Open Comet: An automated tool for comet assay image analysis

被引:490
作者
Gyori, Benjamin M. [1 ,3 ]
Venkatachalam, Gireedhar [1 ,2 ]
Thiagarajan, P. S. [1 ,3 ]
Hsu, David [1 ,3 ]
Clement, Marie-Veronique [1 ,2 ]
机构
[1] Natl Univ Singapore, NUS Grad Sch Integrat Sci & Engn, Singapore 117548, Singapore
[2] Natl Univ Singapore, Yong Loo Lin Sch Med, Dept Biochem, Singapore 117595, Singapore
[3] Natl Univ Singapore, Sch Comp, Singapore 117548, Singapore
来源
REDOX BIOLOGY | 2014年 / 2卷
关键词
Comet assay; Single cell gel electrophoresis; DNA damage; Image processing; Intensity profile analysis; ImageJ plug-in; OXIDATIVE DNA-DAMAGE; INDIVIDUAL CELLS; GEL-ELECTROPHORESIS; ANALYSIS PROGRAM; REPAIR; RADIATION; CANCER;
D O I
10.1016/j.redox.2013.12.020
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 Lime. (C) 2014 The Authors, Published by Elsevier B.V.
引用
收藏
页码:457 / 465
页数:9
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