Dapple is a program for quantitating spots on a two-color DNA microarray image. Given a pair of images from a comparative hybridization, Dapple finds the individual spots on the image, evaluates their qualities, and quantifies their total fluorescent intensities.

Dapple is designed to work with microarrays on glass. The spot-finding techniques used are robust to uneven spot sizes and positional deviations caused by "wobbling" of the arraying robot, as well as image noise and artifacts. As long as your spots are consistently circular, Dapple has a good chance of finding them accurately.

Dapple judges the quality of putative spots automatically using a classifier trained to match the investigator's judgement. In other words, it attempts to replicate the decisions you would make, based on visual inspection of the array, about whether to keep or reject each spot. The inferred qualities of spots are displayed visually, so that the investigator can focus on evaluating a few potentially erroneous spots rather than having to inspect the entire array.