CellProfiler 3.0: Next-generation image processing for biology.

PLoS Biol
Authors
Keywords
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.

Year of Publication
2018
Journal
PLoS Biol
Volume
16
Issue
7
Pages
e2005970
Date Published
2018 07
ISSN
1545-7885
DOI
10.1371/journal.pbio.2005970
PubMed ID
29969450
PubMed Central ID
PMC6029841
Links
Grant list
R35 GM122547 / GM / NIGMS NIH HHS / United States