Abstract
Modern quantitative image analysis techniques have enabled high-throughput, high-content imaging experiments. Image-based profiling leverages the rich information in images to identify similarities or differences among biological samples, rather than measuring a few features, as in high-content screening. Here, we review a decade of advancements and applications of Cell Painting, a microscopy-based cell-labeling assay aiming to capture a cell’s state, introduced in 2013 to optimize and standardize image-based profiling. Cell Painting’s ability to capture cellular responses to various perturbations has expanded owing to improvements in the protocol, adaptations for different perturbations, and enhanced methodologies for feature extraction, quality control, and batch-effect correction. Cell Painting is a versatile tool that has been used in various applications, alone or with other -omics data, to decipher the mechanism of action of a compound, its toxicity profile, and other biological effects. Future advances will likely involve computational and experimental techniques, new publicly available datasets, and integration with other high-content data types.
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Change history
12 December 2024
A Correction to this paper has been published: https://doi.org/10.1038/s41592-024-02578-y
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Acknowledgements
S. Seal acknowledges funding from the Cambridge Centre for Data-Driven Discovery (C2D3) and Accelerate Programme for Scientific Discovery. A.E.C., S. Singh, and S. Seal acknowledge funding from the National Institutes of Health (R35 GM122547 to A.E.C.). O.S. acknowledges funding from the Swedish Research Council (Grants 2020-03731 and 2020-01865), FORMAS (Grant 2022-00940), Swedish Cancer Foundation (22 2412 Pj 03 H), and Horizon Europe (Grant Agreements 101057014 (PARC) and 101057442 (REMEDI4ALL)).
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S. Seal and M.-A.T. designed and performed the systematic review on studies using Cell Painting data. S. Seal, M.-A.T., and A.E.C. wrote the manuscript with extensive discussions with all authors. All of the authors reviewed, edited, and contributed to discussions on the manuscript and approved the final version of the manuscript.
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S. Singh and A.E.C. serve as scientific advisors for companies that use image-based profiling and Cell Painting (A.E.C.: Recursion, SyzOnc, Quiver Bioscience; S. Singh: Waypoint Bio, Dewpoint Therapeutics, DeepCell) and receive honoraria for occasional talks at pharmaceutical and biotechnology companies. J.C.P. and O.S. declare ownership in Phenaros Pharmaceuticals. M.-A.T. and N.G. were formerly employed at AstraZeneca. M.-A.T. and N.G. are currently employed at Recursion Pharmaceuticals. The remaining authors declare no competing interests.
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Supplementary Table 1
Definitions of essential terms in image-based profiling
Supplementary Table 2
90 studies included in this study
Supplementary Table 3
65 studies excluded in this study
Supplementary Table 4
Academic institutions, government agencies, pharmaceutical companies, non-profit organizations that led studies evaluated in this work and/or are members of the JUMPCP or OASIS consortiums.
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Seal, S., Trapotsi, MA., Spjuth, O. et al. Cell Painting: a decade of discovery and innovation in cellular imaging. Nat Methods 22, 254–268 (2025). https://doi.org/10.1038/s41592-024-02528-8
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DOI: https://doi.org/10.1038/s41592-024-02528-8
