title: GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.
abstract: 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/.
authors.forename: Anne
authors.initials: A
authors.lastname: Trinh
authors.forename: Inga H
authors.initials: IH
authors.lastname: Rye
authors.forename: Vanessa
authors.initials: V
authors.lastname: Almendro
authors.forename: Aslaug
authors.initials: A
authors.lastname: Helland
authors.forename: Hege G
authors.initials: HG
authors.lastname: Russnes
authors.forename: Florian
authors.initials: F
authors.lastname: Markowetz
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics; D005260:Female; D005455:Fluorescent Antibody Technique / Q000379:methods; D018740:Genetic Heterogeneity; D006801:Humans; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods; D059010:Single-Cell Analysis / Q000379:methods*; D012984:Software