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| Item Type: | Preprint |
|---|---|
| Title: | 2nd SpatialData hackathon: frameworks, formats and interoperability |
| Creators: |
Manukyan, Artür  ORCID: https://orcid.org/0000-0002-0441-9517, Marconato, Luca ORCID: https://orcid.org/0000-0003-3198-1326, Albert, Marvin ORCID: https://orcid.org/0000-0003-2536-2545, Barnes, Chris ORCID: https://orcid.org/0000-0002-1296-7310, Blume, Alexander ORCID: https://orcid.org/0000-0003-3045-8234, Cerrone, Lorenzo ORCID: https://orcid.org/0000-0001-7337-2313, Crowell, Helena L. ORCID: https://orcid.org/0000-0002-4801-1767, Drummer, Francesca ORCID: https://orcid.org/0009-0002-7156-9125, Gruson, Hugo ORCID: https://orcid.org/0000-0002-4094-1476, Hess, Max ORCID: https://orcid.org/0000-0001-9528-4445, Hu, Taobo ORCID: https://orcid.org/0009-0009-2596-7588, Kedziora, Katarzyna ORCID: https://orcid.org/0000-0001-6524-7731, Kollotzek, Aaron ORCID: https://orcid.org/0009-0009-7142-4015, Macrí, Silvia Maria ORCID: https://orcid.org/0009-0009-2075-8699, Moerth, Eric ORCID: https://orcid.org/0000-0003-1625-0146, Moustafa, Samir ORCID: https://orcid.org/0000-0002-0674-9667, Ozleyen, Selman ORCID: https://orcid.org/0009-0009-2596-7588, Todd, Peter, Sarigün, Ahmet ORCID: https://orcid.org/0009-0003-2715-5344, Stockhaus, Sonja ORCID: https://orcid.org/0009-0005-7712-8154, Varrone, Marco ORCID: https://orcid.org/0000-0002-0538-3464, Vierdag, Wouter Michiel ORCID: https://orcid.org/0000-0003-1666-5421, Zappia, Luke ORCID: https://orcid.org/0000-0001-7744-8565, Zheng, Yimin ORCID: https://orcid.org/0000-0002-0394-9735, Stegle, Oliver ORCID: https://orcid.org/0000-0002-8818-7193 and Akalin, Altuna ORCID: https://orcid.org/0000-0002-0468-0117
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| Abstract: | This preprint outlines the results of the "2nd SpatialData Hackathon" organised by the scverse and Bioconductor teams. The event gathered experts to advance spatial omics through four hackathon tracks: (i) R interoperability, (ii) accessibility and performance of visualization tools, (iii) design modernization for the SpatialData framework, and (iv) file formats and transformations (NGFF). Key achievements include extending the SpatialData, Zarr and bioimaging frameworks to R/Bioconductor ecosystem, improving visualization with 2.5D/3D rendering and a chunked multiscale point representation, introducing cloud-based IO and prototypes for lazy file linking and bidirectional element-table relationships, and developing a language-agnostic conformance test suite for OME-NGFF coordinate transformations. The hackathon fostered collaboration, creating infrastructure prototypes and identifying interoperability challenges. Documented on GitHub, these efforts brought together 24 participants from the US and Europe, promoting a FAIR ecosystem of spatial omics and imaging tools. |
| Keywords: | Bioimaging, Multi-Omics, NGFF, OME-Zarr, Single-Cell, Spatial Omics, Zarr |
| Source: | BioHackrXiv |
| Publisher: | Center for Open Science |
| Article Number: | s6bph_v2 |
| Date: | 29 June 2026 |
| Official Publication: | https://doi.org/10.37044/osf.io/s6bph_v1 |
| Related to: |
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