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

Genome Biol. 2014 Aug 26;15(8):442. doi: 10.1186/s13059-014-0442-y.


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. GoIFISHGoIFISH 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 GoIFISHGoIFISH is highly robust in visual analysis and its accuracy compares favorably to other leading image analysis methods. GoIFISHGoIFISH is freely available at www.sourceforge.net/projects/goifish/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / genetics
  • Female
  • Fluorescent Antibody Technique / methods
  • Genetic Heterogeneity
  • Humans
  • Image Processing, Computer-Assisted / methods*
  • In Situ Hybridization, Fluorescence / methods
  • Single-Cell Analysis / methods*
  • Software*