Open source bioimage informatics tools for the analysis of DNA damage and associated biomarkers

Jens Schneider, Romano Weiss, Madeleine Ruhe, Tobias Jung, Dirk Roggenbuck, Ralf Stohwasser, Peter Schierack, Stefan Rödiger


DNA double-strand breaks (DSBs) are critical cellular lesions that represent a high risk for genetic instability. DSBs initiate repair mechanisms by recruiting sensor proteins and mediators. DSB biomarkers, like phosphorylated histone 2AX (γH2AX) and p53-binding protein 1 (53BP1), are detectable by immunofluorescence as either foci or distinct patterns in the vicinity of DSBs. The correlation between the number of foci and the number of DSBs makes them a useful tool for quantification of DNA damage in precision medicine, forensics and cancer research. The quantification and characterization of foci ideally uses large cell numbers to achieve statistical validity. This requires software tools that are suitable for the analysis of large complex data sets, even for users with limited experience in digital image processing. This includes, for example, pre-processing, transformation and presentation of the data in a less complex structure for further data analysis. There are numerous software solutions for the analysis of foci. This review gives an overview of open source image processing software packages, including graphical user interfaces (GUIs) such as CellProfiler, Icy and ImageJ/Fiji. Software packages like CellProfiler and Icy enable to gain high-content information about DSB biomarkers. Programming languages, like Python, are discussed briefly.