Data Resources#
Looking for test data? IDR Samples aims at covering the different corners of the specification.
After this quick reference, you can find a diverse set of data resources in OME-Zarr format, illustrating the range of scientific stories enabled by the format.
Do you have a data resource in OME-Zarr format that you would like to share? Is there something missing? Please submit an issue or pull request to update this list.
Sample data#
Resources curating OME-Zarr sample data, for demonstration and testing purposes.
Resource |
Description |
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A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions |
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Sample OME-Zarr datasets from the BioImage Archive for testing |
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Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format |
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Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes |
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Close to 500 TB of data in the OME-Zarr 0.5 format |
Data portals#
Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available.
Resource |
Description |
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Cryo-electron tomography (cryoET) data repository |
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A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support |
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The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value |
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A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. |
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A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data |
Datasets#
These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr.
Resource |
Description |
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A collection of of volumetric datasets in OME-Zarr format, including several CT scans. |
Atlases#
These are “atlas”-like datasets, which provide a comprehensive view of a particular biological system. The metadata-rich, streaming-friendly nature of OME-Zarr makes it ideal for sharing and visualizing large, complex datasets that are often associated with atlases.
The WebAtlas pipeline (Li et al, 2024) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging.
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Resource |
Description |
Publication |
Sample |
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Multimodal atlas of zebrafish development including light-sheet imaging |
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ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes (see also S-BIAD2095) |
An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( highlight). |
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An open-access volume electron microscopy atlas of whole cells and tissues |
Other resources#
These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community.
Resource |
Description |
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BRAIN Initiative archive for publishing and sharing neurophysiology data |
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A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. |
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Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. |
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A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. |