Research Article | Open Access
Peter Peer, Luis Galo Corzo, "Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis Research", International Journal of Genomics, vol. 2007, Article ID 089596, 9 pages, 2007. https://doi.org/10.1155/2007/89596
Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis Research
Two-dimensional gel-electrophoresis (2-DE) images show the expression levels of several hundreds of proteins where each protein is represented as a blob-shaped spot of grey level values. The spot detection, that is, the segmentation process has to be efficient as it is the first step in the gel processing. Such extraction of information is a very complex task. In this paper, we propose a novel spot detector that is basically a morphology-based method with the use of a seeded region growing as a central paradigm and which relies on the spot correlation information. The method is tested on our synthetic as well as on real gels with human samples from SWISS-2DPAGE (two-dimensional polyacrylamide gel electrophoresis) database. A comparison of results is done with a method called pixel value collection (PVC). Since our algorithm efficiently uses local spot information, segments the spot by collecting pixel values and its affinity with PVC, we named it local pixel value collection (LPVC). The results show that LPVC achieves similar segmentation results as PVC, but is much faster than PVC.
- J. S. Duncan and N. Ayache, “Medical image analysis: progress over two decades and the challenges ahead,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 22, no. 1, pp. 85–106, 2000.
- S.- E. Ong and A. Pandey, “An evaluation of the use of two-dimensional gel electrophoresis in proteomics,” Biomolecular Engineering, vol. 18, no. 5, pp. 195–205, 2001.
- P. Mahon and P. Dupree, “Quantitative and reproducible two-dimensional gel analysis using Phoretix 2D full,” Electrophoresis, vol. 22, no. 10, pp. 2075–2085, 2001.
- R. D. Appel, J. R. Vargas, P. M. Palagi, D. Walther, and D. F. Hochstrasser, “Melanie II—a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms,” Electrophoresis, vol. 18, no. 15, pp. 2735–2748, 1997.
- P. F. Lemkin and L. E. Lipkin, “2D electrophoresis gel data base analysis: aspects of data structures and search strategies in GELLAB,” Electrophoresis, vol. 4, no. 1, pp. 71–81, 1983.
- P. Cutler, G. Heald, I. R. White, and J. Ruan, “A novel approach to spot detection for two-dimensional gel electrophoresis images using pixel value collection,” Proteomics, vol. 3, no. 4, pp. 392–401, 2003.
- G. W. Horgan and C. A. Glasbey, “Uses of digital image analysis in electrophoresis,” Electrophoresis, vol. 16, no. 3, pp. 298–305, 1995.
- L. Vincent, “Morphological grayscale reconstruction in image analysis: applications and efficient algorithms,” IEEE Transactions on Image Processing, vol. 2, no. 2, pp. 176–201, 1993.
- L. Vincent and P. Soille, “Watersheds in digital spaces: an efficient algorithm based on immersion simulations,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 13, no. 6, pp. 583–598, 1991.
- T. Lindeberg, “Feature detection with automatic scale selection,” International Journal of Computer Vision, vol. 30, no. 2, pp. 79–116, 1998.
- J. Sporring, M. Nielsen, L. M. Florack, and P. Johansen, Eds., Gaussian Scale-Space Theory, Kluwer Academic Publishers, Norwell, Mass, USA, 1997.
- J. C. Russ, The Image Processing Handbook, CRC Press, Boca Raton, Fla, USA, 1995.
- A. K. Jain, R. P. W. Duin, and J. Mao, “Statistical pattern recognition: a review,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 22, no. 1, pp. 4–37, 2000.
- C. Hoogland, J.-C. Sanchez, L. Tonella et al., “The 1999 SWISS-2DPAGE database update,” Nucleic Acids Research, vol. 28, no. 1, pp. 286–288, 2000.
- N. Otsu, “A threshold selection method from grey-level histograms,” IEEE Transactions on Systems, Man, and Cybernetics, vol. 9, no. 1, pp. 62–66, 1979.
- C. F. Taylor, N. W. Paton, K. L. Garwood et al., “A systematic approach to modeling, capturing, and disseminating proteomics experimental data,” Nature Biotechnology, vol. 21, no. 3, pp. 247–254, 2003.
- P. Peer, V. Segura, and F. Solina, “Common open representation of computer vision results in 2DGE research,” Electrotechnical Review, vol. 74, no. 3, pp. 119–124, 2007.
- M. Rogers, J. Graham, and R. P. Tonge, “Statistical models of shape for the analysis of protein spots in two-dimensional electrophoresis gel images,” Proteomics, vol. 3, no. 6, pp. 887–896, 2003.
- E. Bettens, P. Scheunders, J. Sijbers, D. van Dyck, and L. Moens, “Automatic segmentation and modelling of two-dimensional electrophoresis gels,” in Proceedings of IEEE International Conference on Image Processing (ICIP '96), vol. 2, pp. 665–668, Lausanne, Switzerland, September 1996.
Copyright © 2007 Peter Peer and Luis Galo Corzo. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.