Announcements
Papers, public preprints, and community updates, newest first.
2026-08-07 — JUMP-lite: compact, reproducible benchmarking of cell representations
Preprint
JUMP-lite provides a compact subset of JUMP Cell Painting for developing and comparing cell-image representations. The paper also introduces Nahual, an open-source framework for reproducible model deployment.
2025-09-15 — OASIS: multi-omics for chemical safety assessment
Published · Toxicological Sciences
The OASIS Consortium combines Cell Painting, transcriptomics, and proteomics across cell models to improve chemical safety assessment. The initiative aims to make safety testing more predictive of human biology while reducing animal use.
2025-08-07 — Morphological map of under- and overexpression of genes in human cells
Published · Nature Methods
The JUMP Cell Painting genetic dataset captures the effects of perturbing 15,243 human genes through CRISPR knockouts and gene overexpression. Its single-cell images and morphological profiles support exploration of gene functions and relationships.
2025-07-01 — cp_measure: API-first feature extraction for image-based profiling workflows
Preprint
cp_measure brings CellProfiler’s core measurement capabilities into a modular, API-first Python library for morphological feature extraction. It makes image-based profiling easier to integrate into automated analysis workflows.
2025-06-04 — copairs: evaluating profile strength and similarity
Published · Nature Communications
An information-retrieval framework using mean average precision to measure phenotypic activity and consistency.
2025-03-03 — Reproducible image-based profiling with Pycytominer
Published · Nature Methods
Pycytominer is an open-source Python package for processing single-cell measurements into profiles for downstream analysis. It provides reproducible bioinformatics steps for image-based profiling workflows.
2024-12-16 — MotiVE: drug–target interaction prediction
Published · NeurIPS 2024, Datasets and Benchmarks Track
A drug–target interaction graph combining Cell Painting profiles and known relationships to benchmark predictions for unseen compounds and genes.
2024-12-05 — Cell Painting: a decade of discovery and innovation in cellular imaging
Published review · Nature Methods
A review of a decade of Cell Painting advances, from assay protocols and image analysis to biological applications. It covers feature extraction, quality control, batch correction, and integration with other omics data.
2024-09-02 — Cell Painting Gallery: an open resource for image-based profiling
Published · Nature Methods
Cell Painting Gallery provides public image datasets for image-based profiling, including JUMP. The resource supports data discovery and reuse for biological research and computational method development.
2024-08-02 — Batch correction for Cell Painting
Published · Nature Communications
A benchmark of batch-correction methods for integrating JUMP Cell Painting profiles across laboratories and microscopes.