NGFF Café – SpatialData: an open framework for spatial omics with OME-Zarr-based storage

The next NGFF Café on November 26 explores SpatialData, an open framework for storing, analysing and sharing spatial omics data using OME-Zarr.

About the talk

Spatial profiling technologies continue to push throughput, gene counts and resolution to new heights, with datasets growing in scale and availability. SpatialData was developed in 2023 to provide interoperable storage and a modular software infrastructure for these data, with OME-Zarr as its backbone. Meanwhile, the OME-NGFF specification continues to evolve, with an active community effort driving it towards 1.0.

In a talk entitled, "SpatialData: an open framework for spatial omics with OME-Zarr-based storage," Luca Marconato, EMBL, and Tomaz Vieira, DKFZ and EMBL, will present the current state of SpatialData development, covering:

- How the framework ingests data from recently released commercial spatial technologies and represents them in a unified coordinate system

- Ongoing work to align this representation with the OME-NGFF 0.6 specification, including the challenges and design decisions involved

- Core data operations, including spatial queries and annotation transfer, built on an xarray-compatible in-memory model

- The evolving SpatialData specification, its relationship with OME-NGFF, and collaborative efforts across the imaging and single-cell communities towards more open, cross-language spatial data infrastructure

All are welcome: researchers, developers, and anyone working with OME-Zarr or spatial omics data. See you there!