ArticlePatterns (New York, N.Y.)2026
Scalable data harmonization for single-cell image-based profiling with CytoTable.
Article in Patterns (New York, N.Y.), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- 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
- Article
- A morphology and secretome map of pyroptosis.Molecular biology of the cell · 2025Article
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Authors and funding
8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
High-content imaging (HCI) involves the automated acquisition and quantitative analysis of cell phenotypes from microscopy images. These studies often rely on screening, which can involve thousands of chemical or genetic perturbations that produce terabytes of microscopy data. To extract meaningful biological insights, these data must be processed into quantitative features through a technique known as image-based profiling. A major analytical bottleneck is curating the high-dimensional, single-cell data derived from various image-analysis tools. These datasets suffer from inconsistent schemas, inefficient file formats, and undocumented ontological relationships. These challenges reduce reproducibility and slow progress in downstream applications. To solve these issues, we introduce CytoTable, a software package for harmonizing single-cell image-based profiling. CytoTable enables modular, portable, and cross-language data integration through a robust, reproducible, and scalable engine that harmonizes single-cell readouts from multiple image-analysis tools, preparing for feature integration with software in the Cytomining ecosystem such as Pycytominer.
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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.