ArticleNature methods2017
Data-analysis strategies for image-based cell profiling.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 362 papers.
What it found
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Who cites it
362 citing papers in PubMed.
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- Halo: a pretrained model for whole-cell segmentation from nuclei images in spatial transcriptomics.Briefings in bioinformatics · 2026Article
- Functional Vascularization in Tumor Organoid and Tumor-on-Chip Models: Evidence Requirements for Attributing Therapy-Resistance Mechanisms.Bioengineering (Basel, Switzerland) · 2026Review
- 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
- Review
- Data modeling the interplay between single-cell shape, single-cell protein expression, and tissue state.Cell reports methods · 2026Article
- Mapping human microglial morphological diversity via handcrafted and deep learning-derived image features.iScience · 2026Article
- Microscopy Cell Segmentation: Review and Benchmarking of Task-Specific and Foundation Models.Journal of imaging · 2026Review
- From EM to AI: Multiscale imaging of the secretory pathway with insights from plant cells.Journal of microscopy · 2026Review
- Integrating chemical structures as treatments improves representations of microscopy images for morphological profiling.PLoS computational 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
- Impact of regularization methods and outlier removal on unsupervised sample classification.BMC bioinformatics · 2026Article
- DyMamba: dynamic Mamba for microscopy image semantic segmentation.Bioinformatics (Oxford, England) · 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
- High-Content Imaging and Machine Learning Classify Phenotypical Change in Coronary Artery Endothelial Cells Caused by BPS.International journal of molecular sciences · 2026Article
- Cell Painting PLUS: An Iterative Staining-Elution Protocol for High-Content Phenotypic Screenings.Current protocols · 2026Article
302 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
24 authors.
Funding
Abstract
Image-based cell profiling is a high-throughput strategy for the quantification of phenotypic differences among a variety of cell populations. It paves the way to studying biological systems on a large scale by using chemical and genetic perturbations. The general workflow for this technology involves image acquisition with high-throughput microscopy systems and subsequent image processing and analysis. Here, we introduce the steps required to create high-quality image-based (i.e., morphological) profiles from a collection of microscopy images. We recommend techniques that have proven useful in each stage of the data analysis process, on the basis of the experience of 20 laboratories worldwide that are refining their image-based cell-profiling methodologies in pursuit of biological discovery. The recommended techniques cover alternatives that may suit various biological goals, experimental designs, and laboratories' preferences.
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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 Socratic graph.