GenEx software libraries

This page contains the GenEx software libraries for analysis of FISH fluorescence microscopy images. The purpose of the libraries is to detect cell nuclei in the DAPI channel and fluorescence signals contained therein and to evaluate their parameters, including shape and intensity.


This package has been coded in Java on top of the ImageJ library and may be used either as an ImageJ plugin or as a Java package. It can process arbitrary number of signal channels. Main purpose of the library is to take the input set of 2D images from the wide-field fluorescence miscroscope, detect objects contained in these images and filter them using either a simple filter or a classifier. Finally, the parameters of the objects are provided in the form of a CSV file for further analysis. Simple graphical editor is included to provide expert input for object classification.
The pilot application for this library has been in the diagnostics system for mosaic form of the Turner syndrom (chromosomal abnormality in which all or part of one of the X chromosomes is absent or has other abnormalities).

The Java library based on ImageJ can be downloaded here.
The API description the package can be downloaded here (English, pdf format).


This package contains the GenExLib C++ software library for analysis of FISH microscopy images. The purpose of this library is to detect cell nuclei and fluorescence signals contained in the images and to evaluate their shape and intensity parameters. The library is based on the popular OpenCV image processing library. It has been superseeded by the above Java package.

The C++ library can be downloaded here.
Documentation for C++ library can be downloaded here (czech).


The libraries have been developed in the frame of the TA01010931 project "System for support of the FISH method evaluation", supported by Technology Agency of the Czech Republic.