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 t...

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Autores principales: Trinh, Anne, Rye, Inga H, Almendro, Vanessa, Helland, Åslaug, Russnes, Hege G, Markowetz, Florian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167144/
https://www.ncbi.nlm.nih.gov/pubmed/25168174
http://dx.doi.org/10.1186/s13059-014-0442-y
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author Trinh, Anne
Rye, Inga H
Almendro, Vanessa
Helland, Åslaug
Russnes, Hege G
Markowetz, Florian
author_facet Trinh, Anne
Rye, Inga H
Almendro, Vanessa
Helland, Åslaug
Russnes, Hege G
Markowetz, Florian
author_sort Trinh, Anne
collection PubMed
description 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.
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spelling pubmed-41671442014-10-02 GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images Trinh, Anne Rye, Inga H Almendro, Vanessa Helland, Åslaug Russnes, Hege G Markowetz, Florian Genome Biol Software 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. BioMed Central 2014-08-26 2014 /pmc/articles/PMC4167144/ /pubmed/25168174 http://dx.doi.org/10.1186/s13059-014-0442-y Text en © Trinh et al.; licensee BioMed Central Ltd. 2014 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Software
Trinh, Anne
Rye, Inga H
Almendro, Vanessa
Helland, Åslaug
Russnes, Hege G
Markowetz, Florian
GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title_full GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title_fullStr GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title_full_unstemmed GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title_short GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
title_sort goifish: a system for the quantification of single cell heterogeneity from ifish images
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4167144/
https://www.ncbi.nlm.nih.gov/pubmed/25168174
http://dx.doi.org/10.1186/s13059-014-0442-y
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