Hybridized slides are scanned in cy3 and cy5 channels separately by using multiple scanners. We are using GenePix Pro 4.0 from Axon Instruments, QArraymax from Genetix, ArrayWoRx from Applied Precision, and ScanArray Express from PerkinElmer. The Axon scanner uses red and green helium- neon operating at 635 and 532 nm to excite cy5 and cy3 with 10 scanner resolution. Data from each fluorescence channel is collected and stored as separate 16- bit TIFF images. Quality measure values are between 0 and 1. Photomultiplier gain (PMT) settings are adjusted to avoid saturation that happens when the intensity values exceed detection range.

Histograms and preview windows enable to:

• see uniform intensity from both cy3 and cy5 channels
• monitor and adjust saturation spots simultaneously
• quality of image from both channels separately (dye spot or patch that needs extra washing steps)
• distinct background and signal