FoCo: a simple and robust quantification algorithm of nuclear foci

BMC Bioinformatics

Software

Jörg Schaber¹  Lyubomira Ivanova¹  Anastasiya Lapytsko¹  Maja Studencka¹  Gabriel Kollarovic² 

[1] Medical Faculty, Institute for Experimental Internal Medicine, Otto von Guericke University, Pfälzer Platz 2, 39106, Magdeburg, Germany;Medical Faculty, Institute for Experimental Internal Medicine, Otto von Guericke University, Pfälzer Platz 2, 39106, Magdeburg, Germany;Cancer Research Institute, Slovak Academy of Sciences, Vlarska 7, 83391, Bratislava, Slovakia;

关键词: DNA double-strand break;    γH2AX foci;    Fluorescence microscopy;    Image processing;    Single cell analysis;   

DOI  :  10.1186/s12859-015-0816-5

 received in 2015-07-13, accepted in 2015-11-07,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundThe number of γH2AX foci per nucleus is an accepted measure of the number of DNA double-strand breaks in single cells. One of the experimental techniques for γH2AX detection in cultured cells is immunofluorescent labelling of γH2AX and nuclei followed by microscopy imaging and analysis.ResultsIn this study, we present the algorithm FoCo for reliable and robust automatic nuclear foci counting in single cell images. FoCo has the following advantages with respect to other software packages: i) the ability to reliably quantify even densely distributed foci, e.g., on images of cells subjected to radiation doses up to 10 Gy, ii) robustness of foci quantification in the sense of suppressing out-of-focus background signal, and iii) its simplicity. FoCo requires only 5 parameters that have to be adjusted by the user.ConclusionsFoCo is an open-source user-friendly software with GUI for individual foci counting, which is able to produce reliable and robust foci quantifications even for low signal/noise ratios and densely distributed foci.

【 授权许可】

CC BY   
© Lapytsko et al. 2015