title: Adaptive contrast enhancement of two-dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment.
abstract: 2-DE is a powerful technique to discriminate post-translationally modified protein isoforms. However, all steps of 2-DE preparation and gel-staining may introduce unwanted artefacts, including inconsistent variation of background intensity over the entire 2-DE gel image. Background intensity variations limit the accuracy of gel orientation, overlay alignment and spot detection methods. We present a compact and efficient denoising algorithm that adaptively enhances the image contrast and then, through thresholding and median filtering, removes the gray-scale range covering the background. Applicability of the algorithm is demonstrated on immunoblots, isotope-labeled gels, and protein-stained gels. Validation is performed in contexts of (i) automatic gel orientation based on Hough transformation, (ii) overlay alignment based on cross correlation and (iii) spot detection. In gel stains with low background variability, e.g. Sypro Ruby, denoising will lower the spot detection sensitivity. In gel regions with high background levels denoising enhances spot detection. We propose that the denoising algorithm prepares images with high background for further automatic analysis, without requiring manual input on a gel-to-gel basis.
authors.affiliation: Bioinformatics Group, Norut IT, Research Park Tromsø, Tromsø, Norway. werner.van.belle@itek.norut.no
authors.forename: Werner
authors.initials: W
authors.lastname: Van Belle
authors.forename: Gry
authors.initials: G
authors.lastname: Sjøholt
authors.forename: Nina
authors.initials: N
authors.lastname: Anensen
authors.forename: Kjell-Arild
authors.initials: KA
authors.lastname: Høgda
authors.forename: Bjørn Tore
authors.initials: BT
authors.lastname: Gjertsen
mesh_terms: D000465:Algorithms; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods*; D007089:Image Enhancement / Q000379:methods*; D015151:Immunoblotting / Q000379:methods; D009942:Organometallic Compounds / Q000737:chemistry; D012984:Software
chemical_list: D009942:Organometallic Compounds; C515601:Sypro Ruby