Instruction manual

16
Note: The AF frame works only in the area defined by the scan frame.
4. In the Preview window, click the Prescan button. This will give you a more detailed
view of the image area in which the AF function is applied.
5. If necessary, follow steps 7 to 9 (or 10) in the previous scanning scenarios to
define scan settings for your image.
6. Click the Scan (or “Scan to”) button in the Preview window to start the final scan.
This final scan process will include the Auto Focus function to make the image look
clearer and sharper.
6. Important for Scanning Electrophoresis Gels
These hints are copied from the 2D Gel Scanning Guide by Dr. Jörg Bernhardt, with
friendly permission by DECODON GmbH, Greifswald, Germany.
For more detailed information see:
http://www.decodon.com/Support/Howto/Scanning/scanning_2D_gels.html
1. Use grayscale instead of color images.
2. Try to use the complete available grayscale range. Check this using the image
histogram.
3. Choose the image resolution such that the most narrow or smallest spots you
want to analyze have a diameter of at least 5 pixels. Use the image resolution
table as a guide.
4. Scan all gel images using the same orientation.
5. Place each gel at the same position on the scanner plate. Avoid scanning of
large blank areas around the gel.
6. Use presets in the scanner's software to make the scanning process easy and
reproducible. Save resolution and scanning area as presets and reuse them for
all gels in your experiment.
7. Avoid Photoshop and similar general image processing software if you do not
know exactly what you are doing. Use the software that came with your scanner
/ imager for image post-processing.
8. Limit post-processing of images to crop, mirror, and rotation by 90, 180, 270
degrees.
9. Ideally create TIFF files. TIFF images can have different color depths. This is
one of the reasons why TIFF iswidely used as standard image file format (see
below: File Format).
10. Avoid using JPEG files for quantitative analysis.