A fast point pattern matching algorithm for robust spatially addressable bead encoding

Bead encoding is a key problem central to all bead based microarrays. Recently a spatially addressable bead encoding technique has been developed ([1], [2]) that alleviates the need for costly hardware while still allowing high-throughput analysis. This paper proposes a pattern matching based scheme that extends this bead encoding technique´s usability to uncontrolled environments. A novel affine invariant point pattern matching algorithm is developed to achieve this. The proposed algorithm uses local features to overcome the combinatorial explosion problem encountered in matching corrupted point patterns. The use of efficient data structures is emphasized to make the algorithm fast and scalable. The proposed scheme can decode bead identities in assays involving thousands of beads in a few seconds. Evaluation results using both real and simulated data are presented.