Compression of Microarray Images

DNA microarrays have become a tool of paramount importance in the study of gene function, regulation, and interaction across large numbers of genes, and even entire genomes (Hegde et al., 2000; Moore, 2001). Microarray experiments generate pairs of 16 bits per pixel grayscale images (see Fig. 1, for an example). These images, which may require several tens of megabytes in order to be stored or transmitted, are analyzed by software tools that extract relevant information, such as the intensity of the spots and the background level. This information is then used for evaluating the expression level of individual genes (Hegde et al., 2000; Moore, 2001).

[1]  R Sásik,et al.  Microarray truths and consequences. , 2004, Journal of molecular endocrinology.

[2]  N. Lee,et al.  A concise guide to cDNA microarray analysis. , 2000, BioTechniques.

[3]  Ravi Kothapalli,et al.  Microarray results: how accurate are they? , 2002, BMC Bioinformatics.

[4]  Kannan Ramchandran,et al.  Compression of cDNA and inkjet microarray images , 2002, Proceedings. International Conference on Image Processing.

[5]  Glen G. Langdon,et al.  Universal modeling and coding , 1981, IEEE Trans. Inf. Theory.

[6]  Touradj Ebrahimi,et al.  The JPEG 2000 still image compression standard , 2001, IEEE Signal Process. Mag..

[7]  Kannan Ramchandran,et al.  MICROARRAY IMAGE COMPRESSION AND THE EFFECT OF COMPRESSION LOSS , .

[8]  Christodoulos Chamzas,et al.  Technical features of the JBIG standard for progressive bi-level image compression , 1992, Signal Process. Image Commun..

[9]  Arun N. Netravali,et al.  Digital Pictures: Representation, Compression and Standards , 1995 .

[10]  Armando J. Pinho,et al.  Lossless Compression of Microarray Images , 2006, 2006 International Conference on Image Processing.

[11]  David Salomon,et al.  Data Compression: The Complete Reference , 2006 .

[12]  Kannan Ramchandran,et al.  Microarray image compression: SLOCO and the effect of information loss , 2003, Signal Processing.

[13]  Yu Luo,et al.  Gridding and compression of microarray images , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[14]  A. Ortega,et al.  Embedded image-domain adaptive compression of simple images , 1998, Conference Record of Thirty-Second Asilomar Conference on Signals, Systems and Computers (Cat. No.98CH36284).

[15]  N. Faramarzpour,et al.  Lossless DNA microarray image compression , 2003, The Thrity-Seventh Asilomar Conference on Signals, Systems & Computers, 2003.

[16]  Donald A. Adjeroh,et al.  On denoising and compression of DNA microarray images , 2006, Pattern Recognit..

[17]  William A. Pearlman,et al.  A new, fast, and efficient image codec based on set partitioning in hierarchical trees , 1996, IEEE Trans. Circuits Syst. Video Technol..

[18]  Paolo Ferragina,et al.  Text Compression , 2009, Encyclopedia of Database Systems.

[19]  Khalid Sayood,et al.  Introduction to data compression (2nd ed.) , 2000 .

[20]  Qiang Wu,et al.  FAST SEGMENTATION AND LOSSY-TO-LOSSLESS COMPRESSION OF DNA MICROARRAY IMAGES , 2002 .

[21]  S. K. Moore Making chips to probe genes , 2001 .

[22]  Shahram Shirani,et al.  Lossless and lossy compression of DNA microarray images , 2004, Data Compression Conference, 2004. Proceedings. DCC 2004.

[23]  Michael W. Marcellin,et al.  JPEG2000 - image compression fundamentals, standards and practice , 2002, The Kluwer International Series in Engineering and Computer Science.

[24]  D. Cavalieri,et al.  Fundamentals of cDNA microarray data analysis. , 2003, Trends in genetics : TIG.

[25]  Armando J. Pinho,et al.  Lossless Compression of Microarray Images Using Image-Dependent Finite-Context Models , 2009, IEEE Transactions on Medical Imaging.

[26]  Armando J. Pinho,et al.  Lossy-to-Lossless Compression of Images Based on Binary Tree Decomposition , 2006, 2006 International Conference on Image Processing.

[27]  Bin Yu \comprestimation": Microarray Images in Abundance , 2000 .

[28]  Zixiang Xiong,et al.  Microarray BASICA: Background Adjustment, Segmentation, Image Compression and Analysis of Microarray Images , 2003, Proceedings 2003 International Conference on Image Processing (Cat. No.03CH37429).

[29]  Donald A. Adjeroh,et al.  Lossless compression of DNA microarray images , 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

[30]  Rebecka Jörnsten,et al.  Compression of cDNA microarray images , 2002, Proceedings IEEE International Symposium on Biomedical Imaging.

[31]  Guillermo Sapiro,et al.  The LOCO-I lossless image compression algorithm: principles and standardization into JPEG-LS , 2000, IEEE Trans. Image Process..

[32]  G. Blelloch Introduction to Data Compression * , 2022 .

[33]  JORMA RISSANEN,et al.  A universal data compression system , 1983, IEEE Trans. Inf. Theory.