Autonomous system for Web-based microarray image analysis

IEEE Transactions on Nanobioscience
Daniel Bozinov

Abstract

Software-based feature extraction from DNA microarray images still requires human intervention on various levels. Manual adjustment of grid and metagrid parameters, precise alignment of superimposed grid templates and gene spots, or simply identification of large-scale artifacts have to be performed beforehand to reliably analyze DNA signals and correctly quantify their expression values. Ideally, a Web-based system with input solely confined to a single microarray image and a data table as output containing measurements for all gene spots would directly transform raw image data into abstracted gene expression tables. Sophisticated algorithms with advanced procedures for iterative correction function can overcome imminent challenges in image processing. Herein is introduced an integrated software system with a Java-based interface on the client side that allows for decentralized access and furthermore enables the scientist to instantly employ the most updated software version at any given time. This software tool is extended from PixClust as used in Extractiff incorporated with Java Web Start deployment technology. Ultimately, this setup is destined for high-throughput pipelines in genome-wide medical diagnostics labs or microa...Continue Reading

References

Dec 9, 1998·Proceedings of the National Academy of Sciences of the United States of America·M B EisenD Botstein
Oct 12, 2002·Bioinformatics·Ilya ShmulevichWei Zhang
Jan 23, 2003·Bioinformatics·C A Glasbey, P Ghazal
Oct 1, 1997·Journal of Biomedical Optics·Y ChenM L Bittner

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Citations

Aug 21, 2007·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Rastislav Lukac, Konstantinos N Plataniotis
Jan 6, 2005·IEEE Transactions on Nanobioscience·Rastislav LukacAnastasios N Venetsanopoulos
May 15, 2013·Computer Methods and Programs in Biomedicine·Zidong WangXiaohui Liu

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