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An Automatic Gridding and Contour Based Segmentation Approach Applied to DNA Microarray Image Analysis

Authors: Alexandra Oliveros, Miguel Sotaquir√°


DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

Digital Object Identifier (DOI):

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[1] M. B. Eisen and P. O. Brouwn, "DNA arrays for analysis of gene expression," in Methods in Enzymology., vol. 303, 1999, pp. 179-205.
[2] R.S.H. Istepanian, "Microarray image processing: Current status and future directions", IEEE Transactions on Nanobioscience, vol 2, issue 4, pp. 173-175, 2003.
[3] X.Y. Zhang, et al, "Signal processing techniques in genomic engineering", Proceedings of the IEEE, vol. 90 issue 2, pp. 1822-1833, 2002.
[4] M. J. Marton, et al, "Drug Target Validation and Identification of Secondary Drug Target Effects Using DNA Microarrays," Nature Medicine, vol 4, 1998, pp.1293-1301.
[5] Yee Hwa Yang, Michael J. Buckley, Sandrine Dudoit, and Terence P. Speed. "Comparison of Methods for Image Analysis on cDNA Microarray Data". Journal of Computational and Graphical Statistics, vol 11, no 1, 2000, pp 1-29.
[6] Peter Bajcsi. "An overview of DNA grid alignment and foreground separation approaches". EURASIP Journal on applied signal processing, Article ID 80163 , 2006, p.1-13.
[7] M. Katzer, F. Kummert, and G. Sagerer, "Methods for automatic microarray image segmentation," IEEE Transactions on Nanobioscience, vol. 2, no. 4, pp. 202-212, 2003.
[8] M. Eisen, "ScanAlyze," Product Description. Available:
[9] J. Buhler, T. Ideker, and D. Haynor, "Dapple: improved techniques for finding spots on DNA microarrays," Technical Report. UWTR 2000-08- 05, UV CSE, Seattle,Washington, USA.
[10] S. Draghici, Data Analysis Tools for DNA Microarrays, CRC Mathematical Biology and Medicine Series, Chapman & Hall, London, UK, 2003.
[11] A.M. Machado, M.F. Campos, A.M. Siqueira and O.S. Carvalho. "An iterative algorithm for segmenting lanes and gel electrophoresis images". Proceedings of the X Brazilian Symposium on Computer Graphics and Image Processing. Brazil, pp. 140-146, 1997.
[12] J.C. Russ. The Image Processing Handbook. CRC Press & IEEE Press. Florida, 2002.
[13] F. de A. Zampirolli and R. de A. Lotuffo. "Classification of the distance transformation algorithms under the mathematical morphology approach". Proceedings of the 13th Brazilian Symposium on Computer Graphics and Image processing. Brazil, pp. 292-299, 2000.
[14] L. Qin, L. Rueda, A. Ali, A.Ngom, "Spot detection and image segmentation in DNA microarray data," Applied Bioinformatics, 4(1):1- 11, 2005.
[15] Th. Margaritis, K. Marias and D. Kafetzopoulos. "Improved Microarray Spot Segmentation by Combining two Information Channels". 28th IEEE International Conference in Medicine and Biology, Aug. 2006, pp 5850 - 5853.
[16] Iiris Hovatta et al, DNA microarray data analysis, CSC Scientific Computing. Helsinki, 2005.
[17] Rafael Gonzalez and Robert Woods, Digital Image Processing. Prentice Hall, pp 954 2008 N.Brandle, H. Bischof and H. Lapp. "Robust DNA microarray image analysis". Machine Vision and Applications, vol 15, no 1, pp. 11-28, 2003.
[18] Stanford DNA Microarry Database. Available:
[19] P. Bajcsy. "Gridline: automatic grid alignment in DNA microarray scans". IEEE Transactions on Image Processing, vol. 13, no 1, 2004, pp. 15-25.
[20] M. Steinfath, W. Wruck, H. Seidel, H. Lehbrach, U. Radelof and J. O-Brien. "Automated image analysis for array hybridization experiments". Bioinformatics, vol 17, no 7 , 2001 pp. 634-641.
[21] N.Brandle, H. Bischof and H. Lapp. "Robust DNA microarray image analysis". Machine Vision and Applications, vol 15, no 1, pp. 11-28, 2003.