xiao233333/asi-fimsa-workshop-2026
ASI-FIMSA 2026 spatial omics workshop — staged data Small, Colab-sized artifacts derived from the public 10x Genomics Atera whole-transcriptome Xenium preview dataset of FFPE human breast cancer, prepared for a two-hour hands-on workshop at the ASI-FIMSA meeting. Notebooks and build scripts: https://github.com/xiao233333/ASI-FIMSA-workshop-2026 Attribution Derived from Preview Data: Atera In Situ Gene Expression, FFPE Human Breast Cancer. Data © 10x Genomics, used… See the full description on the dataset page: https://huggingface.co/datasets/xiao233333/asi-fimsa-workshop-2026.
Dataset card: CC BY 4.0 attribution, contents, caveats
Upload cci_panel_genes.txt with huggingface_hub
Upload manifest.json with huggingface_hub
Add atera_crop_lr.h5ad (ASI-FIMSA 2026 Staged dataset)
Manifest: Drive mirror live, per-file ids recorded
Checksums for rebuilt Crop
Crop: stamp as-built cell counts into attrs (crop 16006, he_zoom 337)
Manifest: licence recorded as CC BY 4.0, checksums match the live artifacts
Ship voronoi.py so notebooks can fetch it without the GitHub repo
Update checksums for rebuilt Crop
Rebuild Crop: all 16,006 cell boundaries are single Polygons (make_valid could emit MultiPolygon/GeometryCollection, breaking spatialdata-plot's datashader path)
Dataset card: CC BY 4.0 attribution, contents, caveats
Upload crop_window.json with huggingface_hub
Upload atera_cluster_annotation.csv with huggingface_hub
Upload manifest.json with huggingface_hub
Add atera_crop.zarr.zip (ASI-FIMSA 2026 Staged dataset)
Add atera_wholeslide_cells.h5ad (ASI-FIMSA 2026 Staged dataset)
initial commit