CellProfiler 3.0: Next-generation image processing for biology

• DOI: 10.1371/journal.pbio.2005970
• Publication Date: 2018-07-03T16:04:41Z
• Authors: 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
• Keywords: Plug-in; Interface (matter)

CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe 3.0, a new version of software supporting both whole-volume and plane-wise three-dimensional (3D) stacks, increasingly common biomedical research. CellProfiler's infrastructure is greatly improved, provide protocol for cloud-based, large-scale processing. New plugins enable running pretrained deep learning models on images. Designed by biologists, equips researchers with powerful computational tools via well-documented user interface, empowering biologists all fields quantitative, reproducible workflows.