A package for a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. UCSF Spot automatically locates both subarray grids and individual spots. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. UCSF Spot offers a step toward fast and accurate operator-independent results in the quantification of DNA microarray image data.