Unifying Omics Hackathon Series
Bridging scverse and Cell Painting communities at the intersection of image-based profiling, phenomics, and single-cell perturbation analysis.
About the event
Recent advances in Cell Painting and image-based profiling have created an emerging overlap of biological questions addressed by separate computational ecosystems. This hackathon brings together the scverse, CytoData Society, and EU-OPENSCREEN communities for three days of hands-on development at the MDC Berlin, built around three concrete tracks spanning Cell Painting analysis with scverse tooling, single-cell perturbation tools, and scalable model training.
We explicitly welcome analysts and biological scientists experienced in Cell Painting workflows alongside software developers, computational biologists, and ML researchers. The focus is high-throughput image-based profiling of cultured cells (Cell Painting, JUMP-CP, EU-OPENSCREEN), not clinical histopathology, H&E/IHC, or tissue-level imaging. Domain expertise is as critical as technical development: the goal is reusable open-source tools at the intersection of Cell Painting, single-cell perturbation analysis, and phenomics.
For Cell Painting practitioners: the scverse ecosystem provides standardised data structures, composable analysis workflows, and community best practices that have transformed single-cell transcriptomics. The single-cell best practices book illustrates the kind of streamlined, interoperable analyses we could build for image-based profiles, enabling seamless integration with perturbation data. In particular, we believe that the recent engineering efforts made by the tools towards being able to routinely handle large datasets (10+ millions of observations) can be leveraged for Cell Painting.
For ML researchers: Cell Painting generates phenotypic fingerprints of millions of cells across thousands of compounds, making it one of the richest high-throughput biological datasets available. Two good entry points into the field are the reviews by Caicedo et al. and Serrano et al..
Hackathon tracks
Closer to the event, we will publish a set of actionable tasks grouped into these three workstreams. You will later decide which task fits your expertise and interests best. Participants will group around these tasks and then work as a team toward a concrete, shippable outcome over the three days. Workstreams are topically distinct but not siloed: cross-workstream collaboration is encouraged wherever tools or data overlap.
Integrating Scanpy and AnnData into Cell Painting workflows: from raw image ingestion and single-cell segmentation through CellProfiler-compatible feature extraction to population-level profile aggregation, making Cell Painting data fully interoperable with single-cell and perturbation pipelines.
@timtreisApplying pertpy and related tools to large-scale resources such as JUMP-CP and the EU-OPENSCREEN compound collections, exploring multi-omics integration with matched Perturb-seq data, cross-modal mechanism-of-action inference, and uncertainty quantification for actionable hit prioritisation.
Tackling infrastructure challenges of modern Cell Painting resources spanning hundreds of thousands of compounds. Using scverse-native tooling such as annbatch with the EU-OPENSCREEN ECBL dataset to produce proof-of-concept ML pipelines ready for post-event follow-up.
Programme
Wed Sep 2
Thu Sep 3
Fri Sep 4
The team
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Participate
Whether you are an analyst or biological scientist experienced in Cell Painting, a software developer, computational biologist, or ML researcher: if you work at the intersection of Cell Painting and single-cell biology, this event is for you. Apply below or reach out with any questions.
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