Chromosome painting software

chromosome-painting, FISH, M-FISH, CHO-K1
pip install chromawizard==1.2.2


ChromaWizard - Boost your karyotyping workflow

Multicolour image analysis finds its application in a broad range of biological studies, including multiplex-fluorescence in-situ hybridization (M-FISH), which is able to facilitate the analysis of individual chromosomes or segments of chromosome in complex metaphase spreads (chromosome painting). These techniques are used to study and identify numerical and structural chromosome aberrations as observed in many immortalised and cancer cell lines. Currently available image analysis software is mostly offered as a proprietary, expensive software in combination with hardware bundles. These applications are fast and powerful, however, they lack inter- compatibility since they are mostly developed for a specific model organism or hardware system and are not free to use for research purposes. Thus, open software could pave the way for flexible and versatile tools with customizable functionalities depending upon the application needs. To this end we have developed an open source tool for analysing M-FISH based images on the excellent SciPy and OpenCV libraries called "ChromaWizard". We demonstrate functionalities of this tool using Chinese hamster (Cricetulus griseus) and CHO-K1 karyotype paintings with commercially available 12XCHamster (MetaSystems) labeling. "ChromaWizard" is functional and versatile, since it allows the direct inspection of the original hybridization signals and enables the user to assign signals semi-automatically. Finally, the tool is easily customizable and can be further developed for other multicolour image analysis applications.


Linux & MacOS

# Install ChromaWizard
sudo pip3 install chromawizard

Microsoft Windows

ChromaWizard is also available as Conda package. Install Conda for your operating system and type:

conda install -c nauer chromawizard


  • ChromaWizard Tutorial 1