An Automatic Gridding and Contour Based Segmentation Approach Applied to DNA Microarray Image Analysis
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.
[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:
http://rana.lbl.gov/EisenSoftware.htm.
[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:
http://genomewww5.stanford.edu
[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.
[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:
http://rana.lbl.gov/EisenSoftware.htm.
[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:
http://genomewww5.stanford.edu
[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.
@article{"International Journal of Information, Control and Computer Sciences:62679", author = "Alexandra Oliveros and Miguel Sotaquirá", title = "An Automatic Gridding and Contour Based Segmentation Approach Applied to DNA Microarray Image Analysis", abstract = "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.", volume = "2", number = "5", pages = "1720-6", }
