Spatial Omics#
The SpatialData format builds upon OME-Zarr to provide a standard for storing spatial omics data. There are a number of resources that build either on OME-Zarr directly or upon SpatialData.
Links#
Spatial proteomics#
spora ecosystem#
A spora data formats specification 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] a resource containing multiple harmonized spatial proteomics datasets
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. 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. Nature (2026). https://doi.org/10.1038/s41586-026-10884-y (github repo). A spatial proteomics foundation model “VirTues”, pre-trained on parts of the spora data corpus using the spora [io] dataloaders.
other#
Meyer-Bender, M., Vöhringer, H., Schniederjohann, C. et al. Spatialproteomics: an interoperable toolbox for analyzing highly multiplexed fluorescence image data. Nat Methods (2026). https://doi.org/10.1038/s41592-026-03155-1. An xarray/zarr Python toolkit for multiplexed immunofluorescence, using SpatialData for the underlying data representation, in connection with the scverse ecosystem.
Alexander Coulton, Nicholas McGranahan, Odon: an ultra-fast viewer for spatial proteomics, Bioinformatics, Volume 42, Issue 7, July 2026, btag514, https://doi.org/10.1093/bioinformatics/btag514. A viewer for spatial proteomics data built directly for OME-Zarr datasets, with secondary support for SpatialData.