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Updates "spora" links #643

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joshmoore merged 3 commits into from
Nov 1, 2026
Merged

Updates "spora" links #643

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0a23063
Updated spora links, added spora report
bvquerfurth Oct 28, 2026
8abcaf0
Updated spora[data] link
bvquerfurth Oct 29, 2026
06dfe34
Apply suggestion from @lubianat
joshmoore Nov 1, 2026
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8 changes: 5 additions & 3 deletions resources/use-cases/spatial-omics/index.md
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Expand Up @@ -10,10 +10,12 @@ The SpatialData format builds upon OME-Zarr to provide a standard for storing sp

### spora ecosystem

* [A spora data formats specification](https://spora.epfl.ch/docs-data.html) used to harmonize datasets. It stores structured tabular data as `.parquet`, all whole-slide images as `.ome.zarr`, and segmentation masks as `.npz`.
* [spora[data]](https://spora.epfl.ch/datasets.html) a resource containing multiple harmonized spatial proteomics datasets
* [A spora data formats specification](https://spora.epfl.ch/docs/io/format.html) used to harmonize datasets. It stores structured tabular data as `.parquet`, all spatial proteomics and histopathology whole-slide images as `.ome.zarr`, and segmentation and tissue masks as `.npz`.
* [spora[data]](https://spora.bioimagearchive.org/projects/spora) a resource containing multiple harmonized spatial proteomics datasets
* [spora [io]](https://github.com/bunnelab/spora-io) a Python library for accessing spora datasets
* Wenckstern, J., Jain, E., von Querfurth, B. et al. [The Virtual Tissues foundation model resolves spatial proteomics across scales](https://doi.org/10.1038/s41586-026-10884-y). Nature (2026). https://doi.org/10.1038/s41586-026-10884-y ([github repo](https://github.com/bunnelab/virtues#datasets))
* von Querfurth, B., Wenckstern, J., Jain, E. et al. [spora: A Unified Multimodal Dataset and Platform for Spatial Proteomics](
https://doi.org/10.48550/arXiv.2610.24002). NeurIPS Evaluations & Datasets (2026). https://doi.org/10.48550/arXiv.2610.24002 A technical report on spora, alongside a benchmark of spatial proteomics computational methods and foundation models.
* Wenckstern, J., Jain, E., von Querfurth, B. et al. [The Virtual Tissues foundation model resolves spatial proteomics across scales](https://doi.org/10.1038/s41586-026-10884-y). Nature (2026). https://doi.org/10.1038/s41586-026-10884-y ([github repo](https://github.com/bunnelab/virtues#datasets)). A spatial proteomics foundation model "VirTues", pre-trained on parts of the spora data corpus using the spora [io] dataloaders.

## other

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