Difference between revisions of "Journal:ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis"
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'''Keywords''': fluorescence ''in situ'' hybridization (FISH), chromosome painting, open-source image analysis software | '''Keywords''': fluorescence ''in situ'' hybridization (FISH), chromosome painting, open-source image analysis software | ||
==Introduction== | |||
[[wikipedia:Fluorescence in situ hybridization|fluorescence ''in situ'' hybridization]] (FISH) has greatly facilitated the characterization of gene position, chromosomes, and genome organization.[1.] FISH involves the generation and hybridization of loci-specific fluorescence‐labeled nucleic acid probes on to metaphase chromosomes or onto interphase nuclei.[2] The use of this method made gene mapping possible at much higher resolution compared with other physical mapping technologies. [3] FISH was further developed into chromosome painting to simultaneously and unequivocally distinguish chromosomes and their rearrangements in complex karyotypes. Using chromosome-specific probes and combining multiple fluorophores allows the visualization of all chromosomes with individual and unique color combinations. [4] Chromosome painting has proven to be very important not only in diagnostics and in [[cancer]] research, but also in biological research for numerical and structural aberrations, as analysis can be done at the entire genome level. [5, 6] There have been considerable technical improvements for analysis of human and murine samples. However, even though chromosome painting probes become available for a larger number of non‐model species from commercial or specialized labs<ref name="LiehrBasics18">{{cite web |url=http://fish-tl.com/mfish.html |title=Basics and literature on multicolor fluorescence ''in situ'' hybridization application |author=Liehr, T. |work=fish-tl.com |date=2018}}</ref>, this method is still not widely applied due to the absence of open‐source software for analysis. [7] | |||
Revision as of 16:11, 30 December 2019
| Full article title | ChromaWizard: An open-source image analysis software for multicolor fluorescence in situ hybridization analysis |
|---|---|
| Journal | Cytometry Part A |
| Author(s) | Auer, Norbert; Hrdina, Astrid; Hiremath Chaitra; Vcelar, Sabine; Baumann, Martina; Borth, Nicole; Jadhav, Vaibhav |
| Author affiliation(s) | Austrian Centre for Industrial Biotechnology |
| Primary contact | Email: nicole dot borth at boku dot ac dot at |
| Year published | 2018 |
| Volume and issue | 93(7) |
| Page(s) | 749–54 |
| DOI | 10.1002/cyto.a.23505 |
| ISSN | 1552-4930 |
| Distribution license | Creative Commons Attribution-NonCommercial 4.0 International |
| Website | https://onlinelibrary.wiley.com/doi/full/10.1002/cyto.a.23505 |
| Download | https://onlinelibrary.wiley.com/doi/epdf/10.1002/cyto.a.23505 (PDF) |
Abstract
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 publicly 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 their large number of chromosomal rearrangements. The application can be easily adapted to any kind of available labeling kits and is independent of the organism and instrumentation used. 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 also be used for other multicolor applications.
Keywords: fluorescence in situ hybridization (FISH), chromosome painting, open-source image analysis software
Introduction
fluorescence in situ hybridization (FISH) has greatly facilitated the characterization of gene position, chromosomes, and genome organization.[1.] FISH involves the generation and hybridization of loci-specific fluorescence‐labeled nucleic acid probes on to metaphase chromosomes or onto interphase nuclei.[2] The use of this method made gene mapping possible at much higher resolution compared with other physical mapping technologies. [3] FISH was further developed into chromosome painting to simultaneously and unequivocally distinguish chromosomes and their rearrangements in complex karyotypes. Using chromosome-specific probes and combining multiple fluorophores allows the visualization of all chromosomes with individual and unique color combinations. [4] Chromosome painting has proven to be very important not only in diagnostics and in cancer research, but also in biological research for numerical and structural aberrations, as analysis can be done at the entire genome level. [5, 6] There have been considerable technical improvements for analysis of human and murine samples. However, even though chromosome painting probes become available for a larger number of non‐model species from commercial or specialized labs[1], this method is still not widely applied due to the absence of open‐source software for analysis. [7]
Acknowledgements
The authors acknowledge support from the Austrian BMWFW, BMVIT, SFG, Standortagentur Tirol, Government of Lower Austria, and Business Agency Vienna through the Austrian FFG‐COMET‐ Funding Program.
References
- ↑ Liehr, T. (2018). "Basics and literature on multicolor fluorescence in situ hybridization application". fish-tl.com. http://fish-tl.com/mfish.html.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. We also added PMCID and DOI when they were missing from the original reference.
