Automatic registration of microarray images. II. Hexagonal grid

MOTIVATION: In the first part of this paper the author presented an efficient, robust and completely automated algorithm for spot and block indexing in microarray images with rectangular grids. Although the rectangular grid is currently the most common type of grouping the probes on microarray slides, there is another microarray technology based on bundles of optical fibers where the probes are packed in hexagonal grids. The hexagonal grid provides both advantages and drawbacks over the standard rectangular packing and of course requires adaptation and/or modification of the algorithm of spot indexing presented in the first part of the paper. RESULTS: In the second part of the paper the author presents a version of the spot indexing algorithm adapted for microarray images with spots packed in hexagonal structures. The algorithm is completely automated, works with hexagonal grids of different types and with different parameters of grid spacing and rotation as well as spot sizes. It can successfully trace the local and global distortions of the grid, including non-orthogonal transformations. Similar to the algorithm from part I, it scales linearly with the grid size, the time complexity is O (M), where M is total number of grid points in hexagonal grid. The algorithm has been tested both on CCD and scanned images with spot expression rates as low as 2%. The processing time of an image with about 50 000 hex grid points was less than a second. For images with high expression rates (approximately 90%) the registration time is even smaller, around a quarter of a second. SUPPLEMENTARY INFORMATION: http: //fleece. ucsd. edu/~vit/RegistrationSupplement. pdf