Methods for automatic microarray image segmentation

IEEE Transactions on Nanobioscience

Volumn 2, Issue 4, 2003, Pages 202-214

  Katzer, Mathias ^a   Kummert, Franz ^a   Sagerer, Gerhard ^a  

^a BIELEFELD UNIVERSITY   (Germany)

Author keywords

Active contour models; Markov random fields; Microarrays

Indexed keywords

DNA;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; COMPUTER ASSISTED DIAGNOSIS; DNA MICROARRAY; DNA SEQUENCE; EVALUATION; FLUORESCENCE MICROSCOPY; GENE EXPRESSION PROFILING; GENETICS; IMAGE ENHANCEMENT; METHODOLOGY; NANOTECHNOLOGY; PROBABILITY; REPRODUCIBILITY; ROBOTICS; SENSITIVITY AND SPECIFICITY; STATISTICAL MODEL; VALIDATION STUDY;

ALGORITHMS; DNA; GENE EXPRESSION PROFILING; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; MARKOV CHAINS; MICROSCOPY, FLUORESCENCE; MODELS, GENETIC; MODELS, STATISTICAL; NANOTECHNOLOGY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; ROBOTICS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA;

ACOUSTIC NOISE; ALGORITHMS; COMPUTER SOFTWARE; COMPUTER VISION; DATA ACQUISITION; DNA; IMAGE PROCESSING; MATHEMATICAL MODELS; PROBLEM SOLVING; ROBUSTNESS (CONTROL SYSTEMS);

ACTIVE CONTOUR MODELS; GENE EXPRESSION ANALYSIS; MARKOV RANDOM FIELD (MRF); MICROARRAYS;

IMAGE SEGMENTATION;

EID: 3042726883     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2003.817023     Document Type: Article

References (33)

1. M. Eisen and P. Brown, "DNA arrays for analysis of gene expression," Methods Enzymol., vol. 303, pp. 179-205, 1999.
2. Y. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed, "Comparison of methods for image analysis on cDNa microarray data," Univ, California, Berkeley, Tech. Rep. 584, 2001.
3. M. Katzer, F. Kummert, and G. Sagerer, "Robust automatic microarray image analysis," presented at the Proc. Int. Conf. Bioinformatics: North-South Networking, Bangkok, Thailand, 2002.
4. P. Vesanen, "Calibration-free methods in segmentation of cDNA microarray images," in Proc. IS&T/SPIE 12th Symp. Electronic Imaging Science and Technology, 2002, pp. 291-302.
5. M. Katzer, F. Kummert, and G. Sagerer, "A Markov random field model of microarray gridding," in Proc. 18th ACM Symp. Applied Computing, 2003, pp. 72-77.
6. Y. H. Yang, M. J. Buckley, S. Dudoit, and T. P. Speed, "Comparison of methods for image analysis on cDNA microarray data," J. Comput. Graph. Statist., vol. 11, pp. 108-136, 2002.
7. "The chipping forecast II," in Nature Genetics Suppl., 2002, vol. 32, pp. 461-552.
8. T. Okamoto, T. Suzuki, and N. Yamamoto, "Microarray fabrication with covalent attachment of DNA using bubble jet technology," Nature Biotechnol, vol. 18, pp. 438-441, 2000.
9. A. Jain, T. Tokuyasu, A. Snijders, R. Segraves, D. Albertson, and D. Pinkel, "Fully automatic quantification of microarray image data," Genome Res., vol. 12, no. 2, pp. 325-332, 2002.
10. M. Steinfath, W. Wruck, and H. Seidel, "Automated image analysis for array hybridization experiments," Bioinformatics, vol. 17, no. 7, pp. 634-641, 2001.
11. R. Hirata, J. Barrera, and R. F. Hashimoto, "Segmentation of microarray images by mathematical morphology," Real-Time Imaging, vol. 8, no. 6, pp. 491-505, 2002.
12. J. Angulo and J. Serra, "Automatic analysis of DNA microarray images using mathematical morphology," Bioinformatics, vol. 19, no. 5, pp. 553-562, 2003.
13. S. Z. Li, Markov Random Field Modeling in Image Analysis, 2nd ed, ser. Computer Science Workbench. Tokyo, Japan: Springer-Verlag, 2001.
14. R. Kindermann and J. L. Snell, Markov Random Fields and Their Applications, ser. Contemporary Mathematics 1. Providence, RI: American Mathematical Soc., 1980.
15. B. Jähne, Digital Image Processing, 4th ed. Berlin, Germany: Springer Verlag, 1997.
16. W. H. Press, S. A. Teutolski, W. T. Vetterling, and B. P. Flannery, Numerical Recipes in C, 2nd ed. Cambridge, U.K.: Cambridge Univ. Press, 1992.
17. D. Stoyan, W. S. Kendall, and J. Mecke, Stochastic Geometry and Its Applications, 2nd ed. Chichester, U.K.: Wiley, 1995.
18. D. H. Ballard, Computer Vision, 10th ed. Englewood Cliffs, NJ: Prentice-Hall, 1982.
19. F. P. Preparata and M. I. Shamos, Computational Geometry: An Introduction. Berlin, Germany: Springer-Verlag, 1995.
20. P. A. Pevzner, Computational Molecular Biology: An Algorithmic Approach. Cambridge, MA: MIT Press, 2000.
21. M. Katzer, F. Kummert, and G. Sagerer, "Automatische Auswertung von Mikroarraybildern," in Workshop Bildverarbeitung für die Medizin, Leipzig, Germany, 2002.
22. P. B. Chou, P. R. Cooper, M. J. Swain, C. M. Brown, and L. E. Wixson, "Probabilistic network inference for cooperative high and low level vision," in Markov Random Fields: Theory and Applications, R. Chellappa and A. Jain, Eds. Boston, MA: Academic, 1993, pp. 211-243.
23. M. Kass, A. Witkin, and D. Terzopoulos, "Snakes: Active contour models," Int. J. Comput. Vis., vol. 1, no. 4, pp. 321-331, 1988.
24. Y. Chen, E. R. Dougherty, and M. L. Bittner, "Ratio-based decisions and the quantitative analysis of cDNA microarray images," J. Biomed. Opt., vol. 2, no. 4, pp. 364-374, 1997.
25. D. Bozinov and J. Rahnenführer, "Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering," Bioinfonnatics, vol. 18, no. 5, pp. 747-756, 2002.
26. A. A. Amini, S. Tehrani, and T. E. Weymouth, "Using dynamic programming for minimizing the energy of active contours in the presence of hard constraints," in Proc. 2nd Int. Conf. Computer Vision, 1988, pp. 95-99.
27. D. Williams and M. Shah, "A fast algorithm for active contours and curvature estimation," Comput. Vis., Graph. Image Process., vol. 55, no. 1, pp. 14-26, 1992.
28. P. T. Boggs and J. W. Tolle, "Sequential quadratic programming," Acta Numerica, pp. 1-51, 1995.
29. J. Schürmann, Pattern Classification. New York: Wiley, 1996.
30. C. J. C. Burges, "A tutorial on support vector machines for pattern recognition," Data Mining Knowl. Discovery, vol. 2, no. 2, pp. 121-167, 1998.
31. C.-C. Chang and C.-J. Lin. (2001) LIBSVM: A library for support vector machines. Online Available: http://www.csie.ntu.edu.tw/cjlin/libsvm
32. C.-J. Gai, X. Lal, S. Xing, L. Brendel, and V. Walbot, "Gene discovery using the maize genome database ZmDB," Nucleic Acids Res., vol. 28, no. 1, pp. 94-96, 2000.
33. G. Sherlock, T. Hernandez-Boussard, A. Kasarskis, G. Binkley, J. Matese, S. Dwight, M. Kaloper, S. Weng, H. Jin, C. Ball, M. B. Eisen, P. T. Spellman, P. O. Brown, D. Botstein, and J. M. Cherry, "The Stanford microarray database," Nucleic Acids Res., vol. 29, no. 1, pp. 152-155, 2001.