title: A novel multi-scale Hessian based spot enhancement filter for two dimensional gel electrophoresis images.
abstract: Two dimensional gel electrophoresis (2DGE) is a useful method for studying proteins in a wide variety of applications including identifying post-translation modification (PTM), biomarker discovery, and protein purification. Computerized segmentation and detection of the proteins are the two main processes that are carried out on the scanned image of the gel. Due to the complexities of 2DGE images and the presence of artifacts, the segmentation and detection of protein spots in these images are non-trivial, and involve supervised and time consuming processes. This paper introduces a new spot filter for enhancing, and separating the closely overlapping spots of protein in 2DGE images based on the multi-scale eigenvalue analysis of the image Hessian. Using a Gaussian spot model, we have derived closed form equations to compute the eigen components of the image Hessian of two overlapping spots in a multi-scale fashion. Based on this analysis, we have proposed a novel filter that suppresses the overlapping area and results in a better spot separation. The performance of the proposed filter has been evaluated on the synthetic and real 2DGE images. The comparison with three conventional techniques and a commercial software package reveals the superiority and effectiveness of the proposed filter.
authors.affiliation: Faculty of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, Iran.
authors.forename: Sina
authors.initials: S
authors.lastname: Shamekhi
authors.affiliation: Faculty of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, Iran. Electronic address: miranbmh@modares.ac.ir.
authors.forename: Mohammad Hossein
authors.initials: MH
authors.lastname: Miran Baygi
authors.affiliation: Protein-Chemistry Lab., Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
authors.forename: Bahareh
authors.initials: B
authors.lastname: Azarian
authors.affiliation: Faculty of Electrical and Computer Engineering, Tarbiat Modares University, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Gooya
mesh_terms: D000465:Algorithms; D016477:Artifacts; D003198:Computer Simulation; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D007526:Isoelectric Point; D008962:Models, Theoretical; D008970:Molecular Weight; D016011:Normal Distribution; D011506:Proteins / Q000032:analysis*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins
keywords: Detection; Hessian; Proteomics; Segmentation; Spot enhancement filter; Two-dimensional gel electrophoresis