GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images

Molecular analysis has revealed extensive intra-tumor heterogeneity in human cancer samples, but cannot identify cell-to-cell variations within the tissue microenvironment. In contrast, in situ analysis can identify genetic aberrations in phenotypically defined cell subpopulations while preserving tissue-context specificity. GoIFISH is a widely applicable, user-friendly system tailored for the objective and semi-automated visualization, detection and quantification of genomic alterations and protein expression obtained from fluorescence in situ analysis. In a sample set of HER2-positive breast cancers GoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods. GoIFISH is freely available at www.sourceforge.net/projects/goifish/. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-014-0442-y) contains supplementary material, which is available to authorized users.