Media

🎬 Video #

The Cytomining Ecosystem: Open Source Software for Image-Based Profiling

📰 Press #

• CU Anschutz News (July 2026): From Microscopes to Treatments: The Cytomining Ecosystem • Read the article

🎤 Talks #

• SBI2 2025: Cytomining ecosystem overview • Watch on YouTube
• ParslFest 2025: With great Parsl comes great portability: Using Parsl through CytoTable for harmonizing single-cell data • Watch on YouTube · View slides
• CytoData 2020: Pycytominer: a computational ecosystem supporting reproducible image-based profiling • Watch on YouTube

🖼️ Posters #

• OME 2026 Community Meeting: OME-Arrow: Unifying Images, Metadata, and Features in an Interoperable Data Model • View poster
• SBI2 2025: Exploring single-cell images and profiles together with CytoDataFrame • View poster
• SBI2 2024: Single-cell Morphology Quality Control (coSMicQC) • View poster
• SciPy 2023: Cross-language Data Grammar for Single-cell Research Feature Engineering • View poster
• SBI2 2023: CytoTable: High performance and scalable single-cell morphology feature engineering • View poster

📚 Publications #

🔎 Reviews #

• Serrano, E. et al. Progress and new challenges in image-based profiling. Mol. Syst. Biol. 22, 624–658 (2026). doi:10.1038/s44320-026-00197-7
• Caicedo, J.C. et al. Data-analysis strategies for image-based cell profiling. Nat. Methods 14, 849–863 (2017). doi:10.1038/nmeth.4397

🧰 Tools #

Peer-reviewed #

• CytoTable (tool page · GitHub): Bunten, D. et al. Scalable data harmonization for single-cell image-based profiling with CytoTable. Patterns 7, 101514 (2026). doi:10.1016/j.patter.2026.101514
• Pycytominer (tool page · GitHub): Serrano, E. et al. Reproducible image-based profiling with Pycytominer. Nat. Methods 22, 677–680 (2025). doi:10.1038/s41592-025-02611-8
• copairs (tool page · GitHub): Kalinin, A.A. et al. A versatile information retrieval framework for evaluating profile strength and similarity. Nat. Commun. 16, 5181 (2025). doi:10.1038/s41467-025-60306-2
• DeepProfiler (tool page · GitHub): Moshkov, N. et al. Learning representations for image-based profiling of perturbations. Nat. Commun. 15, 1594 (2024). doi:10.1038/s41467-024-45999-1

Preprints #

• buscar (tool page · GitHub): Serrano, E., Li, W.S. & Way, G.P. Single-cell hit calling in high-content imaging screens with Buscar. bioRxiv (2026). doi:10.64898/2026.04.15.718737
• coSMicQC (tool page · GitHub): Tomkinson, J. et al. Stellar quality control for single-cell image-based profiling with coSMicQC. bioRxiv (2025). doi:10.1101/2025.10.14.682427