IEEE Transactions on Pattern Analysis and Machine Intelligence
Microarray image compression: SLOCO and the effect of information loss
Signal Processing - Special issue: Genomic signal processing
High performance scalable image compression with EBCOT
IEEE Transactions on Image Processing
The LOCO-I lossless image compression algorithm: principles and standardization into JPEG-LS
IEEE Transactions on Image Processing
Shape-adaptive discrete wavelet transforms for arbitrarily shaped visual object coding
IEEE Transactions on Circuits and Systems for Video Technology
Gridding and Compression of Microarray Images
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Automating the processing of cDNA microarray images
International Journal of Intelligent Systems Technologies and Applications
JPEG2000 coding techniques addressed to images containing no-data regions
ACIVS'07 Proceedings of the 9th international conference on Advanced concepts for intelligent vision systems
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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.