Storage and transmission of microarray images.

With the recent explosion of interest in microarray technology, massive amounts of microarray images are currently being produced. The storage and transmission of these types of data are becoming increasingly challenging. This article reviews the latest technologies that allow for the compression and storage of microarray images in dedicated database systems.

[1]  Alex E. Lash,et al.  Gene Expression Omnibus: NCBI gene expression and hybridization array data repository , 2002, Nucleic Acids Res..

[2]  P. Brown,et al.  Exploring the metabolic and genetic control of gene expression on a genomic scale. , 1997, Science.

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

[4]  Charles L. Kooperberg,et al.  Improved Background Correction for Spotted DNA Microarrays , 2002, J. Comput. Biol..

[5]  Hong Yan,et al.  Robust adaptive spot segmentation of DNA microarray images , 2003, Pattern Recognit..

[6]  E. Balázs,et al.  Immunodiagnostics for food and feed safety , 2000 .

[7]  Daniel H. Geschwind,et al.  Sharing gene expression data: an array of options , 2001, Nature Reviews Neuroscience.

[8]  J. Goncalves,et al.  Roles and requirements for a research microarray database , 2002, IEEE Engineering in Medicine and Biology Magazine.

[9]  Sergio Contrino,et al.  ArrayExpress—a public repository for microarray gene expression data at the EBI , 2004, Nucleic Acids Res..

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

[11]  John G. Cleary,et al.  Unbounded Length Contexts for PPM , 1997 .

[12]  Rebecka Jörnsten,et al.  On the Bitplane Compression of Microarray Images , 2002 .

[13]  Sorin Draghici,et al.  Gene expression databases and data mining. , 2003, BioTechniques.

[14]  Jürg Bähler,et al.  Getting the most from public microarray data , 2004 .

[15]  Martin Vingron,et al.  Microarray data representation, annotation and storage. , 2002, Advances in biochemical engineering/biotechnology.

[16]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[17]  Terence P. Speed,et al.  Comparison of Methods for Image Analysis on cDNA Microarray Data , 2002 .

[18]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[19]  Dennis B. Troup,et al.  NCBI GEO: mining millions of expression profiles—database and tools , 2004, Nucleic Acids Res..

[20]  Horst Bischof,et al.  Robust DNA microarray image analysis , 2003, Machine Vision and Applications.

[21]  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).

[22]  Hans Lehrach,et al.  Automated image analysis for array hybridization experiments , 2001, Bioinform..

[23]  Musa H. Asyali,et al.  Segmentation of cDNA Microarray Spots Using Markov Random Field Modeling , 2005, Bioinform..

[24]  Nader Karimi,et al.  DNA microarray image compression by pipeline architecture , 2003, The Thrity-Seventh Asilomar Conference on Signals, Systems & Computers, 2003.

[25]  Sergio Contrino,et al.  The ArrayExpress gene expression database: a software engineering and implementation perspective , 2005, Bioinform..

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

[27]  Jens Michael Carstensen,et al.  An Active Lattice Model in a Bayesian Framework , 1996, Comput. Vis. Image Underst..

[28]  Chris A. Glasbey,et al.  Combinatorial image analysis of DNA microarray features , 2003, Bioinform..

[29]  Eero P. Simoncelli,et al.  Image quality assessment: from error visibility to structural similarity , 2004, IEEE Transactions on Image Processing.

[30]  Ajay N. Jain,et al.  Fully automatic quantification of microarray image data. , 2002, Genome research.

[31]  Vitaly L. Galinsky,et al.  Automatic registration of microarray images. I. Rectangular grid , 2003, Bioinform..

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

[33]  Michael F. Miles,et al.  Microarrays: lost in a storm of data? , 2001, Nature Reviews Neuroscience.

[34]  David Botstein,et al.  The Stanford Microarray Database: data access and quality assessment tools , 2003, Nucleic Acids Res..

[35]  Gregory R. Grant,et al.  RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies , 2004, Bioinform..

[36]  R.S.H. Istepanian,et al.  Application of wavelet modulus maxima in microarray spots recognition , 2003, IEEE Transactions on NanoBioscience.

[37]  Margaret Gardiner-Garden,et al.  A Comparison of Microarray Databases , 2001, Briefings Bioinform..

[38]  M. Deen,et al.  Lossy compression of DNA microarray images , 2004, Canadian Conference on Electrical and Computer Engineering 2004 (IEEE Cat. No.04CH37513).

[39]  C. Ball,et al.  Microarray databases: standards and ontologies , 2002, Nature Genetics.

[40]  Franz Kummert,et al.  A Markov Random Field model of microarray gridding , 2003, SAC '03.

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

[42]  Tracy L. Bergemann,et al.  A Statistically Driven Approach for Image Segmentation and Signal Extraction in cDNA Microarrays , 2004, J. Comput. Biol..

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

[44]  Adrian E. Raftery,et al.  Donuts, scratches and blanks: robust model-based segmentation of microarray images , 2005, Bioinform..

[45]  G. Sagerer,et al.  Methods for automatic microarray image segmentation , 2003, IEEE Transactions on NanoBioscience.

[46]  O. Demirkaya,et al.  Segmentation of microarray cDNA spots using MRF-based method , 2003, Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (IEEE Cat. No.03CH37439).

[47]  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..

[48]  Kevin G. Becker,et al.  The sharing of cDNA microarray data , 2001, Nature Reviews Neuroscience.

[49]  Christian J. Stoeckert,et al.  RAD (RNA abundance database): an infrastructure for array data analysis , 2001, SPIE BiOS.

[50]  Musa H. Asyali,et al.  Segmentation of Microarray cDNA Spots Using Markov Random Field Modeling , 2005 .

[51]  D. J. Wheeler,et al.  A Block-sorting Lossless Data Compression Algorithm , 1994 .

[52]  Carlos Caldas,et al.  Microarray segmentation methods significantly influence data precision. , 2004, Nucleic acids research.

[53]  Wen-Liang Hwang,et al.  Gridding spot centers of smoothly distorted microarray images , 2006, IEEE Transactions on Image Processing.

[54]  Gavin Sherlock,et al.  The Stanford Microarray Database accommodates additional microarray platforms and data formats , 2004, Nucleic Acids Res..