Comparative and Functional Genomics 
Volume 2007 (2007), Article ID 89596, 9 pages
doi:10.1155/2007/89596
Research Article

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

Peter Peer1,2 and Luis Galo Corzo1

 1CEIT and Tecnun (University of Navarra), Manuel de Lardizabal 15, San Sebastian 20018, Spain
2Faculty of Computer and Information Science, University of Ljubljana, Tržaška 25, Ljubljana 1000, Slovenia
Received 13 November 2006; Accepted 14 June 2007

Recommended by Stephen Oliver

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.