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Measurements
Various spot measurements can be computed by ImaGene and outputted to a tabdelimited text file. To select measurements that you are interested in you can use
the Measurements panel of Settings dialog.
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Mean – signal and background mean intensity
Median – signal and background median intensity
Mode – signal and background mode intensity (mode corresponds to the pick of
corresponding histogram)
Total – signal and background total intensity (all pixel intensity summed up)
Standard deviation – standard deviation of signal and background intensity
distribution
Area – number of pixels segmented as signal and background
Ignored area – number of pixels in the areas segmented as ignored and directly
touching signal area
Spot area – ignored area plus signal area
Ignored median – median of pixel intensity in ignored area
Area to perimeter ratio – see “Quality Flags” section above
Offset from expected position - – multiple offset measures get outputted,
including X-, Y- and overall offset from expected position for the spot’s adjusted
circle and spot’s center of mass.
Shape regularity - see “Quality Flags” section above