Gridline: automatic grid alignment in DNA microarray scans.

We present a new automatic grid alignment algorithm for detecting two-dimensional (2-D) arrays of spots in DNA microarray images. Our motivation for this work is the lack of automation in high-throughput microarray data analysis that leads to a) spatial inaccuracy of located spots and hence inaccuracy of extracted information from a spot and b) inconsistency of extracted features due to manual selection of grid alignment parameters. The proposed grid alignment algorithm is novel in the sense that 1) it can detect irregularly row- and column-spaced spots in a 2-D array, 2) it is independent of spot color and size, 3) it is general to localize a grid of other primitive shapes than the spot shapes, 4) it can perform grid alignment on any number of input channels, 5) it reduces the number of free parameters to minimum by data driven optimization of most algorithmic parameters, and 6) it has a built-in speed versus accuracy tradeoff mechanism to accommodate user's requirements on performance time and accuracy of the results. The developed algorithm also automatically identifies multiple blocks of 2-D arrays, as it is the case in microarray images, and compensates for grid rotations in addition to grid translations.