Improving 2-DE gel image denoising using contourlets

Proteomics

Volumn 9, Issue 15, 2009, Pages 3877-3888

  Tsakanikas, Panagiotis ^a   Manolakos, Elias S ^a  

^a UNIVERSITY OF ATHENS   (Greece)

Author keywords

2 DE gel images; Contourlets; Denoising; Multiresolution image analysis; Wavelets

Indexed keywords

ARTICLE; CONTOURLET TRANSFORM; FILTER; IMAGE ANALYSIS; IMAGE QUALITY; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL PHENOMENA; NOISE REDUCTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; IMAGE ENHANCEMENT; PROTEINS;

EID: 68549085535     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200701027     Document Type: Article

References (31)

1. Guo, Y., Fu, Z., van Eyk, J. E., A proteomic primer for the clinician. Proc. Am. Thorac. Soc. 2007, 4, 9-17.
2. Dowsey, A. W., High-throughput Image Analysis for Proteomics. Ph.D. Thesis 2005, Department of Computing, Imperial College London.
3. Liebler, D. C., Introduction to Proteomics: Tools for the New Biology, Humana Press, Clifton 2002.
4. Raman, B., Cheung, A., Marten, M. R., Quantitative comparison and evaluation of two commercially available, two-dimensional electrophoresis image analysis software packages, Z3 and Melanie. Electrophoresis 2002, 23, 2194-2202.
5. Marengo, E., Robotti, E., Antonucci, F., Cecconi, D., Numerical approaches for quantitative analysis of two-dimensional maps: a review of commercial software and home-made systems. Proteomics 2005, 5, 654-666.
6. Panek, J, Vohradsky, J., Point pattern matching in the analysis of two-dimensional gel electropherograms. Electrophoresis 1999, 20, 3483-3491.
7. Pleissner, K. P., Hoffmann, F., Kriegel, K., Wenk, C. et al., New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases. Electrophoresis 1999, 20, 755-765.
8. Hoffmann, F., Kriegel, K., Seefeldt, I., Wenk, C. et al., An alternative approach to deal with geometric uncertainties in computer analysis of two-dimensional electrophoresis gels. Electrophoresis 2000, 21, 2637-2640.
9. Efrat, A., Hoffmann, F., Kriegel, K., Schultz, C., Wenky, C., Geometric algorithms for the analysis of 2-D electrophoresis gels. J. Comput. Biol. 2002, 9, 299-315.
10. Kaczmarek, K., Walczak, B., de Jong, S., Vandeginste, B. G. M., Baseline reduction in two dimensional gel electrophoresis images. Acta Chromatogr. 2005, 15, 82-96.
11. Church, S., Advances in two-dimensional gel matching technology. Biochem. Soc. Trans. 2004, 32, 511-516.
12. Rogers, M., Graham, J., Tonge, R. P., Using statistical image models for objective evaluation of spot detection in two-dimensional gels. Proteomics 2003, 3, 879-886.
13. Appel, R. D., Vargas, J. R., Palagi, P. M., Walther, D. et al., Melanie II-a third generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms. Electrophoresis 1997, 18, 2735-2748.
14. Kaczmarek, K., Walczak, B., de Jong, S., Vandeginste, B. G. M., Preprocessing of two-dimensional gel electrophoresis images. Proteomics 2004, 4, 2377-2389.
15. Do, M. N., Vetterli, M., The contourlet transform: an efficient directional multiresolution image representation. IEEE Trans. Image Process. 2005, 14, 2091-2106.
16. Po, D. D-Y., Do, M. N., Directional multiscale modeling of images using the contourlet transform. IEEE Trans. Image Process. 2006, 15, 1610-1620.
17. Tsakanikas, P., Manolakos, I., Effective Denoizing of 2D Gel Proteomics Images Using Contourlets IEEE Proc. ICIP 2007, San Antonio, Texas, USA, September 16-19, 2007, pp. VI: 269-272.
18. Fodor, I., Kamath, C., Denoizing through wavelet shrinkage: an empirical study. SPIE J. Electron. Imaging 2003, 12, 151-160.
19. Graps, A., An introduction to wavelets. IEEE Comput. Sci. Eng. 1995, 2, 50-61.
20. Huang, S. Y., Bai, Z. D., Wavelets, Advanced. Encyclopedia of Physical Science & Technology, 3rd Edn., vol. 17, Academic Press, New York 2002, 753-771.
21. Strang, G., Nguyen, T., Wavelets and Filter Banks, Cambridge Press, Wellesley 1996.
22. Mallat, S. G., A theory for multiresolution signal decomposition: the wavelet representation. IEEE Trans. Pat. Anal. Mach. Intel. 1989, 11, 674-693.
23. Mallat, S. G., Multiresolution approximation and wavelets. Trans. Am. Math. Soc. 1989, 135, 69-87.
24. Donoho, D. L., Ideal spatial adaptation via wavelet shrinkage. Technical Report, Department of Statistics, Stanford University, 1992.
25. Sendur, L., Selesnick, I. W., Bivariate shrinkage with local variance estimation. IEEE Signal Process. Lett. 2002, 9, 438-441.
26. Abramovitch, F. F., Sapatinas, T., Silverman, B., Wavelet thresholding via a Bayesian approach. J. R. Stat. 1998, 60, 725-749.
27. Sendur, L., Selesnick, I.W., Bivariate shrinkage functions for wavelet-based denoising exploiting interscale dependency. IEEE Trans. Signal Process. 2002, 50, 2744-2756.
28. Rogers, M., Graham, J., Tonge, R. P., Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images. Proteomics 2003, 3, 887-896.
29. Garrels, J. I., The QUEST system for quantitative analysis of two-dimensional gels. J. Biol. Chem. 1989, 264, 5269-5282.
30. Anderson, N. L., Taylor, J., Scandora, A. E., Coulter, B. P., Anderson, N. G., The TYCHO system for computer analysis of two-dimensional gel electrophoresis patterns. Clin. Chem. 1981, 27, 1807-1820.
31. Pasquali, C., Frutige, S., Wilkins, M., Hudges, G., Appel, R., Two-dimensional gel electrophoresis of Escherichia coli homogenates: the Escherichia coli SWISS-2DPAGE database. Electrophoresis 1996, 17, 547-555.