EURASIP Journal on Applied Signal Processing 
Volume 2004 (2004), Issue 1, Pages 92-107
doi:10.1155/S1110865704309200

Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images

Jianping Hua,1 Zhongmin Liu,2 Zixiang Xiong,1 Qiang Wu,2 and Kenneth R. Castleman2

 1Department of Electrical Engineering, Texas A&M University, College Station 77843, TX, USA
2Advanced Digital Imaging Research, 2450 South Shore Boulevard, Suite 305, League City 77573, TX, USA
Received 14 March 2003; Revised 23 September 2003

Abstract

This paper presents microarray BASICA: an integrated image processing tool for background adjustment, segmentation, image compression, and analysis of cDNA microarray images. BASICA uses a fast Mann-Whitney test-based algorithm to segment cDNA microarray images, and performs postprocessing to eliminate the segmentation irregularities. The segmentation results, along with the foreground and background intensities obtained with the background adjustment, are then used for independent compression of the foreground and background. We introduce a new distortion measurement for cDNA microarray image compression and devise a coding scheme by modifying the embedded block coding with optimized truncation (EBCOT) algorithm (Taubman, 2000) to achieve optimal rate-distortion performance in lossy coding while still maintaining outstanding lossless compression performance. Experimental results show that the bit rate required to ensure sufficiently accurate gene expression measurement varies and depends on the quality of cDNA microarray images. For homogeneously hybridized cDNA microarray images, BASICA is able to provide from a bit rate as low as 5 bpp the gene expression data that are 99% in agreement with those of the original 32 bpp images.