CellProfiler pipelines for Cell Painting

Standard CellProfiler pipelines used by Pharmbio at Uppsala University for Cell Painting image analysis: illumination correction, quality control, segmentation and feature extraction.

Origin

These pipelines are adapted from the Broad Institute Imaging Platform's Cell Painting pipelines (broadinstitute/imaging-platform-pipelines) and modified for our imaging setup.

Citation

If you use these pipelines, please cite this repository.

Authors

Jonne Rietdijk, Polina Georgiev, Anders Larsson, Maris Lapins — Pharmbio, Uppsala University.

License

BSD 3-Clause — see LICENSE.

References

• Bray M-A, et al. Cell Painting, a high-content image-based assay for morphological profiling using multiplexed fluorescent dyes. Nature Protocols 11, 1757–1774 (2016).
• Cimini BA, et al. Optimizing the Cell Painting assay for image-based profiling. Nature Protocols 18, 1981–2013 (2023).