CellProfiler
GUI-based pipeline tool for high-throughput image analysis, develop an image analysis workflow without the need for programming.
Overview
CellProfiler chains modular image processing steps (illumination correction, segmentation, measurement, export) into a pipeline that can be saved, shared, and run headlessly on many images. It's a common choice for high-content screening and any workflow where the same analysis applies to hundreds or thousands of images.
Key features
- Modular pipeline builder with no scripting required
- Headless batch execution for cluster/HPC processing
- Extensible via Python plugins, including deep-learning segmenters (StarDist, Cellpose)
- Export to tables (CSV) or SQL for downstream analysis
Installation
Download the latest release from cellprofiler.org/releases. Older versions are available via previous releases — some published pipelines only work with a specific CellProfiler version.
CellProfiler with AI tools included
Getting CellProfiler to talk to Cellpose and StarDist is awkward to configure from scratch. Glencoe Software maintains a fork of CellProfiler v4.2.8 with both pre-bundled:
Install this version and the AI modules work out of the box.
Official documentation
Learning resources
Written
- Getting started tutorials — official worked examples covering common pipelines.
- Published example pipelines — adapt a nearby pipeline rather than building from scratch.