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

Abstract

<p/> <p>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 <inline-formula><graphic file="1687-6180-2004-482358-i1.gif"/></inline-formula>% in agreement with those of the original 32 bpp images.</p

Compression of Microarray Images

“…Through segmentation, it is possible to encode the spots and background separately. This is explicitly done in the works of Hua et al (2003;; Jörnsten et al (2003); Jörnsten and Yu (2000;; Jörnsten et al (2002a;; Lonardi and Luo (2004), and more implicilty in the work of Faramarzpour and Shirani (2004);Faramarzpour et al (2003), because, in this case, the separation between the spot area and the background is performed only when the sequence is entropy encoded. Almost all available methods have also a lossy compression version.…”

“…This information is then used for evaluating the expression level of individual genes (Hegde et al, 2000;Moore, 2001). The common approach for microarray compression has been based on image analysis for spot finding (griding followed by segmentation) with the aim of separating the microarray image data into different streams based on pixel similarities (Adjeroh et al, 2006;Faramarzpour and Shirani, 2004;Faramarzpour et al, 2003;Hua et al, 2003;Jörnsten et al, 2003;2002a;Lonardi and Luo, 2004;Zhang et al, 2005). Once separated, the streams are compressed together with the segmentation information.…”

“…A potential drawback of these segmentation based approaches is that different spot placements (e.g., non-rectangular) might compromise their performance. In fact, although initially the rectangular packing was the organization used for spot placement in microarrays, other non-rectangular packings have also been proposed (see Although initially most of the specialized techniques for microarray image compression considered the lossy approach as a reasonable possibility (Faramarzpour and Shirani, 2004;Hua et al, 2003;Jörnsten et al, 2003;2002a), the most recent methods address mainly reversible techniques (Faramarzpour et al, 2003;Lonardi and Luo, 2004;Zhang et al, 2005). Keeping the original images allows future re-analysis by possibly better algorithms.…”

Analysis-Driven Lossy Compression of DNA Microarray Images

“…Nevertheless, if the introduced distortion is smaller than the experimental variability that is inherent to DNA microarrays, the lossy compression can be considered acceptable [1]- [3]. Several generic image compression methods have been adapted or directly applied to DNA microarray images [1], [2], [4]- [6]. However, to the best of the authors' knowledge, no lossy compression technique specifically designed for microarray images has been published.…”

“…This work aims to introduce such a technique with the goal of significantly outperforming existing lossy compressors. (1), which is optically scanned using two different wavelength lasers to produce two microarray images (2).…”