Gellite Manual
Gellite Manual
Gellite Manual
1
Contents
Chapter One- Introduction.................................................................................... 4
1.1 Applications supported..................................................................... 4
1.2 Hardware.......................................................................................... 4
1.2.1 Specifications................................................................................... 4
1.2.2 System Components.................................................................................. 5
1.2.2.1 Darkroom.......................................................................................... 5
1.2.2.2 UV transilluminator...........................................................................
6
1.2.2.3 Filter Draw........................................................................................ 6
1.2.3 Accessories...................................................................................... 6
1.2.3.1 Blue and Visible Light Converters....................................................
6
1.2.3.2 proBLUEVIEW LED transilluminator................................................ 6
1.2.3.3 Thermal Printer................................................................................ 6
1.2.3.4 Analysis Software...................................................................................... 6
1.2.4 Set-up.............................................................................................. 7
1.2.4.1 Installing genePIX Image Capture Software.................................. 7
1.2.4.2 Minimum system requirements....................................................... 7
1.2.4.3 Software Installation........................................................................ 7
1.2.4.4 Installation of hardware information................................................ 7
1.2.4.5 Select Destination Location............................................................. 9
1.2.4.6 Select Start Menu folder.................................................................. 9
1.2.4.7 Device Driver Installation wizard..................................................... 10
1.3 Enabling secure user accounts....................................................... 10
1.4 Setting up hardware........................................................................ 11
Chapter Two- Auto Capture and Manual Image Acquisition............................. 13
2.0 Auto Capture.................................................................................. 13
2.0.1 Sample Selection............................................................................ 14
2.0.2 Dye Selection.................................................................................. 14
2.0.3 Protocol Selection........................................................................... 14
2.0.4 Sample Positioning.......................................................................... 14
2.0.5 Capture Screen............................................................................... 14
2.1 Capturing an image of an agarose EtBr or similar gel..................... 14
2.2 Capturing an image of protein gel (Coomassie, sliver stained) or
other white light image (colony plate, Microtitre plate
etc.)................................................................................................. 16
2.3 Manual Capture.............................................................................. 20
Chapter Three-Exporting, Saving and Printing Images.................................... 25
3.1 Saving Images................................................................................ 26
3.1.1 Saving Annotations......................................................................... 26
3.2 Printing Images............................................................................... 26
3.3 Exporting images to geneQUANT analysis software..................... 27
Chapter Four- Browse, Edit and View Screens.................................................. 28
4.1 Edit Screen..................................................................................... 28
4.2 Annotation Tools............................................................................. 28
4.3 Image Rotation.............................................................................. 31
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4.4 Image Source................................................................................ 31
4.5 Saturation Button.......................................................................... 32
4.6 Enhancement Tools...................................................................... 32
4.7 3D view......................................................................................... 33
4.8 View Images screen...................................................................... 36
4.9 Load Images screen..................................................................... 38
Chapter Five- Configurations............................................................................. 40
5.1 Saving Configurations................................................................... 40
5.1.1 Saving Configurations in Autocapture mode................................ 40
5.1.2 Saving Configurations in Manual mode....................................... 41
5.1.3 Opening Configurations................................................................ 41
Chapter Six- Troubleshooting and General Information................................ 42
6.1 Technical Information.................................................................... 42
6.2 Technical Assistance.................................................................... 42
6.3 Troubleshooting............................................................................ 43
Glossary.............................................................................................................. 44
3
Chapter One- Introduction
The gelLITE system supports multiple applications including DNA/RNA gel
imaging such as EtBr, SYBR Gold, UltraSafe Blue, RunSAFE and visible stained
gels i.e. Coomassie blue and silver stain.
gelLITE is the perfect choice for a low budget gel documentation system. It
features a compact darkroom which has a sliding front door and an internal white
light.
1.2 Hardware
1.2.1 Specification
4
1.2.2 System components
CAMERA
CMOS Digital camera
• USB2 connection
LENS
Superior zoom lens for
exceptional image quality
FILTER DRAWER
Use a range of filters for
extensive choice of
fluorescent applications
SAFETY SWITCH
Protects from accidental
UV exposure when opening
the door
INTERNAL WHITE LIGHT
For sample positioning and
focusing
SLIDING DOOR
Space saving sliding door
TRANSILLUMINATOR (option)
For UV, visible light and blue light
• UV transilluminator slides in
and out of darkroom
• Blue LED light (Ultraslim LED)
‒ sits on a slide in and
out tray
1.2.2.1 Darkroom
5
1.2.2.2 UV transilluminator
1.2.3 Accessories
6
1.2.4 Set-up
Please refer to the Installation quick guide on how to set up the camera and
darkroom.
Please note that Home versions of Windows operating systems are not
supported.
You will need to install the software from an account that has Administrator
rights.
Installation is performed in the following sequence
1. Hardware Information
2. Select destination location
3. Select Start Menu Folder
4. Device Driver Installation Wizard
7
Click ‘Next’
Select from the list the hardware that you have then click ‘Next’
Specify CFR settings you would like to enable. If you are not working within a
CFR compliant environment leave all boxes unchecked. Click ‘Next’
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1.2.4.5 Select Destination Location
Please select the folder in which you would like genePIX to be installed. Select
Browse to explore more folder options. Click ‘Next’
Please select where you would like to create the shortcuts for the program. To
select a different folder click the browse button. Click ‘Next’.
The software is now ready to install. Click ‘Install’ to continue the Installation
process. Click ‘Finish’ to complete the software set up.
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1.2.4.7 Device Driver Installation Wizard
This wizard will now install the software drivers that some computer devices need
in order to complete the installation. Click ‘Next’.
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1.4 Setting up hardware
When using genePIX software for the first time or when you have purchased
additional accessories such as converter screens you need to tell genePIX
software this information.
You can select your preferences on the type of report settings that you would
like. You can select to view or print the full report (Image, File description and
capture properties) or the basic report (image and capture settings).
genePIX software default setting for captured images is to save them as a .sgd
file type. If you prefer you can select from the drop down list to change the saving
default to any of the following file types Tif, Tif-compressed, bmp and jpg.
You can also select to remove screen prompts for converter screens,
automatically hide light and filter messages, reset dynamic field data and select
your regional power frequency.
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Figure 2- User Preferences page
12
Chapter Two- Auto Capture and Manual Image
Acquisition
2.0 Auto Capture
Once the genePIX software has started up the home screen will appear. At first
start up the genePIX software defaults to standard view. The display can be
changed from Standard View to Classic View on the user Preferences screen.
Standard Screen
The basis of auto capture mode is a series of steps that form a structured
workflow. The workflow is very easy to navigate through by using the green
bouncing arrow present in the bottom right hand corner of the screen to move
forward to the next screen (Figure 3). The grey status bar shows the progress of
the workflow, select any of the icons to move between any of the stages that
make up the workflow (Figure 4).
The first step of the workflow is Sample Selection followed by Dye Selection,
Protocol Selection and Sample Positioning. The final stage is the Capture
screen.
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2.0.1 Sample Selection
Select from Gels, blots or manual capture from the home screen.
The capture screen offers a wide range of functions including the ability to save,
print, edit images and analyse the captured image (geneQUANT is required).
The captured image appears in the main window with the summary of the
protocol used present on the right hand side.
Step One
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Step Two
From the home screen screen select the following DNA Agarose.
Step Three
From Dye Selection screen select the dye that you are using either from your
recent selections only or by searching for a dye (N.B. untick recent selections
only to search the full list).
Step Four
Check the ‘Select Light and Filter box’ to see the best imaging condition for your
hardware set-up.
To see more options check the ‘ More Options’ box. To view the non-UV
protocols check the ‘Non-UV protocols only’ box.
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Step Five
Place your sample on top of the transilluminator and close the door. The Sample
Positioning screen will allow you to manually adjust the Lens controls (focus,
zoom and iris settings).
Aperture
Zoom
Focus
N.B. Opening the aperture too far may result in areas of the sample being
saturated, generating a very bright image.
Step Six
The captured image will appear in the main window. The image can now be
saved in various file formats (.sgd, TIFF, JPG and BMP) or printed. You can also
export the image to geneQUANT analysis software.
Step One
16
Step Two
From the Sample Selection screen select the following Gel as Sample Format,
the sample type is Protein and then select that your gel is visibly stained.
Step Three
From Dye Selection screen select the dye that you are using either from your
recent selections only or by searching for a dye (N.B. untick recent selections
only to search the full list).
Step Four
Check the ‘Select Light and Filter box’ to see the best imaging condition for your
hardware set-up
Step Five
If you have a white light converter then place your sample on top of the converter
then place the converter on top of the transilluminator and close the door.
The Sample Positioning screen will allow you to manually adjust the Lens
controls (focus, zoom and iris settings).
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Aperture
Zoom
Focus
N.B. Opening the aperture too far may result in areas of the sample being
saturated, generating a very bright image.
Step Six
The captured image will appear in the main window. The image can now be
saved in various file formats (.sgd, TIFF, JPG and BMP) or printed. You can also
export the image to geneQUANT analysis software.
To ensure that the image you are capturing is not saturated select the ‘Show
Saturation button’ (Figure 5). Saturation will only show when the slider bars have
been moved to each end of the brightness/contrast slider. Over-exposed
(saturated) white bands will show red and over-exposed black areas in blue
(Figure 6).
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genePIX software also has the ability to dynamic field. The dynamic field function
is based on powerful algorithms which corrects for uneven illumination. This
results in an image with a flat, even background whilst maintaining GLP
compliance. To Dynamic field check the box for dynamic fielding (Figure 7) and
then follow the on-screen instructions (Figure 8).
Depending on which type of sample (UV, epi lights or transilluminator white light)
you would like to Dynamic field you may get either of the bottom two messages
shown below.
Or
To freeze the image press (if you have a touch screen monitor) or click the
Capture button (Figure 9). The image is no longer Live. If you wish to abort
capture you can press the ‘Stop’ button at any time (Figure 9).
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2.3 Manual Capture
Manual capture offers you the ability to take complete control of every function of
the system. The manual mode is particularly useful for the more unusual
applications and if you have known imaging parameters that you wish to use.
Once Manual capture has been selected the camera is live. To be able to
position your sample the appropriate lighting and filter combination need to be
selected. Both the lighting and filter menus have a drop-down menu where you
can select from all the available lighting and filters present in your system
(Figure 10).
Once you have selected a light and filter you need to set the exposure time. Use
the +/- buttons to increase or decrease the exposure time (Figure 11). The
exposure time can be entered manually by typing a number directly into the box.
Please enter the exposure time in the following format
hours:minutes:seconds:milliseconds (h:m:s:ms). There is a default exposure time
of 80ms for fluorescent gels.
Auto Capture is designed to capture the maximum available grey scales of the
sample without actually allowing saturation. Therefore, this feature is ideal for
quantifying data (Figure 12).
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To ensure that the image you are capturing is not saturated select the ‘Show
Saturation button’ (Figure 13). Saturation will only show when the slider bars
have been moved to each end of the brightness/contrast slider. Over-exposed
(saturated) white bands will show red and over-exposed black areas in blue
(Figure 14).
genePIX software also has the ability to Dynamic field. The dynamic field function
is based on powerful algorithms which corrects for uneven illumination. This
results in an image with a flat, even background whilst maintaining GLP
compliance. To Dynamic field check the box for dynamic fielding (Figure 15) and
then follow the on-screen instructions (Figure 16).
Depending on which type of sample (UV, epi lights or transilluminator white light)
you would like to Dynamic field you may get either of the bottom two messages
shown below.
21
Or
The histogram tool is very useful for illustrating the distribution of grey scales
within the image (Figure 18). The level of grey scales produced is dependent on
exposure time - up to 65536 grey scales will be displayed (Figure 19).
22
The slider bars present on the left hand side of the screen can be used to adjust
the brightness and contrast of an image and to digitally zoom in or out (Figure
20). Adjust the brightness and contrast by moving the slider tabs up and down.
To return to original settings press the reset button (green arrows). To zoom in
move the slider bar towards the (+) sign and to zoom out move the slider bar
towards the (–) sign.
Figure 20- Manual capture slider bars for brightness and contrast and
digital zoom
To view more information about the captured image select the image information
icon. Once selected the pop up window will display information on dye, filter, light
source, Iris F number, exposure time and the image size. The image information
button also provides information on the range of black and white levels. You can
also point the mouse arrow over a band and the black and white levels and XY
coordinates appear in this box (Figure 22).
The image pool present on the right hand side of the screen contains saved and
unsaved images that have been recently captured in this session. The images
outlined in red are images that have not been saved; images outlined in green
are images which have been saved and the file name will be present (Figure 23).
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Figure 23- Saved and unsaved images
To remove an image from capture screen image pool, select the Close button.
N.B. This will remove the image from every image pool. If the image has not
been saved the software will prompt you to save the image before
removing it.
The image pool also permits the user to select multiple images by checking the
Multi Select Mode box (Figure 25).
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Chapter Three- Exporting, Saving and Printing
Images
The most convenient way to archive or document the complete information about
your experiments is to generate reports.
However, you may just want to export only your gel or blot image(s) for
presentation or publication purposes.
This chapter describes all the ways you can export an image, save and print
images.
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The default is set to Data (*.sgd) which is a secure file and GLP compliant. These
files can only be opened or altered in Cleaver Scientific software packages such
as geneQUANT. SGD files contain all the capture information such as lighting,
filter, exposure times and many more complex details i.e. the camera serial
number.
You can select to save the raw image as a TIFF (16 bit uncompressed or 8 bit
compressed). This format is used when you require all the image data to be
retained. This file option creates a larger file, but will allow you to analyse the
image in other software packages.
To save the displayed image select between *.bmp and *.jpg formats N.B. *.BMP
and *.jpg formats will save as 8-bit files and you will therefore lose quantitative
data. This format should only be used for the export of visual information to
presentation or word processing software, such as Microsoft Powerpoint or
Microsoft Word.
Images captured with genePIX software can be printed using a thermal printer or
any other printer. To print an image you need to press (touch-screen) or click the
following icon (Figure 29).
26
A dialog box will appear showing a print preview. Select Print to print the image
(Figure 30).
To export a captured or saved image simply select the ‘open selected images in
geneQUANT’ button (Figure 31).
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Chapter Four- Browse, Edit and View Screens
The Edit screen offers a variety of functions ranging from image enhancement
and 3D view to changing the resolution of the image for publication purposes
(Figure 32).
The Edit screen has a panel of 3 buttons present on the top left hand side of the
screen allowing you to switch between annotation, enhancement tools and 3D
view (Figure 33).
There are several annotation tools currently available with genePIX software.
The annotation tools will appear automatically when you enter the Edit screen to
access the Enhancement and 3D tools you will need to select the appropriate
icon (Figure 34).
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Figure 34- Annotation Tools
Use the Abc button to add text to your image. Simply click on the
image where you wish to write. Now you can type your text directly
onto the image. To edit the text, double click on it. A window will
appear enabling selection of font, size and style. The text box can
be dragged around the screen as can all the annotation.
This tool can be used when you wish to draw a filled shape. Press
the Fill button then select the shape you wish to draw from the
icons shown in figure 35.
To draw rectangles, circles, freehand shapes, lines and arrows click the
appropriate icon shown below (Figure 35).
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Figure 35- Draw icons
The colour of any annotation can be changed using the colour drop-down menu.
N.B. When using the black and white thermal printer it is recommended to use
white or black annotation for clarity (Figure 36).
Any annotations made will be automatically saved when images are in SGD
format. When saving in other formats, you must check the engrave box to ensure
annotations are saved. See section 3.1 for more information on saving images.
To save any annotation that you have made to your image in a separate file that
can be re-opened over another image, press on (touchscreen) or click the
following icon (Figure 37).
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Figure 37- Save/Load Annotations icon
When you have selected the icon the following dialog box will appear. Select to
save, load or cancel (Figure 38).
The rotate function is available when the annotation and enhancement tools have
been selected. To use the rotate function select the following icon (Figure 39a).
Once this button has been selected the mouse cursor will change to show two
arrows. This cursor can then be used to freely rotate the image (b). To finalise
(fix) the rotation click button (a). To reset the orientation of the image press (c).
a) b) c)
a) b)
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4.5 Saturation button
To show saturation move the slider bars to each end of the brightness/contrast
slider. Over-exposed (saturated) white bands will show red and over-exposed
black areas in blue.
The image enhancement tools allows the user to invert, smooth, sharpen, flip
and crop the image (Figure 42).
Click on this icon to apply a sharpening filter to your image. When this
filter has been applied band edges should become more pronounced
but you may also observe an increase in the graininess of the image.
Click on this icon to apply a smoothing filter. This is useful when the
image has specks of dust or bubbles present. However, this will make
bands appear less sharp.
The Reversal icon will reverse the image to give black bands on a
white background or vice versa. This icon is particularly useful when
trying to see faint bands.
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Speckle correction icon will remove white speckles or ‘hot pixels’ from
the image.
Flip vertical will mirror the image on the vertical plane. This is useful if
the sample has been placed in the cabinet the wrong way round.
Flip horizontal will mirror the image on the horizontal plane. This is
useful if the sample has been placed in the cabinet the wrong way
round.
Select icon allows you to select an area of interest within the captured
image.
The crop icon will crop the selected area of interest and paste into a
separate window; when used together the select and crop processes
will reduce the image size.
4.7 3D View
3D view is a function which enables the user to see a 3D view of their image,
revealing gel thickness and the constrast between peaks on a gel. The 3D view
can be used with any sample type.
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Figure 43- 3D View screen
To control the view use the following controls
The 3D image can also be controlled by clicking and dragging with a mouse to
position as required.
Use the Gamma slider to adjust the gamma of the image to see fainter bands
(Figure 45).
The colour wash button can also be used to emulate different dyes, select the
green colour wash to emulate a SYBR Green DNA gel, the yellow colour wash
imitates a SYBR Gold DNA gel. The Orange, blue and red makes a protein gel
34
appear silver, Coomassie blue and SYPRO red stained respectively. The false
colour can be used to better illustrate faint bands.
The selected image(s) can then be saved, printed, sent to the View screen for
comparison or to the Edit screen for further enhancement (Figure 48).
a) b) c) d)
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Figure 49- Send to geneQUANT icon
The View Images screen allows you to view and compare the images that you
have captured whether they are saved or unsaved and any images brought in
from the Browse Images screen (Figure 50).
The zoom slider can be used to increase or decrease the size of the image
(Figure 51).
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Once you have clicked the ‘Change Layout’ icon the following screen will appear
(Figure 53).
The default setting is set to link all images that are being compared allowing the
zoom and brightness and contrast all images to be altered to the same degree
(Figure 54).
Figure 54- Change Layout screen Zoom and Range slider bars
To adjust the zoom setting of the image(s) use the slider on the left hand side.
Move the slider bar towards the (+) to zoom in and towards the (–) to zoom out.
To adjust the brightness and the contrast use the slider bar on the right hand
side.
To alter the zoom, brightness and contrast of individual images the images will
need to be unlinked. To do this select the numbered icon of the image you wish
to alter under the Link heading (Figure 55). To link images again select the
linked chains icon (Figure 55).
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Figure 55- Linking and Unlinking images
The key identifies which image you have selected and the position of each of the
images that you are comparing (Figure 56).
To exit from the comparison screen simply select the icon without the magnifying
glass from the change layout heading.
The Load images screen allows you to open files that are already saved on your
computer and to open files from external devices such as USB keys.
Use the left hand side of the screen to explore folders on your computer. All
images will be organised by date (Figure 57).
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Figure 57- Browse screen
39
Chapter Five- Configurations
genePIX software can be used to run specific applications with repeatable
workflows and to design custom configurations with a wide variety of settings that
are easily accessable, adaptable and re-usable at any time.
Set up your Protocol by working through the following screens Sample selection,
Dye selection, Protocol selection and Sample positioning. Once you have
captured an image you can save this as a configuration by selecting the following
icon (Figure 58).
A pop-up window will appear where you enter a name for the configuration. You
can at this point select to save the configuration as ‘Lock’ or ‘Make public’. A
‘locked’ configuration means you cannot make any adjustments to the protocol
.‘Make public’ configurations allow you to share configurations with other users
(Figure 59).
You can also modify an existing protocol by selecting the configuration you wish
to edit from the ‘Save Configuration’ dialog box.
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5.1.2 Saving Configurations in Manual mode
Once you have selected the lighting and filter options you wish to use, position
your sample so it is zoomed in and in focus then capture the image. Once you
have captured an image select the configurations icon (Figure 58).
Then enter a name for your configuration and select if you want to ‘Lock’ or
‘Make public’ the configuration (Figure 59).
From the home page you can open saved configurations by simply pressing or
selecting the configuration you wish to open. Once selected the notebook will
enlarge (Figure 60a) enabling you to select whether to open the file (Figure 60b)
or delete the file (Figure 60c).
Once the configuration has been opened you will be taken to the Sample
Positioning screen.
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Chapter Six- Troubleshooting and General
Information
Please visit the Cleaver Scientific website to download the gelLITE technical
literature (This is also available on your genePIX USB memory stick).
Quick Guides
gelLITE Installation
gelLITE Image Capture
42
6.3 Troubleshooting
43
Index
Glossary
The following glossary defines words used in this manual.
Auto Capture- the software will configure the optimal exposure time for your
sample using the maximum number of greyscales from your camera.
Image source- there are two types of image sources, original and processed. If
you have made enhancements to your image such as sharpening, smoothing
and cropping an area this will alter the image source and the image will now be
processed.
Iris- On a CMOS camera the iris is an adjustable aperture used to control the
amount of light coming through the lens.
Dynamic fielding- The dynamic field function corrects for uneven illumination of
light sources.
Speckle correction- will remove white speckles or ‘hot pixels’ (bright spots)
from the image.
44