Information Extraction
ØSpot Intensities
–mean (pixel intensities)
–median (pixel intensities)
ØBackground values
–Local
–Morphological opening
–Constant (global)
–None
ØQuality Information
spot
edge detection
1μm
ØThe total amount of hybridization for a spot is proportional to the total fluorescence at the spot
ØSpot intensity = pixel intensities within a spot
ØLater calculations are based on ratios between Cy5 and Cy3, so we tally in some way the intensity of the spot
ØCan use ratios of medians, means or even modes (if binned)
ØNon-specific hybridization subtracted (area outside the spot)
Mode
Median
Mean