GoIFISH - semi-automated analysis of IFISH images

GoIFISH has been developed for the analysis of IFISH (Immunofluorescence + Fluorescence in situ Hybridisation) images, performing nuclear, membrane and spot detection in order to quantify heterogeneity at the single cell level.

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 allows for the concurrent study of genomic and phenotypic abberations to highlight the diversity within a tissue sample, such as the genomic and phenotypic expression of HER2:

GoIFISH_example

Download and Installation

You can download GoIFISH from http://sourceforge.net/projects/goifish/

Source Code:

Dependencies:

Binaries:
Windows MacOS
Binaries are available for execution outside of the MATLAB environment.
All are dependent on the installation of MATLAB Compiler Runtime (provided in .zip packages).

Reference:

Matlab

Developers

Download

You can download GoIFISH from sourceforge.net

SourceForge

Download statistics

Can be found here!

Other packages

Software
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  • BitPhylogeny - infer intra-tumor phylogenies
  • CRImage - tumor image analysis
  • DANCE - subtype specific drivers of cancer
  • GoIFISH - single cell IFISH analysis
  • HTSanalyzeR - functional annotation
  • lol - lots of lassos
  • MEDICC - intra-patient copy number comparison
  • nem - nested effects models
  • OncoNEM - oncogenetic NEMs
  • PAN - posterior associa- tion networks
  • RedeR - graph visualiza- tion and analysis
  • RTN - network recon- struction and analysis
  • SANTA - spatial analysis of network associations
Data @ Bioconductor