ReviewNature protocols2023
Optimizing the Cell Painting assay for image-based profiling.
Review in Nature protocols, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 95 papers.
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Who cites it
95 citing papers in PubMed.
- Functional immune profiling translates T cell dynamics into predictive biomarkers for myeloma immunotherapy.Leukemia · 2026Article
- A host-centric morphological profiling approach to identify repurposed antiviral drugs.iScience · 2026Article
- Cell Painting in activated cells illuminates phenotypic dark space and drug mechanisms of action.Nature communications · 2026Article
- A High-Content Imaging Pipeline to Investigate Subcytotoxic Effects in RTgill-W1 Cells.Environmental science & technology · 2026Article
- Structure-based scaffold hopping reveals strategies to overcome oncogenic KIT and PDGFRA mutation-driven drug-resistance in GIST.Nature communications · 2026Article
- Subcellularly Resolved 3D Translatome in Mouse Oocytes and Early Embryos.bioRxiv : the preprint server for biology · 2026Article
- CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies.Nature communications · 2026Article
- Leveraging Morphological Profiling for Mechanistic Elucidation of Metal-Based Anticancer Compounds.JACS Au · 2026Article
- Spatial multi-omics identifies early synaptic pruning and context-specific dopaminergic vulnerability in synucleinopathies.Nature communications · 2026Article
- A one-week automated genome-wide optical pooled screen using OttoSeq.Genome biology · 2026Article
- Retrieval-Based Evaluation of Cell Painting Feature Spaces Reveals Differences in the Preservation of Biologically Meaningful Phenotypic Similarity.International journal of molecular sciences · 2026Article
- A comprehensive pharmacological survey across heterogeneous patient-derived glioblastoma stem cell models.iScience · 2026Article
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- The one-week automated genome-wide optical pooled screen.bioRxiv : the preprint server for biology · 2026Article
- Article
- Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings.Current protocols · 2026Article
- Predicting DNA damage response using synthetic cell painting profiles and experimental analysis.iScience · 2026Article
- BESTDR Enables Bayesian Quantification of Mechanism-Specific Drug Responses.Cancer research · 2026Article
- Unlocking the potential of computational phenotypic drug discovery: methods, challenges, and future directions.NPJ systems biology and applications · 2026Review
- A scalable approach to resolving variants of uncertain significance.bioRxiv : the preprint server for biology · 2026Article
35 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
35 authors.
Funding
Abstract
In image-based profiling, software extracts thousands of morphological features of cells from multi-channel fluorescence microscopy images, yielding single-cell profiles that can be used for basic research and drug discovery. Powerful applications have been proven, including clustering chemical and genetic perturbations on the basis of their similar morphological impact, identifying disease phenotypes by observing differences in profiles between healthy and diseased cells and predicting assay outcomes by using machine learning, among many others. Here, we provide an updated protocol for the most popular assay for image-based profiling, Cell Painting. Introduced in 2013, it uses six stains imaged in five channels and labels eight diverse components of the cell: DNA, cytoplasmic RNA, nucleoli, actin, Golgi apparatus, plasma membrane, endoplasmic reticulum and mitochondria. The original protocol was updated in 2016 on the basis of several years' experience running it at two sites, after optimizing it by visual stain quality. Here, we describe the work of the Joint Undertaking for Morphological Profiling Cell Painting Consortium, to improve upon the assay via quantitative optimization by measuring the assay's ability to detect morphological phenotypes and group similar perturbations together. The assay gives very robust outputs despite various changes to the protocol, and two vendors' dyes work equivalently well. We present Cell Painting version 3, in which some steps are simplified and several stain concentrations can be reduced, saving costs. Cell culture and image acquisition take 1-2 weeks for typically sized batches of ≤20 plates; feature extraction and data analysis take an additional 1-2 weeks.This protocol is an update to Nat. Protoc. 11, 1757-1774 (2016): https://doi.org/10.1038/nprot.2016.105.
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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.