Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis Research

Peer, Peter; Corzo, Luis Galo

doi:https://doi.org/10.1155/2007/89596

International Journal of Genomics

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Research Article | Open Access

Volume 2007 | Article ID 089596 | https://doi.org/10.1155/2007/89596

Local Pixel Value Collection Algorithm for Spot Segmentation in Two-Dimensional Gel Electrophoresis Research

Peter Peer^1,2and Luis Galo Corzo¹

Academic Editor: Stephen Oliver

Received13 Nov 2006

Accepted14 Jun 2007

Published27 Sept 2007

Abstract

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.

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Copyright

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.

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