Configuration from

those displayed (which will be overwritten by you saving your new Configuration),
or enter a name for your new Configuration in the Enter configuration name
here… box, eg ECL chemi.

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By default when you save the Configuration that you have just created, the software will
only allow you to access it. This behaviour can be modified using the two checkboxes at
the bottom left of the pop-up.

• Use the Lock checkbox to prevent adjustments being made to the

Configuration.

• Use the Make public checkbox to make the Configuration accessible to other

Users.

The new saved Configuration ECL Blot appears on the Home screens, eg on the Standard View Home
screen:

NEW CONFIGURATION - ADDED TO TOP OF LIST

By default when you save the Configuration that you have just created, the
software will only allow you to access it. This behaviour can be modified using the
two checkboxes at the bottom left of the pop-up.

• Use the Lock checkbox to prevent adjustments being made to the

Configuration.

• Use the Make public checkbox to make the Configuration accessible to other

Users.

In Auto Image Capture Mode

To create a Configuration in Auto Image Capture mode:

3. Work through the workflow for the type of test sample that you are going to image, i.e.

Step 1 - Sample selection, Step 2 - Dye selection, Step 3 - Protocol selection, Step 4 ­Sample positioning, and capture an image.

4. Once the image has been captured the Saved Protocols pop-up appears.

SAVED PROTOCOLS POP-UP

(i) Select the Yes button.
The Save Configuration pop-up appears.

ChemiLite system 51

SAVE CONFIGURATION POP-UP

(ii) Follow the prompt in the pop-up and either select an existing Configuration from

those displayed (which will be overwritten by you saving your new Configuration),
or enter a name for your new Configuration in the Enter configuration name
here… box, eg Blot Chemi.

By default when you save the Configuration that you have just created, the software will
only allow you to access it. This behaviour can be modified using the two checkboxes at
the bottom left of the pop-up.

• Use the Lock checkbox to prevent adjustments being made to the

Configuration.

• Use the Make public checkbox to make the Configuration accessible to other

Users.

(iii) Select the OK button to save the Configuration.

The new saved Configuration Blot chemi appears on the Home screens, eg on the Classic View Home
screen:

NEW CONFIGURATION - ADDED TO TOP OF LIST

In Manual Image Capture Mode

To create a Configuration in Manual Image Capture mode:

5. Work through the Manual Image Capture process described previously and capture an

image.

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6. Select the Save Protocol icon from the Image Action icons.

(i) Select the Save Protocol icon .

The Save Configuration pop-up appears.

SAVE CONFIGURATION POP-UP

(ii) Follow the prompt in the pop-up and either select an existing Configuration from

those displayed (which will be overwritten by you saving your new Configuration),
or enter a name for your new Configuration in the Enter configuration name
here… box, eg Manual Capture 1.

By default when you save the Configuration that you have just created, the software will
only allow you to access it. This behaviour can be modified using the two checkboxes at
the bottom left of the pop-up.

• Use the Lock checkbox to prevent adjustments being made to the

Configuration.

• Use the Make public checkbox to make the Configuration accessible to other

Users.

(iii) Select the OK button to save the Configuration.

The new saved Configuration Manual Capture 1 appears on the Home screens, eg on the Classic
View Home screen:

Save icon

Print icon

Edit icon

Save Protocol

Analyse icon
View Images

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NEW CONFIGURATION - ADDED TO TOP OF LIST

Using Configurations

All accessible previously created and saved Configurations/Protocols appear on the Home screens.

STANDARD VIEW HOME SCREEN CLASSIC VIEW HOME SCREEN

Opening a Configuration

System protocols are pre-installed configurations that the user can use for imaging some of
the more common applications.
To open and use a system Protocol from the Home screen:

• On the home screen select the ‘System Protocols’ tab

• Select the Protocol you wish to use

If the protocol is in Auto Image Capture mode the system will display the Sample Positioning
screen. if the protocol is in the Manual Image Capture mode the system will display the
revelant Manual Capture screen with the difined protocols displayed.

7. Position the sample and complete the the appropriate Automatic or Manual Image

Capture process as described previously.

To open and use an existing Configuration/Protocol from the Home screen:

8. On the Home screen select the Configuration you want to use.

On the Standard View Home screen you can sort and search saved configurations:

Sort By options are: Last Used, Title, Author, Type/Dye.
Search is by entering text in the Search title here... field. There is also a Clear button to

clear entered search text.
The software will configure your ChemiLite Instrument based on the data in the
Configuration file and will take you to the following point in the image capture process:
If the Configuration is in Auto Image Capture mode the system will display the Sample
Positioning screen, as shown below:

ChemiLite system 54

AUTOMATIC CAPTURE SAMPLE POSITIONING

If the Configuration is in Manual Image Capture mode the system will display the relevant
Manual Capture screen with the defined protocols displayed, typically as shown below:

TYPICAL MANUAL CAPTURE SAMPLE POSITIONING

9. Position the sample and complete the appropriate Automatic or Manual Image Capture

process as described previously.

Deleting a Configuration

To delete a Configuration from the Home screen:

10. Select the Delete Configuration button in the Configuration that you want to

delete.

DELETE CONFIGURATION POP-UP

11. In the Delete Configuration pop-up select the Yes button.

12. The selected Configuration is deleted and is no longer visible on the Home screen.

Editing a Saved Configuration

All accessible previously created and saved Configurations/Protocols appear on the Home screen.

ChemiLite system 55

STANDARD VIEW HOME SCREEN CLASSIC VIEW HOME SCREEN

To edit a previously saved Configuration, first open the Configuration as described previously. Then
use the normal controls/actions available on the Auto Image Capture Sample Positioning screen or
Manual Capture screen to change the settings.

• For Auto Image Capture Sample Positioning screen refer to Automatic Image Capture

Mode.

• For Manual Capture screen refer to Manual Image Capture Mode.

If you make changes to an existing Configuration and want to save the new Configuration as a new
Configuration, refer to Creating and Saving a Configuration.

ChemiLite system 56

IMAGE FUNCTIONS

Load Images Screen

Previously saved images can be located and browsed through from the Home screen.

STANDARD VIEW HOME SCREEN CLASSIC VIEW HOME SCREEN

Select the Load Images icon on the Standard View Home screen or the Load Images icon

on the Classic View Home screen. This displays the Load Images screen.

LOAD IMAGES SCREEN

• By default the software navigates to the default save location and displays thumbnail size

images of all the saved images at that location. The software also maps the current drives
that it can detect and connect to and displays this in the standard Windows format in the
left hand pane. Images saved in other locations can be displayed by navigating to their
location using the tree structure displayed in the left hand pane.

• Recovered images at the default save location are displayed in the central pane. Also

displayed at the top of the central pane is the drive/folder path.

• Images displayed in the central pane of the Load Images screen can be sorted by two

parameters; Sort by Name or Sort by Date. Select one of the two icons at the top of the
central image pane.

SORT ICONS

• Sort by Name sorts the files in the displayed drive/folder alphabetically with 'A' at

the top.

ChemiLite system 57

• Sort by Date sorts the files in the displayed drive/folder by date with the most

recent at the top.

• Series images can be identified by a pattern of overlapping images in the top right hand

corner of the thumbnail image, as shown below:

SERIES IMAGE THUMBNAIL

• If more images than can be displayed are available then a scroll bar appears, scrolling

allows you to display the initially non-displayed images.

• Selecting an image or images in the central pane adds the selected image or images to the

Selected Images pane. At the same time the image(s) selected in the central pane turn
green, as shown below.

SELECTED IMAGES

• To de-select an image, select the image again in the central pane or select the red Dismiss

icon in the corner of the image in the Selected Images pane.

Image Actions from Load Images Screen

Once you have located your image(s) using the Load Images screen there are two image actions
available; View Images and Edit. The two Image Action icons are displayed at the bottom of the
Load Images screen.

• Initially these icons are initially greyed-out (unavailable), only becoming active once an

image has been selected.

• Selecting the View Images icon opens the View Images screen with the image(s) selected

on the Load Images screen displayed in the view pane.

• Selecting the Edit icon opens the Image Edit screen with the image(s) selected on the Load

Images screen displayed in the Selected Images pane.

Edit icon

View Images

ChemiLite system 58

• For the actions that can be performed using these screens refer to View Images Screen

and Image Edit Screen sections of this Guide.

View Images Screen

The View Images screen is used to view and compare captured images. Images can be saved or
unsaved. The View Images screen can be accessed as follows:

STANDARD VIEW HOME SCREEN CLASSIC VIEW HOME SCREEN

• The View Images function is only available when captures have been made during the

current GenePix session and images have been saved, are unsaved, or when previously
saved images have been selected using the Load Images function.

• From the Standard View Home screen - by selecting the View Images icon .

• From the Classic View Home screen - by selecting the View Images icon .

• The View Images screen can also be accessed from any other screen displaying the View

Images icon in the Image Action icons.

Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

Save icon

Print icon

Edit icon

Save Protocol

Analyse icon
View Images

ChemiLite system 59

VIEW IMAGES SCREEN - SINGLE VIEW IMAGES SCREEN - SINGLE

IMAGES ONLY DISPLAYED AND MULTIPLEXED IMAGES DISPLAYED

View Images Screen - Single Images

Single image captures selected for viewing are all displayed in a division of the main left hand pane
labelled Single Images.

View Images Screen - Multiplexed Images

Multiple image capture files, e.g. multiplexed images, selected for viewing are each displayed in a
division of the main left hand pane labelled with name given to the multiplexed image file, e.g.
marker and chemi image.sgd. The multiplexed image plus all of its constituent separate image
captures, if saved, are displayed.

View Images Screen - Image Display Options

The View Images screen or the images displayed on it can be altered in several ways using the
following options:

• Zoom

• Change Layout

• Manage Images

• Hide/Show

ChemiLite system 60

ZOOM
Images are displayed as thumbnails on the View Images screen. The size of the images
can be changed by adjusting the Zoom Slider control.

ZOOM SLIDER

CHANGE LAYOUT
Two options are available using the Change Layout controls.

CHANGE LAYOUT CONTROLS

By default the View Images screen opens with the File Display button selected and
the Compare button greyed-out (unavailable). The Compare button becomes active

once files are selected in the View Images main pane.
Up to four images can be selected and compared. Selecting the Compare button

displays the Compare Images version of the View Images screen.

VIEW IMAGES - COMPARE IMAGES SCREEN

The left hand pane contains the following controls for each individual image:

• The Gamma slider changes the tone of the overall image. With reference to the

histogram mentioned previously, the Gamma function changes the relative
brightness of the recorded midrange tones by shifting them either towards the
dark end or the white end of the graph, without changing the extreme dark or
extreme white values. This gives the recorded image an overall darker or lighter
appearance.

GAMMA SLIDER

• Scroll bars allow you to view the entire area of an image. A horizontal scroll bar

appears when the Zoom function is used on an image.

The right hand pane contains the following controls:

• The Change Layout controls.

ChemiLite system 61

• The Link controls.

TWO IMAGES - LINKED

TWO IMAGES - UNLINKED

THREE IMAGES

The default setting is for images being compared to be unlinked. The numbers
in the Link boxes correspond to the positions of the images in the left hand
pane.
With the images unlinked, adjustments made using the Scroll bars or the Zoom
and Range controls are applied only to the selected image. The selected image
is indicated in the Link boxes by the selected image number being outlined red.

Images can be linked by selecting the Link button. With the images linked,
adjustments made using the Scroll bars or the Zoom and Range controls are
applied equally to all of the linked images.
Selecting one of the images in the left hand pane or one of the numbered Link
boxes unlinks the images.
Unlinked images can be zoomed into and panned around by positioning the
cursor over the selected image and when the cursor changes hold and drag to
move the image around in its viewing window.

A Histogram button is displayed for each image, below the vertical Scroll
bar. Selecting this displays a histogram or graphical representation of the
distribution of grey scales recorded by the camera sensor; with black to the
extreme left, white to the extreme right.

HISTOGRAM DISPLAY

The Histogram button turns red to indicate that the function has been selected.
Selecting the button again cancels the Histogram function.
The histogram is a graph showing the number of pixels in the image at each
different intensity value found in that image. For a 16-bit image there are a
possible 65535 different intensities so the histogram will graphically display 256
numbers showing the distribution of pixels amongst those grayscale values. If
the graph is bunched up to the left it indicates that not many grayscale levels
have been captured and the red lines on the histogram graph may need to be
adjusted to see bands. If the graph reaches to the far right (65535 grayscales)
this indicates that the image may be saturated.
The image Key.

ChemiLite system 62

IMAGE KEY

The Key displays the filenames of the displayed images. As with the Link
controls, the Key numbers correspond to the image positions in the left hand
pane.

• The Zoom and Range controls.

ZOOM AND RANGE CONTROLS

The Digital Zoom slider allows you to zoom in or out of the displayed image.
Dragging the slider towards the + sign zooms in, dragging the slider towards the

- sign zooms out.
Contrast is a measure of how bright highlights are in an image. Brightness is a
measure of how bright shadows are in an image. Use the Contrast slider to
control how bright the lightest objects in an image are displayed. Use the
Brightness slider to control how bright dark objects in an image are displayed.

Selecting the File Display button when on the View Images - Compare Images screen
takes you back to the standard View Images screen.
MANAGE IMAGES
Two options are available using the Manage Images controls.

MANAGE IMAGES CONTROLS

Selecting the Close button closes only the selected image file(s).
Selecting the Close All button closes all image files.
HIDE/SHOW

Selecting the arrow (inactive) (active)next to an
image title on the View screen hides the image(s) associated with that title, i.e. the
thumbnails are not displayed but the image title is still displayed. This provides more area
for the other images to be displayed in. The up arrow changes to a down arrow.
Hidden images can be displayed again by selecting the down arrow.

Digital Zoom slider

Contrast / Brightness
sliders

ChemiLite system 63

View Images Screen - Combining Single Images into a New Multiplexed Image

More than one single image can be combined to produce a new mutliplexed image using the Create
Multiplexed Image icon which is displayed with the Image Action icons at the bottom right of

the screen. The Multiplexed Image icon only becomes active once files are selected in the View
Images main pane.
Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected

To create a new multiplexed image:

13. In the Single Images display, select the images that you want to combine. This function

14. can also be utilised from the Change Layout - Compare function, in which case the

images are already selected, i.e. the images you have selected to compare.

CREATE MULTIPLEXED IMAGE - IMAGES SELECTED

15. Select the Create Multiplexed Image button . This displays the Create Multiplexed

Image pop-up. This shows what the multiplexed image will look like.

Options are available using the Set Type of Composite Image buttons; Create
Monochrome Image.

MULTIPLEXED IMAGE - MONOCHROME IMAGE

Create Multiplexed

Image icon

Save icon

Print icon

Analyse icon
Edit icon

ChemiLite system 64

16. Select the OK button to create the multiplexed image or select the Cancel button to

cancel the multiplexed image creation. The multiplexed image created is displayed on
the View Images screen.

MULTIPLEXED IMAGE CREATED

The newly created multiplexed image now has its own row in the main left hand pane,
the multiplexed image plus all of the selected constituent images are displayed.

Image Edit Screen

The Image Edit screen provides a wide variety of image manipulation options. The Image Edit screen
can be accessed from other screens by selecting the Edit icon from the Image Action icons.

Image Edit Screen - Image Editing Main Options

The Image Edit screen provides a variety of image editing options grouped into four main options:

• General

• Annotate

• Enhance

• 3D View

By default the Image Edit screen opens in General mode.
Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

Save icon

Print icon

Edit icon

Save Protocol

Analyse icon
View Images

ChemiLite system 65

IMAGE EDIT SCREEN - GENERAL MODE

The other main option modes are selected using the buttons in the top left hand pane.

IMAGE EDIT SCREEN - MAIN OPTION SELECTION BUTTONS

Image Edit Screen - General Option

The General option provides a range of basic image manipulation tools. The lower left hand pane of
the General screen provides the following controls/functions:

• Image Source

• Rotation

• Copy Image

• Other

Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

GENERAL CONTROLS/FUNCTIONS

General button

Enhance button

Annotate button

3D View button

ChemiLite system 66

IMAGE SOURCE
As you make changes to an image file the GenePix Image Capture software makes a copy
of the file to which the changes are made. There are therefore two versions of the image
file; the original unchanged image file, and the changed image file. The Image Source
function allows you to view either of these two files. To view the unchanged file select

the View Original Image button . To view the changed file select the View Processed
Image button .

ROTATION
Displayed images can be rotated freely by selecting the Allow Rotation button .

Once the image has been rotated the new image orientation can be fixed by selecting the
Allow Rotation button a second time. Image orientation can be reset to its original

position by selecting the Reset Rotation button .

COPY IMAGE
An image can be copied to the Windows Clipboard by selecting the Copy button

. This allows you to paste the image into another package.

OTHER
The Other functions provided are Saturation and Colour.
The Saturation function can be used to check if areas of the image are going to be over­exposed; over-exposed white bands will be highlighted in red on the image, over-exposed
black bands will be highlighted in blue on the image. This function is useful if the Select
AutoExpose Area function has been used. Please note that saturated bands are not

quantifiable. To use this function select the Saturation button .
The Colour function can be used to improve the appearance of an image by changing the
colour of the coloured bands to produce a greater colour contrast, this can make seeing

faint bands more visible. Select the Default button and select a new colour
from the drop-down menu. To reject a colour and return to the original setting select
Default from the drop down menu.

ChemiLite system 67

OTHER FUNCTIONS - DEFAULT COLOUR MENU

The Default function can also be used to applied a colour wash that emulates different
dyes.

• Select the green colour wash to emulate a SYBR Green DNA gel.

• Select the yellow colour wash to emulate a SYBR Gold DNA gel.

• The orange-blue-red colour wash makes a protein gel appear silver, Coomassie

blue and SYPRO red stained.

If the image being edited is a multiplex image, the colour change is applied to all of the
individual exposure captures but not the composite image. To apply the colour change to
the composite image as well check the Use in Composite checkbox.

Image Edit Screen - Annotate Option

The Annotate option provides a means of adding both textual and graphical annotations to an
image. The lower left hand pane of the Annotate screen provides the following controls/functions:

• Image Source

• Annotation Tools

• Copy and Paste

• Edit

Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

ChemiLite system 68

ANNOTATE CONTROLS/FUNCTIONS

IMAGE SOURCE
This function is as described previously in Image Edit Screen - General Option.
ANNOTATION TOOLS
The following image annotation tools are available:

Select tool
Pan tool
Text tool
Fill/No Fill tool
Rectangle tool
Ellipse tool

Polygon tool
Line tool
Arrow tool
Select Colour tool
Select Line Style tool

The Select tool enables you to select text or objects that you have added to an image.
The Pan tool enables you to pan around an image if you have enlarged it so that not all of
the image is viewable in the central image viewing pane. Select the tool icon and then
click and drag or touch and drag to move the image around.
The Text tool enables you to add text in text boxes to your image. Select the tool and
position the cursor roughly where want the annotation to appear and left click/tap, and
then start typing. Using the Select tool you can then position the text box exactly where
you want it, and resize the text box horizontally and vertically. Double clicking/tapping
the text enables you to change the text and the text parameters using the pop-up
dialogue boxes shown below.

ChemiLite system 69

TEXT POP-UP 1 TEXT POP-UP 2

The font selection pop-up dialogue box is opened by selecting the Select Font
button on the text dialogue box.
The parameters you can change are:

• The text itself. The text previously typed in the text box appears in the Text box.

This text can be edited directly.

• Text direction (horizontal or vertical)

• Font

• Size

• Style (normal/italic/oblique) and (normal/bold)

The Fill/No Fill tool enables you to fill shapes that you have added to the image. Select
the shape, then select a colour for the fill using the Select Colour tool.
The Rectangle tool enables you to add 4-sided shapes to an image. Draw the shape, then
select it using the Select tool, and the shape can be positioned by dragging and resized
using the visible 'handles'. A rectangle can be filled using the Fill/No Fill and Select Colour
tools. The outline of a rectangle can be coloured and the style of the line can be changed
using the Select Colour and Select Line Style tools.
The Ellipse tool enables you to add ellipses (circles) to an image. Draw the shape, then
select it using the Select tool, and the shape can be positioned by dragging and resized
using the visible 'handles'. An ellipse can be filled using the Fill/No Fill and Select Colour
tools. The outline of an ellipse can be coloured and the style of the line can be changed
using the Select Colour and Select Line Style tools.
The Polygon tool enables you to add freehand shapes to an image. Draw the shape, then
right click/double tap to stop drawing. Using the Select tool the shape can be 're-shaped'
using the visible 'handles'. Shapes can be filled using the Fill/No Fill and Select Colour
tools. The outline of the shape can be coloured and the style of the line can be changed
using the Select Colour and Select Line Style tools.
The Line tool enables you to draw straight lines, at any angle and of any length, on an
image. Draw the line, then select it using the Select tool, and the line can be positioned
by dragging and resized using the visible 'handles'. The line can be coloured and the style
of the line can be changed using the Select Colour and Select Line Style tools.
The Arrow tool enables you to draw a straight line with an arrowhead at one end, at any
angle and of any length, on an image. Draw the arrow, then select it using the Select tool,
and the arrow can be positioned by dragging and resized using the visible 'handles'. The
arrow can be coloured and the style of the arrow can be changed using the Select Colour
and Select Line Style tools.
The Select Colour and Select Line Style tools are used as described above.

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COPY AND PASTE
The Copy and Paste function enables you to copy and paste annotations created as
described above. If the paste function is used on the same image, then the pasted
annotation appears directly transposed over the top of the source annotation. The pasted
annotation can then be dragged to where it is required and modified/changed as
described previously. A copied annotation can also be pasted into a different image,
where it can be modified/changed as described previously.
To copy an annotation of any type, first select the annotation, then select the Copy

Selected Annotations button . To paste the copied annotation, first select the
destination image, then select the Paste Annotations button .

EDIT
The Edit function enables you to align and delete annotations created as described
above. The align and delete functions only apply to annotations which have been
selected.
To align annotations, first select the annotations (more than one selection is made by
holding down the Ctrl key on the PC keyboard), select the Align Selected Annotations

button , then from the drop-down menu select the alignment direction.

ANNOTATION ALIGNMENT DROP-DOWN MENU

To delete annotations, first select the annotations, then select the Delete Selected

Annotations button .

Note: The Delete key on the PC keyboard can also be used to delete selected annotations.

Image Edit Screen - Enhance Option

The lower left hand pane of the Enhance screen provides the following controls/functions:

• Image Source

• Enhancement Tools

• Resolution

Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

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ENHANCE OPTION TOOLS/CONTROLS/FUNCTIONS

IMAGE SOURCE
This function is as described previously in Image Edit Screen - General Option.
ENHANCEMENT TOOLS
The following image enhancement tools are available:

Sharpen tool
Smooth tool
Invert tool
Speckle Correct tool

Flip Vertical tool
Flip Horizontal tool
Define area to be cropped

tool
Crop area tool

The Sharpen tool applies a sharpening filter to the selected image. The sharpening filter
should make the edges of bands more pronounced. However, there may also be an
increase in graininess.
The Smooth tool applies a smoothing filter to the selected image. This can be useful if the
image has specks of dust or bubbles present. However, there may also be a reduction in
band sharpness.
The Invert tool reverses the image, i.e. white appears black, black appears white. This can
be useful when trying to view very faint bands on an image.
The Speckle Correct tool can be used to remove white speckles or 'hot pixels' from an
image.
The Flip Vertical tool mirrors the selected image in the vertical plane. This can be useful if
the sample has been placed in the Darkroom the wrong way round.
The Flip Horizontal tool mirrors the selected image in the horizontal plane. This can be
useful if the sample has been placed in the Darkroom the wrong way round.
The Define area to be cropped tool enables you to select an area of the selected image
so that you can isolate the chosen portion of the image from the rest of the image in
order to view that portion more closely. Select the Define area to be cropped icon and

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draw a rectangle that covers the area you want to examine. The rectangle is outlined in
pink and filled with a transparent pink fill. Select the fill area and the selection rectangle
can be accurately positioned by dragging and resized using the visible 'handles'. This
enables you to finely control the selected area of interest. Selecting the Define area to be
cropped tool once more cancels the selection rectangle just made, but leaves the cursor
in selection mode, allowing you to restart the selection process. Selecting the Define area
to be cropped tool twice more cancels the selection rectangle just made and also cancels
the selection function.
Once you have defined the area you want to examine more closely using the Define area
to be cropped tool, select the Crop area tool to perform the crop function. The defined
area is 'cut out' of the image, the rest of the image is discarded, and the cropped or 'cut
out' selection is enlarged to the full viewing area.

RESOLUTION
The Resolution tool can be used to change the resolution of the selected image. When
the Enhancement Tools option is selected the system displays the current/default
resolution of the selected image in the Resolution box.
To change the resolution of the current displayed image select the Resolution tool and
select a new resolution from the drop-down menu.

RESOLUTION MENU

The options displayed in the Resolution drop-down menu depend on the resolution that
the image is captured at, an example is shown below:

Default image resolution

New selection

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RESOLUTION MENU

Note: If you use the Resolution option, you can make and undo one change of image resolution.

Having made a change and used the Undo button to revert to the original resolution, the
Resolution option is greyed out and is unavailable. To try another resolution you must
dismiss the image and reload it from the Load Images screen.

Image Edit Screen - General / Annotate / Enhance Options Common Controls

The central image viewing pane of the General, Annotate and Enhance options of the Image Edit
Screen provide a common set of image controls.
Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

IMAGE SLIDER CONTROLS

The following controls are available to adjust the display of a captured image.

IMAGE SLIDER CONTROLS

The Zoom slider allows you to zoom in or out of the displayed image. Dragging the slider
towards the + sign zooms in, dragging the slider towards the - sign zooms out.

Zoom (digital) slider

Invert (Image Inversion)

button

Contrast / Brightness
sliders

Gamma slider

Auto Levels (Reset)

button

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The Gamma slider changes the tone of the overall image. With reference to the
histogram mentioned previously, the Gamma function changes the relative brightness of
the recorded midrange tones by shifting them either towards the dark end or the white
end of the graph, without changing the extreme dark or extreme white values. This gives
the recorded image an overall darker or lighter appearance.
Contrast is a measure of how bright highlights are in an image. Brightness is a measure of
how bright shadows are in an image. Use the Contrast slider to control how bright the
lightest objects in an image are displayed. Use the Brightness slider to control how bright
dark objects in an image are displayed.
If you make changes using the sliders you can undo the changes by selecting the Auto
Levels icon.
Use the Invert button to invert the image, i.e. white appears black, black appears white.
This can help when making changes with the slider controls. Selecting the Invert button a
second time changes the image back to how it was originally.

CAPTURED IMAGE INFORMATION

Select the Image Information icon . This displays a pop-up window displaying
captured image information. The information displayed is as follows:

• Dye

• Image capture date / time

• Filter

• Light

• Exposure time

• Iris f number

• Image size

• Range (range of grey scales captured)

IMAGE INFORMATION POP-UP WINDOW

The Image Information icon turns red. Selecting the Image Information icon a second
time closes the pop-up window.

IMAGE HISTOGRAM

Select the Histogram button . This displays a histogram or graphical representation of
the distribution of grey scales recorded by the camera sensor; with black to the extreme
left, white to the extreme right.

HISTOGRAM DISPLAY

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The Histogram button turns red to indicate that the function has been selected. Selecting
the button again cancels the Histogram function.
The histogram is a graph showing the number of pixels in the image at each different
intensity value found in that image. For a 16-bit image there are a possible 65535
different intensities so the histogram will graphically display 256 numbers showing the
distribution of pixels amongst those grayscale values. If the graph is bunched up to the
left it indicates that not many grayscale levels have been captured and the red lines on
the histogram graph may need to be adjusted to see bands. If the graph reaches to the
far right (65535 grayscales) this indicates that the image may be saturated.

Image Edit Screen - 3D View Option

The 3D View screen presents the selected image in three-dimensional form, revealing gel thickness,
and with the peaks representing (and being proportional to) the distribution of grey scales recorded
by the camera sensor.

IMAGE EDIT SCREEN - 3D VIEW OPTION

The lower left hand pane of the 3D View version of the screen provides the following
controls/functions:

• Image Source

• Other

• Gamma

Note: Selected function buttons turn red. They stay red and the function remains active until the

function button is re-selected.

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3D VIEW OPTION CONTROLS/FUNCTIONS

IMAGE SOURCE
This function is as described previously in Image Edit Screen - General Option.
OTHER
The Saturation and Default functions are as described previously in Image Edit Screen -
General Option.

GAMMA
The Gamma slider changes the tone of the overall image. With reference to the
histogram mentioned previously, the Gamma function changes the relative brightness of
the recorded midrange tones by shifting them either towards the dark end or the white
end of the graph, without changing the extreme dark or extreme white values. This gives
the recorded image an overall darker or lighter appearance.

IMAGE EDITING FUNCTIONS
The central image viewing pane of the 3D View option of the Image Edit Screen provides
the following functions for altering the view of the displayed image:

Pan Up control
Reset Pan button
Pan Down control
Pan Left control
Pan Right control

Rotate Right control
Rotate Forward control
Rotate Anti-clockwise control
Reset Rotation button
Rotate Clockwise control
Rotate Backward control
Rotate Left control

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Selecting an action by clicking or tapping on an icon once moves the image in the relevant
direction by a programmed amount or step. The image can be moved in the relevant
direction continuously by 'holding down' the icon.
Selecting either of the Reset icons resets the image back to its original position.
The Zoom control, located in the upper left hand corner of the viewing pane,
magnifies/reduces the size of the image within the viewing pane.

ZOOM SLIDER

The Scale control, located in the lower left hand corner of the viewing pane,
increases/decreases the vertical axis used to display the distribution of grey scales
information.

SCALE SLIDER

Image Edit Screen - All Options Common Controls

ACTION ICONS
All four of the Image Edit main option screens provide the same Action icons across the
bottom of the screen.
The left hand group of Action icons is as follows:

• Selecting the Load Images icon takes you back to the Browse Images screen,

allowing you to search for images.

• Selecting the View Images icon takes you back to the View Images screen,

allowing you to view and compare captured images.

•

Home icon

Load Images icon

View Images

icon

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The right hand group of Action icons is as follows:

•

• The Undo last change icon only becomes active once you have performed an

action on an image, e.g. added an annotation. Selecting the active Undo last
change icon takes you back to the position you were in prior to your last action,

e.g. the annotation you just added is removed.

• The Save/Load Annotations icon saves any annotations that you have made on

an image into a separate annotation file. This separate annotation file can be
opened and the annotations applied to more than one image. This is useful when
capturing a series of similar images which need to be annotated identically for
comparison purposes.

Selecting the Save/Load Annotations icon calls up a Save/Load Annotations
dilaogue box which you use to either save your annotations to a particular file, or
load a previously saved set of annotations.

SAVE / LOAD ANNOTATIONS DIALOGUE BOXES

RIGHT HAND PANE
The right hand pane of all four of the Image Edit main option screens provides the same
information.
The right hand pane contains the image pool of images selected for editing. Each image is
displayed in the image pool as a thumbnail. If more than one image thumbnail is
displayed, the currently displayed image is highlighted yellow. To change the image
displayed, select the image in the right hand pane.

Undo last change icon

Save/Load

Annotations icon

Save icon

Analyse icon
Print icon

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At the bottom of the right hand pane there are two buttons for dismissing images from
the image pool, as follows:

REMOVE / REMOVE ALL BUTTONS

Selecting the Remove button dismisses the currently selected image from
the image pool.

Selecting the Remove All button dismisses all images from the image
pool.

Common Screen Functions and Tools

The following general Action icons are available when using the GenePix Image Capture software:

The Home icon when selected takes you back to the GenePix Image Capture Home
screen.

The Save icon is used to save captured/modified images.
The Print icon is used to print an image.
The Analyse icon is used to export an image to the GeneQUANT Software package for

further analysis.

Action icons can only be selected once they are active, i.e. they are coloured in.

Saving Images

Any time that an image is captured or in some way changed, e.g. annotated, colour washed for
increased contrast, etc, and the Save icon is active, using the GenePix Image Capture software you
have the opportunity to save the image.

Select the Save icon from the bottom of the screen. This displays the standard Windows™ Save
As screen.

SAVE AS SCREEN

• By default the software navigates to the default or last used save location.

Structured Data **.sgd

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• A different save location can be specified using the drives display down the left hand side

and/or the Save in: field.

• You can specifiy a name for your file using the File name: field. The GenePix Image Capture

software will give the image a default name of imageX, where X is a sequential number
starting at 1.

• You can specify a file type for your file using the Save as type: field. The GenePix software

defaults to the Structured Data format file ( *.sgd ). Other file types available are:

SAVE FILE FORMAT TYPES

Select file destination, filename and file type, then select the Save button.

Note: For all file types the image will be saved as captured. This will save the image as originally
captured- any brightness and contrast adjustments that have been made to the image since capture
will not be saved. To save any changes to your image in Tiff, jpeg and bmp formats please use export
to publication button.

SAVING ADDITIVE SERIES IMAGES

If you have captured a set of images using the Manual Capture - Additive Series function, the Save
function changes. You can select from the following options:

OPTION 1 Save the additive image plus all constituent images, as a single file.
Select the Save icon , the following message pop-up will appear:

SAVING ADDITIVE SERIES CAPTURE POP-UP

Select the Together button, you get the Save As screen.
Select file save location, name and type as detailed previously, or accept the system
defaults.
The system saves all of the images in the series; each of the individual captures plus the
additive image, in a single .sgd file.
OPTION 2 Save all constituent captured images, as discrete files.

Select the Save icon , the following message pop-up will appear:

SAVING ADDITIVE SERIES CAPTURE POP-UP 1

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Select the Individually button, the following message pop-up will appear:

SAVING ADDITIVE SERIES CAPTURE POP-UP 2

Select the All button to continue, you get a copy of the Save As screen for each of the
captured images.
Select file save location, name and type as detailed previously for each image file. Select
the Save button.
Once each capture has been saved, the following message pop-up will appear:

SAVING DISPLAYED IMAGE POP-UP

Make your choice based on the message and how you intend to use the saved image.
Select the As displayed button to save the image as it appears on the screen - complete
with any brightness and contrast adjustments that have been made to the image.
Select the As captured button to save the image as it was originally captured - any
brightness and contrast adjustments that have been made to the image since capture will
not be saved.

Note: This process saves all of the captured images, but only the captured images, it does not

save the additive image.

OPTION 3 Save selected constituent captured images, as discrete files.
Select the image you want to save.

Select the Save icon , the following message pop-up will appear:

SAVING ADDITIVE SERIES CAPTURE POP-UP 1

Select the Individually button, the following message pop-up will appear:

SAVING ADDITIVE SERIES CAPTURE POP-UP 2

Select the Selected button to continue, you get the Save As screen.
Select file save location, name and type as detailed previously for the image file. Select the
Save button.

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Once the image has been saved, the following message pop-up will appear:

SAVING DISPLAYED IMAGE POP-UP

Make your choice based on the message and how you intend to use the saved image.
Select the As displayed button to save the image as it appears on the screen - complete
with any brightness and contrast adjustments that have been made to the image.
Select the As captured button to save the image as it was originally captured - any
brightness and contrast adjustments that have been made to the image since capture will
not be saved.

Note: This process saves only a single selected captured image, it does not save the additive

image.

Once you have saved your selected image, you then have the option of choosing and
saving another image from the series. In this way you can choose to save as many or as few
images from a series as you want.

SAVING MULTIPLEXED IMAGES

If you have captured or created a multiplexed image the Save function changes. You can select from
the following options:

OPTION 1 Save the combined image plus all constituent images, as a single file.
Select the combined image.

Select the Save icon , the following message pop-up will appear:

SAVING MULTIPLEX CAPTURE POP-UP

Select the Together button, you get the Save As screen.
Select file save location, name and type as detailed previously.
OPTION 2 Save the combined image plus all constituent images, as discrete files.
Select the combined image.

Select the Save icon , the following message pop-up will appear:

SAVING MULTIPLEX CAPTURE POP-UP

Select the Individually button, you get a non-compliance message pop-up:

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SAVING NON-GLP IMAGE! POP-UP

Note: Saving the constituent image files of a multiplexed image as discrete files is considered to

be non-GLP laboratory practice as it means that an individual file could be deleted and the
full audit trail of the multiplexed image would therefore be lost.

Select the Yes button to continue, you get a copy of the Save As screen for each of the
images (the combined image plus each of the individual constituent images).
Select file save location, name and type as detailed previously for each image file.
OPTION 3 Save selected image(s) in any selected combination.
Select the images you want to save.

Select the Save icon , you get a copy of the Save As screen for each of the selected
images.
Select file save location, name and type as detailed previously for each image file.
OPTION 4 Saving an edited multiplexed image.
If you are in Image Edit mode and you make a change to a multiplexed image and then

select the Save icon , the following message pop-up will appear:

SAVING MULTIPLEX CAPTURE POP-UP

Select the Together button, you get the Save As screen.
Select file save location, name and type as detailed previously.
Select the Individually button, the following message pop-up will appear:

EDITED IMAGE SAVING MULTIPLEX CAPTURE POP-UP

Select the Selected button you get a copy of the Save As screen for each of the selected
images.
Select file save location, name and type as detailed previously for each image file.
Select the All button, you get a non-compliance message pop-up:

SAVING NON-GLP IMAGE! POP-UP

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Note: Saving the constituent image files of a multiplexed image as discrete files is considered to

be non-GLP laboratory practice as it means that an individual file could be deleted and the
full audit trail of the multiplexed image would therefore be lost.

Select the Yes button to continue, you get a copy of the Save As screen for each of the
images (the combined image plus each of the individual constituent images).
Select file save location, name and type as detailed previously for each image file.

Export for publication

Export for publication feature in GenePIX allows the user to adjust the resolution, contrast
and brightness of an image ensuring that it is of publication quality. The user can also select to save
the image in the following file formats Tiff, Bmp and Jpg.

EXPORT FOR PUBLICATION-POP_UP

Printing

Any time that an image is captured, viewed, or in some way changed, e.g. annotated, colour washed
for increased contrast, etc, and the Print icon is active, using the GenePix Image Capture software
you have the opportunity to print the image.
Note: The Print dialogue box will change depending on the version of Windows™ that you are

using.

ChemiLite system 85

TYPICAL PRINT DIALOGUE BOX

Select your printer in the Printer box, Name: field.
Select the range of pages you want to print in the Print range box.
Select the printer settings you want to use by selecting the Properties... button.
Select the number of copies you want to print in the Copies box, Number of copies: field.

What is printed depends on the selections made on the User Preferences screen, as follows:

• Full Report - checking this checkbox sets the Instrument to generate a Full Report for each

test. The Full Report content can be controlled using the additional checkboxes, check to
include the feature:

• Image

• File Description

• Capture Properties

• Basic Report - checking this checkbox sets the Instrument to generate a Basic Report for

each test. Additional features are:

• Basic Report Image Only - if the checkbox is checked, the printed report contains

only the captured image for the test. If not checked, the report contains the
image plus some basic information, e.g. filename / username / date / time /
sample / filter, etc.

• Preview Before Printing - if the checkbox is checked, the screen displays a

preview of the report before it is printed. If not checked, the report is printed
without a preview being displayed. If this option is checked when you select more
than one image and then select print you have to go through a print preview
stage for each image.

The print function is actioned by selecting the Print icon from the bottom of the screen.
What is printed also depends on the following:

• Printing from the View Images screen.

• Printing from the Image Edit screen.

• Printing a single image capture.

• Printing an additive series capture.

• Printing a multiplex capture.

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SINGLE IMAGE CAPTURE

From View Images, single images can be selected and printed individually or multiple single
images can be selected and printed collectively.
From Image Edit, single images can be selected and printed individually.

ADDITIVE SERIES CAPTURES

OPTION 1
From View Images, to print the constituent images:
Select the additive image.

Select the Print icon . The Printing series capture dialogue box is displayed.

PRINTING SERIES CAPTURE DIALOGUE BOX

Select the All button. All of the constituent image captures print. The additive image does
not print.
OPTION 2
From View Images, to print the additive image:
Select the additive image.

Select the Print icon . The Printing series capture dialogue box is displayed.

PRINTING SERIES CAPTURE DIALOGUE BOX

Select the Display button. The additive image prints (blank sheet).
OPTION 3
From View Images, to print a single constituent image:
Select the constituent image.

Select the Print icon .
The selected constituent image prints.
OPTION 4
From View Images, to print more than one constituent image:
Select the constituent images.

Select the Print icon .
The selected constituent images print.
OPTION 5
From Image Edit, to print all of the constituent images:
Select any one of the constituent image thumbnails.

Select the Print icon . The Printing series capture dialogue box is displayed.

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PRINTING SERIES CAPTURE DIALOGUE BOX

Select the All button. All of the constituent image captures print. The additive image does
not print.
OPTION 6
From Image Edit, to print any one constituent image:
Select one of the constituent image thumbnails.

Select the Print icon . The Printing series capture dialogue box is displayed.

PRINTING SERIES CAPTURE DIALOGUE BOX

Select the Display button. The selected constituent image prints.

MULTIPLEX CAPTURES

OPTION 1
From View Images, to print the multiplexed image plus the constituent images:
Select the multiplex image.

Select the Print icon . The Printing multiplex dialogue box is displayed.

PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the All button. The multiplexed image (blank page) plus all of the constituent images
print.
OPTION 2
From View Images, select the additive image:

Select the Print icon . The Printing multiplex dialogue box is displayed.

PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the Display button. The currently displayed image prints.
OPTION 3
From View Images, to print a single constituent image:
Select the constituent image.

Select the Print icon .

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The selected constituent image prints.
OPTION 4
From View Images, to print more than one constituent image:
Select the constituent images.

Select the Print icon .
The selected constituent images print.
OPTION 5
From Image Edit, to print the multiplexed image plus the constituent images:
Select the multiplexed image from the thumbnails.

Select the Print icon . The Printing multiplex dialogue box is displayed.

PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the All button. The multiplexed image plus all of the constituent images print.
OPTION 6
From Image Edit, to print the multiplexed image:
Select the multiplexed image from the thumbnails.

Select the Print icon . The Printing multiplex dialogue box is displayed.

PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the Display button. The selected multiplexed image prints.
OPTION 7
From Image Edit, to print the multiplexed image plus the constituent images:
Select one of the constituent image thumbnails.

Select the Print icon . The Printing multiplex dialogue box is displayed.

PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the All button. The multiplexed image plus all of the constituent images print.
OPTION 8
From Image Edit, to print any one constituent image:
Select one of the constituent image thumbnails.

Select the Print icon . The Printing series capture dialogue box is displayed.

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PRINTING MULTIPLEX CAPTURE DIALOGUE BOX

Select the Display button. The selected constituent image prints.

FULL REPORT PRINT OPTIONS

If the Full Report option is selected on the User Preferences screen, when you select the
Print icon you can view pages of the report and access the print settings screens using

the icons at the top of the screen.

The following actions are available:

Zoom in
Zoom out
No zoom

Printer Setup
Print
Previous
Next

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EXIT WITHOUT PRINTING

Having made your selections, if for some reason having previewed the report, either Full or Basic,
you do not want to print the report you can exit the Print function without printing by selecting the
Report icon at the top left of the screen and selecting Close from the drop-down menu.

EXIT WITHOUT PRINTING

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OPERATOR MAINTENANCE

Looking After a ChemiLite Instrument

A ChemiLite Instrument does not require regular maintenance or calibration other than occasional
checking and cleaning.

Cleaning a ChemiLite Instrument

WARNING

Switch off the instrument and unplug the mains power cord from the electrical
supply.

The outside of the ChemiLite Instrument can be cleaned using a soft lint-free cloth, moistened if
required with a little water. Mild detergent may be used, if necessary. Do not use abrasive or solvent
based cleaning materials. Always perform a patch test on an inconspicuous area before you clean
the entire surface.
Surfaces which may become contaminated with biochemical materials/reagents, e.g. the interior
surfaces of the Darkroom, the Black Tray, can be cleaned using a soft lint free cloth and a non­fluorescent cleaning agent such as; a neutral detergent or 70% ethanol solution.
Avoid spilling any liquid into the body of the instrument and clean any external spills immediately. If
any liquid enters the main body of the instrument, make the instrument inoperative and contact the
supplier.

Contacting Cleaver

If it becomes necessary to contact Cleaver Scientific the following information will be required:

• Unit Serial Number

• Camera

• GenePix Image Capture Version

• Database Version

The Unit Serial Number can be found on a sticker on the back of the Darkroom. The other system
information can be found from the GenePix Imager Capture software Home screens, as shown
below:

STANDARD VIEW HOME SCREEN

On the Standard View Home screen, select the icon in the Title Bar. The About GenePix Image
Capture pop-up appears: