ArticleNature methods2025
Reproducible image-based profiling with Pycytominer.
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Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43citing papers in PubMed
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43 citing papers in PubMed.
- Deciphering senescence-associated mechanisms through cell painting & transcriptomics.npj aging · 2026Article
- A host-centric morphological profiling approach to identify repurposed antiviral drugs.iScience · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Reconstructing EBV reactivation and DNA damage response kinetics in morphologic pseudotime.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Scalable data harmonization for single-cell image-based profiling with CytoTable.Patterns (New York, N.Y.) · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Single-cell hit calling in high-content imaging screens with Buscar.bioRxiv : the preprint server for biology · 2026Article
- Predicting DNA damage response using synthetic cell painting profiles and experimental analysis.iScience · 2026Article
- A scalable approach to resolving variants of uncertain significance.bioRxiv : the preprint server for biology · 2026Article
- Multiplexed high-content imaging uncovers morphological diversity of lymphocyte activation and dysfunction.bioRxiv : the preprint server for biology · 2026Article
- Analyzing Cell Painting PLUS Data Using Cell Profiler and KNIME Analytics Platform.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Combined neocortical protein and morphological profiling of reactive microglia across Alzheimer's and Creutzfeldt-Jakob disease.Acta neuropathologica communications · 2025Article
- SubCell: Proteome-aware vision foundation models for microscopy capture single-cell biology.bioRxiv : the preprint server for biology · 2025Article
- Computational prediction of mutagenicity through comprehensive cell painting analysis.Mutagenesis · 2025Article
- Reconstructing EBV reactivation and DNA damage response kinetics in morphologic pseudotime.bioRxiv : the preprint server for biology · 2025Article
- Image-Based Profiling in Live Cells Using Live Cell Painting.Bio-protocol · 2025Article
- Alternate dyes for image-based profiling assays.SLAS discovery : advancing life sciences R & D · 2025Article
- The Integrated Stress Response Pathway Improves Aged Murine Muscle Stem Cell Activation andbioRxiv : the preprint server for biology · 2025Article
- Prediction of cellular morphology changes under perturbations with a transcriptome-guided diffusion model.Nature communications · 2025Article
- A quadratic paradigm describes the relationship between phenotype severity and variation.Nature communications · 2025Article
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Authors and funding
28 authors.
Erik SerranoDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
Srinivas Niranj ChandrasekaranImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-8874-9988
Dave BuntenDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.ORCID http://orcid.org/0000-0001-6041-3665
Kenneth I BrewerIndependent Researcher, San Francisco, CA, USA.
Jenna TomkinsonDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
Roshan KernDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.ORCID http://orcid.org/0000-0002-5605-4759
Michael BornholdtImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Stephen J FlemingData Sciences Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1885-4405
Ruifan PeiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
John ArevaloImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1138-5036
Hillary TsangImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Vincent RubinettiDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.
Callum Tromans-CoiaImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Tim BeckerImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9615-0799
Erin WeisbartImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-6437-2458
Charlotte BunneImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-1431-103X
Alexandr A KalininImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-4563-3226
Rebecca SenftImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Stephen J TaylorDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA.ORCID http://orcid.org/0000-0002-7279-7798
Nasim JamaliImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Adeniyi AdeboyeImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Hamdah Shafqat AbbasiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Allen GoodmanImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Juan C CaicedoImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
Anne E CarpenterImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-1555-8261
Beth A CiminiImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9640-9318
Shantanu SinghImaging Platform, Broad Institute of MIT and Harvard, Cambridge, MA, USA. shantanu@broadinstitute.org.ORCID http://orcid.org/0000-0003-3150-3025
Gregory P WayDepartment of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, USA. gregory.way@cuanschutz.edu.ORCID http://orcid.org/0000-0002-0503-9348
Funding
Computational Bioscience Program Training GrantT15LM009451 · NLM · UNIVERSITY OF COLORADO DENVER · PI Katherina Kechris-Mays, Arjun Krishnan · 2007 to 2026
$11.7MExtracting rich information from biological imagesR35GM122547 · NIGMS · BROAD INSTITUTE, INC. · PI Anne E. Carpenter · 2017 to 2026
$6.2MHuman Frontier Science Program (HFSP) RGY0081/2019Massachusetts Life Sciences Center (MLSC) Bits to Bytes Capital CallMassachusetts Life Sciences Center (MLSC) Data Science Internship ProgramNIGMS NIH HHS R35 GM122547NLM NIH HHS T15 LM009451U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM) T15LM009451
Abstract
Advances in high-throughput microscopy have enabled the rapid acquisition of large numbers of high-content microscopy images. Next, whether by deep learning or classical algorithms, image analysis pipelines commonly produce single-cell features. To process these single cells for downstream applications, we present Pycytominer, a user-friendly, open-source Python package that implements the bioinformatics steps key to image-based profiling. We demonstrate Pycytominer's usefulness in a machine-learning project to predict nuisance compounds that cause undesirable cell injuries.
Indexed as
Computational BiologyImage Processing, Computer-AssistedSingle-Cell AnalysisSoftwareAlgorithmsHumansMachine LearningMicroscopyReproducibility of Results
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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.