Segmentation of complementary DNA microarray images by wavelet-based markov random field model

IEEE Transactions on Information Technology in Biomedicine

Volumn 13, Issue 6, 2009, Pages 1068-1074

  Athanasiadis, Emmanouil I ^a   Cavouras, Dionisis A ^b   Glotsos, Dimitris Th ^b   Georgiadis, Pantelis V ^a   Kalatzis, Ioannis K ^b   Nikiforidis, George C ^a  

^a UNIVERSITY OF PATRAS   (Greece)

^b UNIVERSITY OF WEST ATTICA   (Greece)

Author keywords

CDNA microarray; Image segmentation; Markov random field (MRF); Wavelet

Indexed keywords

CDNA MICROARRAY; COEFFICIENT OF DETERMINATION; COEFFICIENT OF VARIATION; DNA MICROARRAY IMAGES; FUZZY C-MEANS ALGORITHMS; HARD THRESHOLDING; MARKOV RANDOM FIELD (MRF); MARKOV RANDOM FIELD MODEL; MARKOV RANDOM FIELDS; MATCHING FACTOR; MEAN ABSOLUTE ERROR; MICROARRAY IMAGES; REPRODUCIBILITIES; STATIONARY WAVELET TRANSFORMS; VERTICAL COMPONENT; WAVELET;

DIGITAL IMAGE STORAGE; DNA; FUZZY RULES; FUZZY SYSTEMS; GENES; HIDDEN MARKOV MODELS; IMAGE SEGMENTATION; NUCLEIC ACIDS; STRUCTURAL FRAMES; WAVELET TRANSFORMS;

IMAGE MATCHING;

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER SIMULATION; DNA MICROARRAY; FUZZY LOGIC; IMAGE PROCESSING; METHODOLOGY; PROBABILITY; REPRODUCIBILITY;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER SIMULATION; FUZZY LOGIC; IMAGE PROCESSING, COMPUTER-ASSISTED; MARKOV CHAINS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; REPRODUCIBILITY OF RESULTS;

EID: 70449602231     PISSN: 10897771     EISSN: None     Source Type: Journal    
DOI: 10.1109/TITB.2009.2032332     Document Type: Article

References (31)

1. Y. H. Yang, M. J. Buckley, S. Duboit, and T. P. Speed, "Comparison of methods for image analysis on cDNA microarray data," J. Comput. Graph. Statist., vol.11, pp. 108-136, 2002.
2. A. Lehmussola et al., "Evaluating the performance of microarray segmentation algorithms," Bioinformatics, vol.22, pp. 2910-2917, 2006.
3. A. A. Ahmed et al., "Microarray segmentation methods significantly influence data precision," Nucleic Acids Res., vol.50, p. 32, 2004.
4. M. Schena, D. Shalon, R. W. Davis, and P. O. Brown, "Quantitative monitoring of gene expression patterns with a complementary DNA microarrray," Science, vol.270, pp. 467-470, 1995.
5. M. B. Eisen. (1999). ScanAlyze. [Online]. Available: http://rana.lbl.gov/ EisenSoftware.htm
6. Axon Instruments, Inc. 1999. GenPix 4000 A User's guide.
7. Gene Sifter data center. (2008). [Online].Available: http://www. genesifter.net/web/dataCenter.html
8. M. J. Buckley. (2000). The Spot User's Guide. CSIRO Mathematical and Information Science. [Online]. Available: http://www.cmis.csiro.au/IAP/Spot/ spotmanual.htm
9. ImaGene, ImaGene 6.1 User Manual. (2008). [Online]. Available: http://www.biodiscovery.com/index/papps-webfiles-action
10. R. Adams and L. Bischof, "Seeded region growing," IEEE Trans. Pattern Anal. Mach. Intell., vol.16, no.6, pp. 641-647, Jun. 1994.
11. D. Tran, M. Wagner, Y. W. Lau, and M. Gen, "Fuzzy methods for voicebased person authentication," IEEJ (Inst. Elect. Eng. Jpn.) Trans. Electron., Inf. Syst., vol.124, no.10, pp. 1958-1963, 2004.
12. J. L. DeRisi, V. R. Iyer, and P. O. Brown, "Exploring the metabolic and genetic control of gene expression on a genomic scale," Science, vol.278, pp. 680-686, 1997.
13. T. Srinark and C. Kambhamettu, "A microarray image analysis system based on multiple snakes," J. Biol. Syst. Spec. Issue, vol.12, pp. 127-157, 2004.
14. K. Blekas, N. P. Galatsanos, and I. Georgiou, "An unsupervised artifact correction approach for the analysis of DNA microarray images," in Proc. IEEE Int. Conf. Image Process. (ICIP), 2003, vol.2, pp. 165-168.
15. K. Blekas, N. Galatsanos, A. Likas, and I. E. Lagaris, "Mixture model analysis of DNA microarray images," IEEE Trans. Med. Imag., vol.24, no.7, pp. 901-909, Jul. 2005.
16. S. Z. Li, Markov Random Field Modeling in Computer Vision. New York: Springer-Verlag, 2001.
17. O. Demirkaya, M. H. Asyali, and M.M. Shoukri, "Segmentation of cDNA microarray spots using markov radom field modeling," Bioinformatics, vol.21, pp. 2994-3000, 2005.
18. H. Noba, M. N. Shirazi, and E. Kawaguchi, "MRF-based texture segmentation using wavelet decomposed images," Pattern Recog., vol.35, pp. 771-782, 2002.
19. E. Athanasiadis, D. Cavouras, P. Spyridonos, I. Kalatzis, and G. Nikiforidis, "An automatic microarray image gridding technique based on continuous wavelet transform," Lecture Notes Comput. Sci., vol.4673, pp. 854-870, 2007.
20. J. E. Fowler, "The redundant discrete wavelet transform and additive noise," IEEE Signal Process. Lett., vol.12, no.9, pp. 629-632, Sep. 2005.
21. P. Sakellaropoulos, L. Costaridou, and G. Panayiotakis, "A wavelet-based spatially adaptive method for mammographic contrast enhancement," Phys. Med. Biol., vol.48, pp. 787-803, 2003.
22. D. Tran and M. Wagner, "Fuzzy C-means clustering-based speaker verification," in Lecture Notes in Computer Science: Advances in Soft Computing-AFSS 2002, N. R. Pal and M. Sugeno, Eds. New York: Springer-Verlag, 2002, pp. 318-324.
23. J. L. DeRisi, V. R. Iyer, and P. O. Brown, "Exploring the metabolic and genetic control of gene expression on a genomic scale," Science, vol.278, pp. 680-686, 1997.
24. Stanford University, School of Medicine, Palo Alto, CA. (2008). [Online]. Available: http://cmgm.stanford.edu/pbrown/scanner.html
25. S. Geman and D. Geman, "Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images," IEEE Trans. Pattern Anal. Mach. Intell., vol.6, no.6, pp. 721-741, Nov. 1984.
26. H. Deng and D. A. Clausi, "Unsupervised segmentation of synthetic aperture radar sea ice imagery using a novel markov random field model," IEEE Trans. Geosci. Remote Sens., vol.43, no.3, pp. 528-538, Mar. 2005.
27. D. L. Donoho and I. M. Johnstone, "Ideal spatial adaptation by wavelet shrinkage," Biometrika, vol.81, pp. 425-455, 1994.
28. C. S. Burrus, R. A. Gopinath, and H. Guo, Introduction to Wavelets and Wavelet Transfroms. Englewood Cliffs, NJ: Prentice Hall, 1998.
29. Y H. Yang, S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai, and T. P. Speed, "Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation," Nucleic Acid Res., vol.30, no.4 -15, 2002.
30. G. F. Reed, F. Lynn, and B. D. Meade, "Use of coefficient of variation in assessing variability of quantitative assays," Clinical Diagnostic Laboratory Immunology, vol.9, no.6, pp. 1235-1239, 2002.
31. The MathWorks, Inc. Software, Novi, MI, MATLABR.