for the semi-automated analysis of IFISH images

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GoIFISH has been developed for the analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection.

Users can manually edit segmentation results, perform background adjustments, construct heatmaps, topology maps, and perform cell classification. All results can be exported for further analysis.

GoIFISH has been developed in MATLAB, however binaries are provided to run the program outside of the MATLAB environment. Source code is also available for download.

To cite this software:
"GoIFISH: A system for the quantification of single cell heterogeneity from IFISH images"
Trinh A, Rye IH, Almendro V, Helland A, Russness HG, Markowetz F
May 2014

GoIFISH Web Site


  • Automatic segmentation of nuclei, membranes and spots
  • Manual refinement of segmentation results
  • Generation of heatmaps and topology maps
  • Real time cell classification
  • Background intensity adjustment to account for auto-fluorescence
  • Export segmentation results, cell properties in .png/.txt or .mat format for further analysis
  • Save current project to continue at later date


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