t within
GeneSnap
(if the program does not open automatically
simply double-click on the GeneSnap desktop icon).
You will now see the GeneSnap User box.
Type your name into the space and click the OK button. This is now your configuration and any
changes you make to the way you use or set-up the program can be stored as defaults under your
name. Each user can enter a name or title for their own individual user preferences so that
whenever you start G:BOX Chemi XT16 and enter your name at the log-in stage the system adapts
for your preferred settings. In future you only need to select your name from the drop down list.
GeneSnap will now fully open and you will see an image capture window. To ensure the best
performance of the G:BOX Chemi XT16 camera allow 30mins for cooling.
To obtain a live image, click on the green live button within the image
capture window.
The image capture window will now show the current camera view.
For UV excitation place the gel sample on the transilluminator.
For visible dyes place the gel sample on the visible light converter. The
converter should then be placed directly on top of the transilluminator.
For chemiluminescence imaging see page 3 of this Guide.
Use the lighting control drop down menu to select which light source comes
on when the image is live. Select No Light for chemiluminescence
(alternatively choose the Chemi configuration).
For UV excitable dyes select Transilluminator (alternatively select the Gel
configuration).
For visible light converter applications select Transilluminator.
Use the filter wheel drop down menu to select the appropriate filter for your
application. For chemiluminescence imaging select No filter to maximise light
entering the camera (No filter will be automatically selected if the Chemi
configuration has been chosen in the previous step). If a filter slider has
been fitted move the slider to the appropriate position (left blank, middle
Etbr/UV filter, ND filter).
For UV excitable dyes choose the appropriate filter (refer to Application
note 10 on the Syngene website for choice of optimal filters).
For visible light converter applications select the Neutral Density filter. 2
With the darkroom door closed, use the buttons beneath the door to move the sample tray until the
image of the sample can be seen to fill the screen, thereby achieving maximum resolution. For ease of
use it is suggested that the well line (for 1D gels) is at the top of the image.
Adjust the lens focus and aperture rings (only the Navitar lens has adjustable aperture) until the
image is sharp.
Further controls
Exposure time - Above we "grabbed" an image in real time using the standard exposure setting of the
camera. However, in some instances you may wish to extend the exposure time to resolve fainter bands
or collect chemiluminescent images. In this case click the arrows on the Exposure time bar to
increase (or decrease) the exposure time. The window shows how much exposure time you have set. The
arrows on the right allow you to change the units of the exposure time.
Neutral Fielding (NF)
This allows the capture of images corrected for uneven illumination (not applicable for
chemiluminescence). See Neutral Fielding Quick Guide for more details.
Binning and Increased Effective Pixels
The G:BOX Chemi XT16 system has a high resolution camera chip: 4.2 million pixels. Binning or merging
pixels will increase the sensitivity of the camera for low light levels. Consequently, chemiluminescent
imaging can be achieved with much shorter exposure times.
GeneSnap offers multiple levels of binning including no binning, 2x2, 3x3, 4x4, 6x6, and 8x8 binning.
Each level of binning will result in corresponding decrease in resolution, and this must be considered
when selecting which level to use.
In addition, selecting effective pixels up to 6.3 million pixels is available. When using effective pixels
this will result in an increase in image size and this must be considered when selecting this feature.
6) Adjust position of
sample tray
7) Adjust focus and
aperture
8) Focus indicator
9) Set exposure
time
10) NF
11) Binning and
Increased Effective
Pixels
It is advisable to use the *focus indicator to achieve the best focus. The
focus indicator shows when the focus condition (amount of contrast) in
the picture is increasing or decreasing. If the contents of the picture
change suddenly, it stops indicating for a period of one second and
appears grey. If the focus condition is improving the bands in the
indicator will move upwards. Bands will move downwards if the focus
condition is getting worse. If the focus condition is the best that has
been measured, the indicator shows a bright green colour. This bright
colour automatically appears at the beginning of focusing as the camera
has not seen a better condition so far. If the focus condition is below the
best seen the indicator shows a pale green colour.
When the camera is live start adjusting the focus and the bands will move
upwards as the focus is improving. Once the focus has gone through the
optimum condition the bands will start to go downwards and appear pale
green. Now turn the focus back to return to the optimum setting and when
it appears bright green you have achieved the best focus and the image
can be grabbed. To re-set the focus click on the Re-set icon (eye) at the
top of the focus indicator.
Bright Grey Pale
An additional indication on this control panel is the darkroom "door open" warning. The pictorial of the
darkroom will show if the darkroom door is open or closed.
Please note that no binning is
equivalent to 1x1 binning 12) Saturation detection
13) Auto exposure
14) Chemiluminescence
imaging tips
Auto exposure G:BOX Chemi XT16 has a unique auto-exposure system leaving the software to decide
the optimal exposure setting. The image will have no saturated areas and be fully quantifiable. This
setting should only be used when capturing images of fluorescent samples. It is especially useful when
the gel is dark or if the bands are very faint. To activate this function simply click on the AUTO
EXPOSE button.
Depending upon the gel this can take several seconds to achieve (a progress indicator shows the
automatic exposure control is operating).
Once the process is complete the "grabbed" image is displayed in the image window and the lighting is
automatically switched off. We do not recommend use of Auto exposure for chemiluminescence.
Highest value is just
below 65535
Saturation - Clicking the Show Saturation icon when you have a live image will show if the camera is over
exposed.
Red coloured shading indicates overexposure of white. Blue coloured shading indicates underexposure.
The optimum exposure time is one showing no red shading.
The G:BOX Chemi XT16 has a very wide dynamic range which means that higher levels of light can be
detected by the camera before it reaches saturation point.
To check for saturation on a grabbed image, click on the Histogram icon.
A graph will be displayed indicating how many grey shades have been detected by the camera, from 0 -
65535. Provided that all areas of the image are within this range, it is within the linear range of the
camera, and quantification may be performed with confidence. The best image is that which utilises the
full dynamic range of the camera and this can be checked by viewing the histogram of the grabbed
image.
Please note that for dyes that
have a lower dynamic range
compared to the camera e.g.
silver or coomassie then it will not
be possible to utilise the full
dynamic range of the camera.
Chemiluminescence imaging tips
Place the sample on the centre of the UV transilluminator or visible light converter converter. It is
recommended that you place the membrane between two sheets of acetate film.
Ensure that No light and No filter is selected (alternatively choose the Chemi configuration).
Ensure that the lens aperture is set to fully open.
You may wish to select one of the binning modes - see above.
Now select the Series Capture button from the image capture window.
Select the required number of frames and whether or not these should be added (adding is
recommended).
Exposure time may be entered individually for each frame or the same time used throughout. A single
long exposure may be set if required.
GeneSnap will display your series of images- simply select that which is most appropriate, which
should be the one with the largest dynamic range but containing no saturation.
3 15) Printing
16) Saving
17) Motorised sample tray
override
18) UV safety override
4
GBCXT16IC01H
Printing - When an image is "grabbed" the PRINT icon is available.
Click this to send a copy of the image to the thermal printer for a hard copy output.
Saving the image - You have the choice of either selecting FILE/SAVE AS or FILE/EXPORT. In the
first case the image can be saved in the Syngene secure SGD format for true GLP. With the second
option, the image can be saved in a range of formats including TIF, BMP, GIF, PCX, TGA, WPG, and
JPEG. Images can then be exported to other software packages.
For more detailed information concerning capture and enhancement including custom user
configurations, annotation, filter and colour overlays, image browser etc. - please refer to the full
manual supplied.
Motorised sample tray override - You may wish for the motorised sample tray to be moved when the
door is open, in order to position the sample. This is achieved by pushing one of the sample tray
buttons (up or down) at the same time as pressing the black button positioned 5cms below the round
shiny door magnet. Note the transilluminator that the sample is placed on needs to be pushed to the
back of the darkroom otherwise the sample tray will not move (contact with the