a digital image processing - based system and method are disclosed for quantitatively assessing nucleic acid species expressed in a microarray . the microarray is a grid of a plurality of sub - grids of the nucleic acid species . the system includes a scanner that has a digital scanning sensor that scans the microarray and transmits from an output a digital image of the microarray , and a computer that receives the digital image of the microarray from the scanner and then processes the digital image , detecting an expression signal of the nucleic acid species , segmenting the expression signal , calculating a measure of the segmented expression signal , and providing the measure at the output of the computer . prior to segmenting the expression signal for a nucleic acid species , the expression signal is characterized by a center pixel in the digital image and an approximate radius around the center pixel . the computer segments the expression signal by tentatively classifying pixels within the approximate radius as signal pixels and those outside the approximate radius as background pixels , determining major intensity modes for the signal pixels and for the background pixels , and using the major intensity modes , reclassifying the signal and background pixels depending on each pixel &# 39 ; s intensity relative to the major intensity modes .