Quick Summary: Use of the Axon Scanner
The GenePix 4200A scanner should be turned on before the computer is powered up so that the
computer can identify the scanner.
1. Switch on the power supply and then switch on the scanner .
2. Double click on “GenePix Pro 6.1” to open the application. The scanner will initialize
itself, DO NOT PROCEED until it has finished. Allow to warm for 15-30 minutes
prior to scan. If an error box is shown on the screen, reboot/restart the computer and
double click on program again.
3. Open the scanner door and then open the slide platform by lifting the tab at the front.
4. Place the slide face DOWN onto the platform with the barcode at the front. Move the
lever on the left side of the platform and confirm that the slide is lying flat on the stage.
5. Close the platform and be sure that the front “clicks” closed (should not be too hard)
6. Close the scanner door by sliding it to the right.
7. Set the PMT value for each channel (635: red for Cy5 and 532: green for Cy3) using
the hardware setting button.
8. Do a preview scan by pressing the “fast forward“ button (tool button at top right of the
screen, if you place the cursor over the tools their function will pop up).
9. Check the Histogram tab for balanced signals which span the whole dynamic range.
To adjust the lasers to achieve a color balance ( ratio ~1), press the “hardware settings”
button
and adjust the PMT gain for each laser (For example: if the image is too
red, increase the 532nm PMT or decrease the 635nm PMT) .
10. Re-scan the slide in “Preview” mode to check if the new settings have been effective in
balancing the signals If the image is too light, you can adjust the brightness and
contrast using the sliders on the left side of the screen (This only adjusts the way it
looks and not the actual values)
Auto PMT could be used to find the appropriate PMT value to reach Ration 1.0 but GAL file
should be applied before using Auto-PMT.
11. Set the scan area by pressing the “scan area” button on the left side of the screen
and drawing a square around the area to be included in the “data” scan ( Click and
drag mouse from top left of the area to the bottom right).
12. Press the “Data Scan” button
to acquire the final scan.
13. Press the “Open/Save” button
and choose “Save Images” to save your images.
Type in a name for your images in the “File Name:” box. Choose “single-image TIFF”
14. Eject the slide by either clicking ton the “Eject” button on the right side of the desktop
or by sliding open the scanner door, lifting the latch and removing the slide.
15. If you have no more slides to scan and you have checked the schedule to confirm that
no one else is coming to use the scanner please switch off the scanner and power
supply.
16. Please use Demo mode of the GenePix software for data analysis (this will ensure that
the lasers will last longer)
Auto PMT could be used to find the appropriate PMT value to reach Ration 1.0 but GAL file
should be applied before using Auto-PMT.
Note: To ensure everyone has an opportunity to use the scanner, please limit your
booking for 2 hours per day. If your scanner is free after your time is up, you may
remain until somebody else needs it.
If you cannot make your booking, please cancel it on the calendar. Due to the size of
the image and the number of users, your files cannot remain on the drive indefinitely. It
is therefore recommended that users copy their files to a CD immediately after saving
them and then delete the files from the hard drive.