ArticleMolecular biology of the cell2021
Predicting cell health phenotypes using image-based morphology profiling.
Article in Molecular biology of the cell, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- A host-centric morphological profiling approach to identify repurposed antiviral drugs.iScience · 2026Article
- Maximum Matching Accuracy: An Instance Segmentation Evaluation Metric Utilizing Globally Optimal Matching.ArXiv · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Predicting DNA damage response using synthetic cell painting profiles and experimental analysis.iScience · 2026Article
- Unlocking the potential of computational phenotypic drug discovery: methods, challenges, and future directions.NPJ systems biology and applications · 2026Review
- Leveraging AI for cell biology discovery.Biochemical Society transactions · 2026Review
- Synthetic lethality in cancer drug discovery: challenges and opportunities.Nature reviews. Drug discovery · 2026Review
- PhenoProfiler: advancing phenotypic learning for image-based drug discovery.Nature communications · 2025Article
- Label-Free Longitudinal Imaging of Single Cell Drug Response with a 3D-Printed Cell Culture Platform.Analytical chemistry · 2025Article
- Evolution of the PRNT: Merging tradition and innovation to set the gold standard in the era of automation.Human vaccines & immunotherapeutics · 2025Review
- Joint profiling of cell morphology and gene expression during in vitro neurodevelopment.eLife · 2025Article
- Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.PLoS computational biology · 2025Article
- Quantitative analysis of human umbilical vein endothelial cell morphology and tubulogenesis.Journal of microscopy · 2025Article
- High-Throughput Microfluidic Technologies for Rapidly Screening Pollutant-Induced Cell Health Effects.ACS bio & med chem Au · 2025Article
- Alternate dyes for image-based profiling assays.SLAS discovery : advancing life sciences R & D · 2025Article
- A machine learning-based analysis method for small molecule high content screening of three-dimensional cancer spheroid morphology.Molecular pharmacology · 2025Article
- Article
- A versatile information retrieval framework for evaluating profile strength and similarity.Nature communications · 2025Article
- A morphology and secretome map of pyroptosis.Molecular biology of the cell · 2025Article
- CellPHIE: Integrating Pathway Discovery With Pooled Profiling of Perturbations Uncovers Pathways of Huntington's Disease, Including Genetic Modifiers of Neuronal Development and Morphology.bioRxiv : the preprint server for biology · 2025Article
15 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Genetic and chemical perturbations impact diverse cellular phenotypes, including multiple indicators of cell health. These readouts reveal toxicity and antitumorigenic effects relevant to drug discovery and personalized medicine. We developed two customized microscopy assays, one using four targeted reagents and the other three targeted reagents, to collectively measure 70 specific cell health phenotypes including proliferation, apoptosis, reactive oxygen species, DNA damage, and cell cycle stage. We then tested an approach to predict multiple cell health phenotypes using Cell Painting, an inexpensive and scalable image-based morphology assay. In matched CRISPR perturbations of three cancer cell lines, we collected both Cell Painting and cell health data. We found that simple machine learning algorithms can predict many cell health readouts directly from Cell Painting images, at less than half the cost. We hypothesized that these models can be applied to accurately predict cell health assay outcomes for any future or existing Cell Painting dataset. For Cell Painting images from a set of 1500+ compound perturbations across multiple doses, we validated predictions by orthogonal assay readouts. We provide a web app to browse predictions: http://broad.io/cell-health-app. Our approach can be used to add cell health annotations to Cell Painting datasets.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.