title: OpenComet: an automated tool for comet assay image analysis.
abstract: Reactive species such as free radicals are constantly generated in vivo and DNA is the most important target of oxidative stress. Oxidative DNA damage is used as a predictive biomarker to monitor the risk of development of many diseases. The comet assay is widely used for measuring oxidative DNA damage at a single cell level. The analysis of comet assay output images, however, poses considerable challenges. Commercial software is costly and restrictive, while free software generally requires laborious manual tagging of cells. This paper presents OpenComet, an open-source software tool providing automated analysis of comet assay images. It uses a novel and robust method for finding comets based on geometric shape attributes and segmenting the comet heads through image intensity profile analysis. Due to automation, OpenComet is more accurate, less prone to human bias, and faster than manual analysis. A live analysis functionality also allows users to analyze images captured directly from a microscope. We have validated OpenComet on both alkaline and neutral comet assay images as well as sample images from existing software packages. Our results show that OpenComet achieves high accuracy with significantly reduced analysis time.
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore.
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Gyori
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
authors.forename: Gireedhar
authors.initials: G
authors.lastname: Venkatachalam
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore.
authors.forename: P S
authors.initials: PS
authors.lastname: Thiagarajan
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; School of Computing, National University of Singapore, Singapore.
authors.forename: David
authors.initials: D
authors.lastname: Hsu
authors.affiliation: NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore ; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
authors.forename: Marie-Veronique
authors.initials: MV
authors.lastname: Clement
mesh_terms: D000465:Algorithms; D000818:Animals; D001331:Automation; D002460:Cell Line; D020552:Comet Assay / Q000379:methods*; D004249:DNA Damage / Q000187:drug effects; D061827:Dimensional Measurement Accuracy; D006861:Hydrogen Peroxide / Q000494:pharmacology; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D051381:Rats; D012984:Software
chemical_list: D006861:Hydrogen Peroxide
keywords: Comet assay; DNA damage; Image processing; ImageJ plug-in; Intensity profile analysis; Single cell gel electrophoresis