Protocols: Scanning

Here is the protocol for scanning slides with the [which scanner is it?].

  1. Choose a meaningful name for the experiment, so that the eventual file names will be recognizable.
  2. 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.)
  3. Set the "A" channel to scan Cy5 and the "B" channel to scan Cy3.
  4. 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.
  5. Set the offsets in both channels to zero.
  6. 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.
  7. 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.
  8. Proceed to the data upload protocol.

©2003-2010 The University of Texas MD Anderson Cancer Center
1515 Holcombe Blvd, Houston, TX 77030
1-800-392-1611 (USA) / 1-713-792-6161      Legal Statements