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ChromaWizard: An open source image analysis software for multicolor fluorescence in situ hybridization analysis
Author(s) -
Auer Norbert,
Hrdina Astrid,
Hiremath Chaitra,
Vcelar Sabine,
Baumann Martina,
Borth Nicole,
Jadhav Vaibhav
Publication year - 2018
Publication title -
cytometry part a
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.316
H-Index - 90
eISSN - 1552-4930
pISSN - 1552-4922
DOI - 10.1002/cyto.a.23505
Subject(s) - software , computer science , fluorescence in situ hybridization , multiplex , metaphase , karyotype , biology , bacterial artificial chromosome , computational biology , comparative genomic hybridization , chromosome , bioinformatics , genetics , genome , gene , programming language
Multicolor image analysis finds its applications in a broad range of biological studies. Specifically, multiplex fluorescence in situ hybridization (M‐FISH) for chromosome painting facilitates the analysis of individual chromosomes in complex metaphase spreads and is widely used to detect both numerical and structural aberrations. While this is well established for human and mouse karyotypes, for which species sophisticated software and analysis tools are available, other organisms and species are less well served. Commercially available software is proprietary and not easily adaptable to other karyotypes. Therefore, a publically available open source software that combines flexibility and customizable functionalities is needed. Here we present such a tool called “ChromaWizard” which is based on popular scientific image analysis libraries (OpenCV, scikit‐image, and NumPy). We demonstrate its functionality on the example of primary Chinese hamster ( Cricetulus griseus ) fibroblasts metaphase spreads and on Chinese Hamster Ovary cell lines known for the large number of chromosomal rearrangements. The application can be easily adapted to any kind of available labeling kits and is independent of the used organism and instrumentation. It allows direct inspection of the original hybridization signals and enables either manual or automatic assignment of colors, making it a functional and versatile tool that can be used also for other multicolor applications.