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Vol. 12, Issue 2, 325-332, February 2002

METHODS
Fully Automatic Quantification of Microarray Image Data

Ajay N. Jain,1,2,3,4 Taku A. Tokuyasu,1,2 Antoine M. Snijders,1,2 Richard Segraves,1 Donna G. Albertson,1,2,3 and Daniel Pinkel1,3

1 Comprehensive Cancer Center, 2 Cancer Research Institute, and 3 Department of Laboratory Medicine, University of California, San Francisco, California 94143, USA

DNA microarrays are now widely used to measure expression levels and DNA copy number in biological samples. Ratios of relative abundance of nucleic acids are derived from images of regular arrays of spots containing target genetic material to which fluorescently labeled samples are hybridized. Whereas there are a number of methods in use for the quantification of images, many of the software systems in wide use either encourage or require extensive human interaction at the level of individual spots on arrays. We present a fully automatic system for microarray image quantification. The system automatically locates both subarray grids and individual spots, requiring no user identification of any image coordinates. 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. We present a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying the pixels in each spot, the system yields more accurate estimates of ratios than systems assuming spot circularity. The software, called UCSF Spot, runs on Windows platforms and is available free of charge for academic use.

Present address: 4University of California, San Francisco, Cancer Center, Box 0128, San Francisco, CA 94143-0128, USA.

12:325-332 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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