Journal
PLOS BIOLOGY
Volume 16, Issue 7, Pages -Publisher
PUBLIC LIBRARY SCIENCE
DOI: 10.1371/journal.pbio.2005970
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Funding
- National Institutes of Health [2R01GM089652-05A1, 1R35GM122547-01]
- Allen Institute for Cell Science
- Deutsche Forschungsgemeinschaft (DFG research fellowship) [5728]
- Google Accelerated Sciences
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CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler's infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.
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