2nd SpatialData Hackathon: Frameworks, Formats and Interoperability
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 lazyfile 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.
Citation
@misc{manukyan2026,
author = {Manukyan, Artur and Marconato, Luca and Barnes, Chris and
Albert, Marvin and Özleyen, Selman and Drummer, Francesca and
Vierdag, Wouter-Michiel and Zappia, Luke and Gruson, Hugo and
Varrone, Marco and Hess, Max and Moerth, Eric and Stegle, Oliver and
Akalin, Altuna and Zheng, Yimin and TaoBo, H U and Macri, Silvia
Maria and Sarıgün, Ahmet and Blume, Alexander and Kollotzek, Aaron
and Crowell, Helena and Cerrone, Lorenzo and Stockhaus, Sonja and
Moustafa, Samir},
title = {2nd {SpatialData} {Hackathon:} {Frameworks,} {Formats} and
{Interoperability}},
date = {2026-06-07},
url = {https://doi.org/10.37044/osf.io/s6bph_v2},
doi = {10.37044/osf.io/s6bph_v2},
langid = {en},
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
lazyfile 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.}
}