PLoS Biology (Jul 2018)

CellProfiler 3.0: Next-generation image processing for biology.

  • Claire McQuin,
  • Allen Goodman,
  • Vasiliy Chernyshev,
  • Lee Kamentsky,
  • Beth A Cimini,
  • Kyle W Karhohs,
  • Minh Doan,
  • Liya Ding,
  • Susanne M Rafelski,
  • Derek Thirstrup,
  • Winfried Wiegraebe,
  • Shantanu Singh,
  • Tim Becker,
  • Juan C Caicedo,
  • Anne E Carpenter

DOI
https://doi.org/10.1371/journal.pbio.2005970
Journal volume & issue
Vol. 16, no. 7
p. e2005970

Abstract

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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.