On 18–19 May 2026, the Human Cell Atlas hosted a Spatial Cell Segmentation Hackathon at Mirai House, the 10x Genomics EMEA headquarters in the Leiden Bio Science Park, Netherlands. The two-day hybrid event brought teams together to tackle one of the hardest problems in imaging-based spatial transcriptomics: accurately segmenting individual cells from imaging spatial transcriptomics (iST) data.
Open Problems organised the benchmarking infrastructure for the hackathon. In preparation for the meeting, we presented the proposed benchmark design (the datasets, task API, methods, and evaluation metrics) so that teams could spend the hackathon building and comparing segmentation methods against a shared, reproducible standard rather than ad-hoc pipelines.
That groundwork produced a new Open Problems benchmark: task_spatial_segmentation.