Microarray BASICA: background adjustment, segmentation, image compression and analysis of microarray images

Abstract

This paper presents Microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression and analysis of microarray images. BASICA uses the fast Mann-Whitney test-based algorithm introduced in J. Hua et al., (2002) to segment microarray images, and post-processing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with background adjustment, are then used for the independent compression of foreground and background. We introduce a new distortion measure for microarray image compression and devise a coding scheme by modifying the object-based embedded block coding with optimized truncation (object-based EBCOT) algorithm J. Hua et al., (2002) to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that BASICA can extract sufficiently accurate genetic information at bitrates as low as 43bpp.