Here is the protocol for scanning slides with the [which scanner is
- Choose a meaningful name for the experiment, so that the
eventual file names will be recognizable.
- Set the resolution to X = 3248 and Y = 1248. (This corresponds
roughly to a resolution of 20 microns; it is one-half the maximum in
each direction. It should produce image files that are approximately 8
megabytes in size. With our spot size, this should also produce spots
that are approximately 16 pixels in diameter, contained in a box that
is 20x20 pixels.)
- Set the "A" channel to scan Cy5 and the "B" channel to scan Cy3.
- Set the color map (LUT) in the "A" channel to be a scale from
black at 0 to red at nearly saturated, with white for saturated
pixels. Set an analogous color map for the "B" channel, using green
instead of red.
- Set the offsets in both channels to zero.
- Do preliminary scans in both channels. Adjust the gains
interactively and independently until you can see only a few pixels
in each channel that are saturated.
- After you are satisfied with the gains in each channel, perform a
final scan and save the files. Record the gain that was used for each
channel in a notebook. You will need this when you upload the image
files to the database.
- Proceed to the data upload protocol.
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