New Spot Matching Algorithm for Protein 2-DE Images Based on Geometric Blocking and Gray Hierarchical_Journal of Biomedical Engineering

Authors：

TANGHao ,  XIONGBangshu , OUQiaofeng , LIJun

Key Laboratory of Nondestructive Test of Ministry of Education, Nanchang Hangkong University, Nanchang 330063, China;

Corresponding author：

XIONGBangshu, Email: xiongbs@126.com

Keywords：

2-DE gel image; protein spot matching; grey hierarchical; geometric blocking; shape context

DOI：

10.7507/1001-5515.20140090

Video：

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Abstract Full text Figures/Tables Video References Cited by

To reduce the mismatching and non-matching in the protein two-dimension electrophoresis (2-DE) images, we proposed an auto-matching algorithm based on gray hierarchical and geometric blocking in this study. Firstly, protein spots in the gel images were divided into groups by gray level and geometric position, and then a method based on shape context and normalized correlation was used for coarse matching in protein spots. Secondly, matched pairs in coarse matching were set as feature points, and the precise matching in the rest of not matched protein spots was accomplished by the method of geometric correlation and similarity criterion. Finally, local affine transformation was used in the verification of matching results to remove non-matching and mis-matching points. The algorithm was applied to different 2-DE gel images. The results showed that the new matching algorithm could reduce the non-matching and mis-matching spots, and increase the matching accuracy.

Citation： TANGHao, XIONGBangshu, OUQiaofeng, LIJun. New Spot Matching Algorithm for Protein 2-DE Images Based on Geometric Blocking and Gray Hierarchical. Journal of Biomedical Engineering, 2014, 31(3): 487-492,498. doi: 10.7507/1001-5515.20140090 Copy

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12.	BELONGIE S, MALIK J, PUZICHA J. Shape matching and object recognition using shape contexts[J]. IEEE Trans Pattern Anal Mach Intell, 2002, 24(4):509-522.

1. O'FARRELL P H. High resolution two-dimensional electrophoresis of proteins[J]. J Biol Chem, 1975, 250(10):4007-4021.
2. RABILLOUD T, CHEVALLET M, LUCHE S, et al. Two-dimensional gel electrophoresis in proteomics:past, present and future[J]. J Proteomics, 2010, 73(11):2064-2077.
3. DOWSEY A W, DUNN M J, YANG G Z. Automated image alignment for 2D gel electrophoresis in a high-throughput proteomics pipeline[J]. Bioinformatics, 2008, 24(7):950-957.
4. WANG X Y, FENG D D. Hybrid registration for two-dimensional gel protein images[C]//Proceedings of 3rd Asia-Pacific Bioinformatics Conference. London:Imperial College Press, 2005:1-10.
5. MATUZEVIČIUS D, SERACKIS A, NAVAKAUSKAS D. Application of k-means and MLP in the automation of matching of 2DE gel images[C]//Proceedings of the 20th International Conference on Artificial Neural Networks. Berlin:Springer-Verlag, 2010:541-550.
6. AL-TAM, DOS ANJOS A, SHAHBAZKIA H R. 2-D electrophoresis gel matching using proximity graphs[C]//International Conference on Environment and BioScience. Singapore:IACSIT Press, 2011:16-21.
7. 熊邦书,陈乐平,欧巧凤,等.基于分层策略的凝胶图像间蛋白点匹配算法[J].中国生物医学工程学报,2012,31(3):422-427.
8. KACZMAREK K, WALCZAK B, DE JONG S, et al. Matching 2D gel electrophoresis images[J]. J Chem Inf Comput Sci, 2003, 43(3):978-986.
9. SORZANO C Ó S, THÉVENAZ P, UNSER M. Elastic reg-istration of biological images using vector-spline regularization[J]. IEEE Trans Biomed Eng, 2005, 52(4):652-663.
10. HORAUD R, FORBES F, YGUEL M, et al. Rigid and articulated point registration with expectation conditional maximization[J]. IEEE Trans Pattern Anal Mach Intell, 2011, 33(3):587-602.
11. ROGERS M, GRAHAM J. Robust and accurate registration of 2-D electrophoresis gels using point-matching[J]. IEEE Trans Image Process, 2007, 16(3):624-635.
12. BELONGIE S, MALIK J, PUZICHA J. Shape matching and object recognition using shape contexts[J]. IEEE Trans Pattern Anal Mach Intell, 2002, 24(4):509-522.

Journal of Biomedical Engineering

New Spot Matching Algorithm for Protein 2-DE Images Based on Geometric Blocking and Gray Hierarchical

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