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OpenApr 9, 2026
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Per-frame metadata in UAPI
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsarea: readersFormat readers, converters, data ingestFormat readers, converters, data ingestStatus: Open.#155 In czbiohub-sf/iohub;identify optimal chunk size for computational imaging, DL, and visualization workflows
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsperformanceSpeed and memory usage of the codeSpeed and memory usage of the codeStatus: Open.#33 In czbiohub-sf/iohub;Universal entry points
area: readersFormat readers, converters, data ingestFormat readers, converters, data ingestdesign discussionNeeds design input before implementationNeeds design input before implementationhelp wantedExtra attention is neededExtra attention is neededStatus: Open.#40 In czbiohub-sf/iohub;support ome-ngff on s3
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsarea: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)Status: Open.#209 In czbiohub-sf/iohub;Add TIFF examples
area: readersFormat readers, converters, data ingestFormat readers, converters, data ingestdocumentationImprovements or additions to documentationImprovements or additions to documentationStatus: Open.#212 In czbiohub-sf/iohub;- Status: Open.#188 In czbiohub-sf/iohub;
Nice to have:
__repr__functions for ngff nodesarea: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsgood first issueGood for newcomersGood for newcomersStatus: Open.#265 In czbiohub-sf/iohub;Positionshould be a subclass ofBaseFOVarea: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsdesign discussionNeeds design input before implementationNeeds design input before implementationStatus: Open.#249 In czbiohub-sf/iohub;CLI to update metadata of zarr stores
area: cliCommand-line interfaceCommand-line interfacearea: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsStatus: Open.Fix copying sub-stores
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsupstreamIssues with upstream dependenciesIssues with upstream dependenciesStatus: Open.Choose a faster default compressor
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsperformanceSpeed and memory usage of the codeSpeed and memory usage of the codeStatus: Open.Test against ome-zarr-models-py 1.0
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsciContinuous integrationContinuous integrationStatus: Open.- Status: Draft (not ready).
Zarr-python 3 cannot read old data with empty channels
area: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)upstreamIssues with upstream dependenciesIssues with upstream dependenciesStatus: Open.OME-Zarr v0.5 (Zarr v3) Review Updates
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsarea: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)Status: Open.Add a quiet option for
iohub convert/TiffConverterarea: cliCommand-line interfaceCommand-line interfacearea: readersFormat readers, converters, data ingestFormat readers, converters, data ingestStatus: Open.#391 In czbiohub-sf/iohub;Implement parallelized zarr conversion
area: cliCommand-line interfaceCommand-line interfacearea: readersFormat readers, converters, data ingestFormat readers, converters, data ingestperformanceSpeed and memory usage of the codeSpeed and memory usage of the codeStatus: Open.#383 In czbiohub-sf/iohub;