#acl ChrisSeidel:read,write,delete,revert All:read
= Agilent Microarray Scanner =
Agilent makes a scanner for scanning DNA microarrays labeled with Cy5 and Cy3. The following are some brief notes (circa 2007):
 * The scanner is NOT self balancing. It has no ability to balance the Red and Green channels.
 * The TIF images produced by the scanner are dual layer images. When opening them in Axon GenePix, the green image is first and must be assigned wavelength 532, followed by assigning the red image 635.

The software that drives the scanner is clunky and horrible to use, but it's functional once you get used to it. It appears to be designed for scanning arrays in batch where attention to detail is not much of an option. If you want to pay close attention to one array - it's absolutely terrible.

People who use this scanner (i.e. people from Rick Young's Lab) actually tell me that they scan the arrays on the Agilent scanner, but then open the images in GenePix to check the scan for color balance - then go back to the Agilent scanner to make adjustments! Agilent strikes again with Bad Design.