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PLoS Biol DOI:10.1371/journal.pbio.2005970

CellProfiler 3.0: Next-generation image processing for biology.

Publication TypeJournal Article
Year of Publication2018
AuthorsMcQuin, C, Goodman, A, Chernyshev, V, Kamentsky, L, Cimini, BA, Karhohs, KW, Doan, M, Ding, L, Rafelski, SM, Thirstrup, D, Wiegraebe, W, Singh, S, Becker, T, Caicedo, JC, Carpenter, AE
JournalPLoS Biol
Date Published2018 07
KeywordsAnimals, Cell Nucleus, Deep Learning, DNA, Humans, Image Processing, Computer-Assisted, Imaging, Three-Dimensional, Induced Pluripotent Stem Cells, Mice, RNA, Messenger, Software

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.


Alternate JournalPLoS Biol
PubMed ID29969450
PubMed Central IDPMC6029841
Grant ListR35 GM122547 / GM / NIGMS NIH HHS / United States