Background Intensity
ØA spot’s measured intensity includes a contribution of non-specific hybridization and other chemicals on the glass.
ØFluorescence intensity from regions not occupied by DNA can be different from regions occupied by DNA .
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ScanAlyze
ImaGene
GenePix
ØFocuses on small regions around spot mask.
ØDetermine median/mean pixel values in this region.
Spot intensities =
mean intensity for each pixel within the circle surrounding a spot  – mean (median) intensity of the background pixels immediately surrounding the spot
SNR (signal-to-noise ratio) = Median signal intensity / Median noise value
, where signal = foreground, noise = background
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