From 0a23063066ca69269ae2f887c2dce284d9e1aa44 Mon Sep 17 00:00:00 2001 From: Benedikt von Querfurth <50669691+bvquerfurth@users.noreply.github.com> Date: Wed, 28 Oct 2026 23:37:09 +0100 Subject: [PATCH 1/3] Updated spora links, added spora report --- resources/use-cases/spatial-omics/index.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/resources/use-cases/spatial-omics/index.md b/resources/use-cases/spatial-omics/index.md index 336d773a..6fdf6c5d 100644 --- a/resources/use-cases/spatial-omics/index.md +++ b/resources/use-cases/spatial-omics/index.md @@ -10,10 +10,13 @@ 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) 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]( +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 From 8abcaf0942996f0d966f7fce5215d8730d506df0 Mon Sep 17 00:00:00 2001 From: Benedikt von Querfurth <50669691+bvquerfurth@users.noreply.github.com> Date: Thu, 29 Oct 2026 10:22:22 +0100 Subject: [PATCH 2/3] Updated spora[data] link --- resources/use-cases/spatial-omics/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/use-cases/spatial-omics/index.md b/resources/use-cases/spatial-omics/index.md index 6fdf6c5d..87af473a 100644 --- a/resources/use-cases/spatial-omics/index.md +++ b/resources/use-cases/spatial-omics/index.md @@ -11,7 +11,7 @@ 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/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) a resource containing multiple harmonized spatial proteomics datasets +* [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 * 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]( From 06dfe348819454542b97cbbb5b7c87a9e5004247 Mon Sep 17 00:00:00 2001 From: Josh Moore Date: Sun, 1 Nov 2026 09:29:54 +0100 Subject: [PATCH 3/3] Apply suggestion from @lubianat Co-authored-by: Tiago Lubiana --- resources/use-cases/spatial-omics/index.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/resources/use-cases/spatial-omics/index.md b/resources/use-cases/spatial-omics/index.md index 87af473a..d4d3f91c 100644 --- a/resources/use-cases/spatial-omics/index.md +++ b/resources/use-cases/spatial-omics/index.md @@ -14,8 +14,7 @@ The SpatialData format builds upon OME-Zarr to provide a standard for storing sp * [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 * 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]( -https://doi.org/10.48550/arXiv.2610.24002). A technical report on spora, alongside a benchmark of spatial proteomics computational methods and foundation models. +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