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PLoS Biol. 2018 Jul 3;16(7):e2005970. doi: 10.1371/journal.pbio.2005970. eCollection 2018 Jul.

CellProfiler 3.0: Next-generation image processing for biology.

Author information

1
Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America.
2
Skolkovo Institute of Science and Technology, Skolkovo, Moscow Region, Russia.
3
Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
4
Allen Institute for Cell Science, Seattle, Washington, United States of America.

Abstract

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.

PMID:
29969450
PMCID:
PMC6029841
DOI:
10.1371/journal.pbio.2005970
[Indexed for MEDLINE]
Free PMC Article

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