From 7 to 11 December 2026, the German Network for Bioinformatics Infrastructure (de.NBI) hosts the 5th BioHackathon Germany at Hotel Freizeit In in Göttingen. Open Problems and SpaceHack, a spatial transcriptomics hackathon series that has produced community benchmarks and best practices over its previous editions, are joining forces there with the project OpenProblems.Bio x SpaceHack 5.0: Multi-Modal Spatial Benchmarking and FAIR Data Standards, led by Naveed Ishaque (BIH at Charité) and Malte Lücken (Helmholtz Munich).
Spatial omics technologies now generate data at a scale and diversity that outstrips our ability to evaluate the methods analysing them. Over five days, we will port existing spatial benchmarks onto the Open Problems platform, define new spatial tasks, and build the data infrastructure that lets both communities draw on FAIR community datasets.
Subprojects
The work is split over parallel subprojects:
- Multimodal niche detection
- Spatial trajectory inference
- Spatial cell-cell communication
- Spatial and single-cell integration
- Spatial proteomics preprocessing
- Foundation model evaluation
- Cell segmentation evaluation
- Spatial segmentation simulation
- Porting existing benchmarks to Open Problems
- Loaders for the BioImage Archive and other FAIR spatial data resources (e.g. LaminLabs SpatialDB), so that community datasets become directly usable for continuous, reproducible benchmarking
Who should join
We welcome method developers, tool maintainers, data infrastructure engineers and tissue biologists. Contributions range from implementing a metric or a dataset loader to defining what a task should measure in the first place. All outputs are open source and land in a platform that keeps evaluating methods long after the hackathon ends.
Taking part
The hackathon is hybrid. On-site places are fully booked, but you can still register to join remotely. The programme starts on Monday 7 December at 13:00 with the project presentations and ends on Friday 11 December with the final reports from each project. The full programme and travel information are on the event website.
Let’s bring the Open Problems and SpaceHack communities and new contributors together for this joint effort! And thanks to de.NBI for hosting the BioHackathon.
