Computational protocol: The Focinator   a new open source tool for high throughput foci evaluation of DNA damage

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Protocol publication

[…] The macro “Focinator” was programmed as a macro for automated quantitative and qualitative analysis of foci with the open-source software ImageJ, a public domain Java image processing program developed at the National Institutes of Health (NIH) [, ]. ImageJ is designed with an open architecture and provides extensibility via Java plugins and automation with macros. Custom-built tools can be developed to solve image processing or analysis problems. [, ]. ImageJ is available for Windows, Mac OS, Mac OS X and Linux. It has its own ImageJ macro language that is able to control ImageJ procedures and the automation of action series including variables and user-defined functions. The macro, instructions and support are obtainable at addition, a tool for batch mode and import of data from foci-count and ROI analysis was developed: the batch mode was programmed using R, a free software environment for programming []. The R-script allows automated opening of images, foci evaluation and the direct export of foci data in a Microsoft Excel spreadsheet. Excel spreadsheets enable further statistical analysis as well as easy export into other statistical software. […]

Pipeline specifications

Software tools ImageJ, FoCo
Application Microscopic phenotype analysis
Organisms Mus musculus
Diseases Nervous System Diseases, Prostatic Neoplasms