CellProfiler 3.0: Next-generation image processing for biology

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


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Nucleus / metabolism
  • DNA / metabolism
  • Deep Learning
  • Humans
  • Image Processing, Computer-Assisted*
  • Imaging, Three-Dimensional
  • Induced Pluripotent Stem Cells / cytology
  • Induced Pluripotent Stem Cells / metabolism
  • Mice
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Software*


  • RNA, Messenger
  • DNA