Journal article
PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images
Bioinformatics (Oxford, England), Vol.38(2), pp.594-596
01/03/2022
DOI: 10.1093/bioinformatics/btab589
PMCID: PMC8722751
PMID: 34390579
Abstract
Our increasing ability to resolve fine details using light microscopy is matched by an increasing need to quantify images in order to detect and measure phenotypes. Despite their central role in cell biology, many image analysis tools require a financial investment, are released as proprietary software, or are implemented in languages not friendly for beginners, and thus are used as black boxes. To overcome these limitations, we have developed PyJAMAS, an open-source tool for image processing and analysis written in Python. PyJAMAS provides a variety of segmentation tools, including watershed and machine learning-based methods; takes advantage of Jupyter notebooks for the display and reproducibility of data analyses; and can be used through a cross-platform graphical user interface or as part of Python scripts via a comprehensive application programming interface.
PyJAMAS is open-source and available at https://bitbucket.org/rfg_lab/pyjamas.
Supplementary data are available at Bioinformatics online.
Details
- Title: Subtitle
- PyJAMAS: open-source, multimodal segmentation and analysis of microscopy images
- Creators
- Rodrigo Fernandez-Gonzalez - Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON M5G 1X8, CanadaNegar Balaghi - University of TorontoKelly Wang - University of TorontoRay Hawkins - University of TorontoKatheryn Rothenberg - Ted Rogers Centre for Heart ResearchChristopher McFaul - University of TorontoClara Schimmer - University of TorontoMichelle Ly - University of TorontoAna Maria do Carmo - University of TorontoGordana Scepanovic - Ted Rogers Centre for Heart ResearchGonca Erdemci-Tandogan - University of TorontoVeronica Castle - University of Toronto
- Resource Type
- Journal article
- Publication Details
- Bioinformatics (Oxford, England), Vol.38(2), pp.594-596
- Publisher
- Oxford University Press (OUP)
- DOI
- 10.1093/bioinformatics/btab589
- PMID
- 34390579
- PMCID
- PMC8722751
- ISSN
- 1367-4803
- eISSN
- 1367-4811
- Grant note
- ER14-10-170 / Government of Ontario Tier II Canada Research Chair in Quantitative Cell Biology and Morphogenesis University of Toronto XSeed Program and the GPU Seeding Program of NVIDIA Corporation 418438-13 / Natural Sciences and Engineering Research Council of Canada 30279 / Canada Foundation for Innovation 156279 / CIHR Translational Biology and Engineering Program of the Ted Rogers Centre for Heart Research
- Language
- English
- Date published
- 01/03/2022
- Academic Unit
- Biology
- Record Identifier
- 9984696717002771
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