ArticlePloS one2013
Multiplex cytological profiling assay to measure diverse cellular states.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 152 papers.
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Who cites it
152 citing papers in PubMed.
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- Generative machine learning unlocks the first proteome-wide image of human cells.bioRxiv : the preprint server for biology · 2026Article
- Combinatorial prediction of therapeutic perturbations using causally inspired neural networks.Nature biomedical engineering · 2026Article
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- Large scale compound selection guided by cell painting reveals activity cliffs and functional relationships.Communications biology · 2026Article
- Quality Control Measures and Statistical Strategies to Address the Challenges of High-Content Phenotypic Data.Methods in molecular biology (Clifton, N.J.) · 2026Article
- The Cell Painting PLUS Method: Phenotypic Profiling Using Iterative Staining-Elution Cycles.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A pooled Cell Painting CRISPR screening platform enables de novo inference of gene function by self-supervised deep learning.Nature communications · 2025Article
- PhenoProfiler: advancing phenotypic learning for image-based drug discovery.Nature communications · 2025Article
- Generalizable morphological profiling of cells by interpretable unsupervised learning.Nature communications · 2025Article
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
- Joint profiling of cell morphology and gene expression during in vitro neurodevelopment.eLife · 2025Article
- Backbone Alterations in Cyclic Peptides Influence Both Membrane Permeability and Biological Activity.Journal of medicinal chemistry · 2025Article
- Chr:17q21.31 locus risk haplotype H1 susceptibility to ferroptosis is mediated by endolysosomal pathway.Cell death & disease · 2025Article
- Smaller scale, same impact: replicating high-throughput phenotypic profiling in a medium-throughput lab for use in chemical risk assessment.Archives of toxicology · 2025Article
- Computational prediction of mutagenicity through comprehensive cell painting analysis.Mutagenesis · 2025Article
- Dual-Mode Wheat Germ Agglutinin Labeling - A Versatile Cell Segmentation Strategy for High-Resolution LA-ICP-TOFMS Bioimaging.Analytical chemistry · 2025Article
- A machine learning-based analysis method for small molecule high content screening of three-dimensional cancer spheroid morphology.Molecular pharmacology · 2025Article
92 more citing papers are in PubMed but not listed here.
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Authors and funding
13 authors.
Funding
Abstract
Computational methods for image-based profiling are under active development, but their success hinges on assays that can capture a wide range of phenotypes. We have developed a multiplex cytological profiling assay that "paints the cell" with as many fluorescent markers as possible without compromising our ability to extract rich, quantitative profiles in high throughput. The assay detects seven major cellular components. In a pilot screen of bioactive compounds, the assay detected a range of cellular phenotypes and it clustered compounds with similar annotated protein targets or chemical structure based on cytological profiles. The results demonstrate that the assay captures subtle patterns in the combination of morphological labels, thereby detecting the effects of chemical compounds even though their targets are not stained directly. This image-based assay provides an unbiased approach to characterize compound- and disease-associated cell states to support future probe discovery.
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Registered trials
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