This software is designed to detect(segment) DNA fiber from DNA fluorescence image and subsequently perform fiber quantification and categorization. A software graphical user interface (GUI) is developed associated with the algorithm for more flexible DNA fiber analysis. User can perform manual, semi-auto, and fully auto DNA quantification analysis using the software.
DNA fiber fluorescence image has been widely used for DNA replication and repair dynamics study. Traditional DNA fiber quantification is relied on manual examination of DNA fluorescence image via image processing platform. This process is time-consuming and laborious and may suffer from inter-observer variation. An automatic DNA fiber analysis software is hence needed. The dedicated software is able to accurately detect and quantify DNA fiber from DNA fluorescence image.
- Matlab source code
- A compiled Windows executable.
- associated documentation
Please cite this paper if you are using this software in your research:
* Automatic DNA replication tract measurement to assess replication and repair dynamics at the single molecule level
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Journal: Bioinformatics
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Manuscript ID BIOINF-2022-0413.R1, Category: Original Paper
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Complete List of Authors: LI, Longjie; Institute of Molecular and Cell Biology; Bioinformatics Institute KOLINJIVADI, Arun Mouli; Lee Kong Chian School of Medicine ONG, Kok Haur; Bioinformatics Institute; Institute of Molecular and Cell Biology Young, David; Institute of Molecular and Cell Biology; University of California, San Francisco, UCSF Weill Institute for Neurosciences, Department of Psychiatry and Behavioral Sciences Marini, Gabriel Pik Liang; Bioinformatics Institute Chan, Sock Hoai; National Cancer Center, Cancer Genetics Service, Division of Medical Oncology; Duke-NUS Medical School, Oncology Academic Clinical Program CHONG, Siao Ting; Lee Kong Chian School of Medicine CHEW, Ee Ling; National Cancer Center, Cancer Genetics Service, Division of Medical Oncology Lu, Haoda; Bioinformatics Institute Gole, Laurent; Institute of Molecular and Cell Biology YU, Weimiao; Bioinformatics Institute, Computational Digital Pathology Lab; Institute of Molecular and Cell Biology NGEOW, Joanne; Lee Kong Chian School of Medicine; National Cancer Center, Cancer Genetics Service, Division of Medical Oncology; DukeNUS Medical School, Oncology Academic Clinical Program
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Keywords: DNA damage and repair, Automatic fibre quantification, Human-machine interface, Cancer carcinogenesis, Replication forks