Dapple: Improved Techniques for Finding Spots on DNA Microarrays

A key step in experiments using DNA microarrays is locating the thousands of individual spots in a scanned array image. Each spot provides quantitative information about a distinct DNA sequence, so it is imperative that spots be found and quantitated accurately. Spot finding is complicated by variations in the positions and sizes of spots and by the presence of artifacts and background noise in microarray images. We describe Dapple, a new spot finding implementation for microarrays on glass slides. Dapple finds spots using morphological information which is robust to both variation and artifacts. It achieves high spot finding throughput and accuracy by learning to evaluate the quality of candidate spots from examples supplied by the user. Dapple’s techniques are useful for improving the accuracy of data acquisition from