Workflow

Biology

Plug-in

Gibbs isotherm

Operating system

Biochemistry

Computer science

Computational biology

Modular design

Software

Bioinformatics

Database

Interface (matter)

Image (mathematics)

Data science

Artificial intelligence

Pulmonary surfactant

Programming language

PLoS Biology

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.

CellProfiler 3.0: Next-generation image processing for biology