ArticleCytometry. Part A : the journal of the International Society for Analytical Cytology2023
Assessing the performance of the Cell Painting assay across different imaging systems.
Article in Cytometry. Part A : the journal of the International Society for Analytical Cytology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Retrieval-Based Evaluation of Cell Painting Feature Spaces Reveals Differences in the Preservation of Biologically Meaningful Phenotypic Similarity.International journal of molecular sciences · 2026Article
- Transitive prediction of small-molecule function through alignment of high-content screening resources.Nature biotechnology · 2026Article
- Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings.Current protocols · 2026Article
- The Cell Painting PLUS Method: Phenotypic Profiling Using Iterative Staining-Elution Cycles.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Alternate dyes for image-based profiling assays.SLAS discovery : advancing life sciences R & D · 2025Article
- Prediction of Bioactive Metabolites from AmericanJournal of natural products · 2025Article
- Triple-effect correction for Cell Painting data with contrastive and domain-adversarial learning.Nature communications · 2025Article
- Cell Painting PLUS: expanding the multiplexing capacity of Cell Painting-based phenotypic profiling using iterative staining-elution cycles.Nature communications · 2025Article
- Bridging imaging-based in vitro methods from biomedical research to regulatory toxicology.Archives of toxicology · 2025Review
- Review
- Cell Painting: a decade of discovery and innovation in cellular imaging.Nature methods · 2025Review
- Insights into the Identification of iPSC- and Monocyte-Derived Macrophage-Polarizing Compounds by AI-Fueled Cell Painting Analysis Tools.International journal of molecular sciences · 2024Article
- A Decade in a Systematic Review: The Evolution and Impact of Cell Painting.bioRxiv : the preprint server for biology · 2024Article
- Article
- Unleashing the potential of cell painting assays for compound activities and hazards prediction.Frontiers in toxicology · 2024Review
- Optimizing the Cell Painting assay for image-based profiling.Nature protocols · 2023Review
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Authors and funding
17 authors.
Funding
Abstract
Quantitative microscopy is a powerful method for performing phenotypic screens from which image-based profiling can extract a wealth of information, termed profiles. These profiles can be used to elucidate the changes in cellular phenotypes across cell populations from different patient samples or following genetic or chemical perturbations. One such image-based profiling method is the Cell Painting assay, which provides morphological insight through the imaging of eight cellular compartments. Here, we examine the performance of the Cell Painting assay across multiple high-throughput microscope systems and find that all are compatible with this assay. Furthermore, we determine independently for each microscope system the best performing settings, providing those who wish to adopt this assay an ideal starting point for their own assays. We also explore the impact of microscopy setting changes in the Cell Painting assay and find that few dramatically reduce the quality of a Cell Painting profile, regardless of the microscope used.
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