Spot addressing for microarray images structured in hexagonal grids

Authors:
Nikolaos Giannakeas;Fanis Kalatzis;Markos G. Tsipouras;Dimitrios I. Fotiadis
Affiliations:
Laboratory of Biological Chemistry, Medical School, University of Ioannina, GR 45110 Ioannina, Greece and Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science ...;Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, GR 45110 Ioannina, Greece;Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, GR 45110 Ioannina, Greece;Unit of Medical Technology and Intelligent Information Systems, Dept. of Materials Science and Engineering, University of Ioannina, GR 45110 Ioannina, Greece
Venue:
Computer Methods and Programs in Biomedicine
Year:
2012

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Abstract

In this work, an efficient method for spot addressing in images, which are generated by the scanning of hexagonal structured microarrays, is proposed. Initially, the blocks of the image are separated using the projections of the image. Next, all the blocks of the image are processed separately for the detection of each spot. The spot addressing procedure begins with the detection of the high intensity objects, which are probably the spots of the image. Next, the Growing Concentric Hexagon algorithm, which uses the properties of the hexagonal grid, is introduced for the detection of the non-hybridized spots. Finally, the Voronoi diagram is applied to the centers of the detected spots for the gridding of the image. The method is evaluated using spots generated from the scanning of the Beadchip of Illumina, which is used for the detection of Single Nucleotide Polymorphisms in the human genome, and uses hexagonal structure for the location of the spots. For the evaluation, the detected centers for each of the spot in the image are compared to the centers of the annotation, obtaining up to 98% accuracy for the spot addressing procedure.