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:
Download and Installation
You can download GoIFISH from http://sourceforge.net/projects/goifish/
Source Code:
- source code and example images are available here
Dependencies:
- MATLAB Version 7.11 (2010b)
- MATLAB toolboxes: Image Processing Toolbox, Statistics Toolbox
- Bio-formats for image conversion to .tiff or .mat
Binaries:
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:
-
GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images
A. Trinh, I.H. Rye, V. Almendro, A. Helland, H.G. Russnes^, F. Markowetz^
Genome Biology, 2014, 15:442
PMID:25168174 | doi:10.1186/s13059-014-0442-y
