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- Status: Open.#442 In czbiohub-sf/iohub;
Consolidated Metadata
area: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)Status: Open.#435 In czbiohub-sf/iohub;Update CI to use ODIC Trusted Publishing
ciContinuous integrationContinuous integrationStatus: Open.#428 In czbiohub-sf/iohub;Switch to Typer for CLI
area: cliCommand-line interfaceCommand-line interfaceStatus: Open.Downsampling for Labels
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)design discussionNeeds design input before implementationNeeds design input before implementationStatus: Open.#423 In czbiohub-sf/iohub;WARNING:iohub.ngff.nodes:Cannot read first position metadata.
area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collectionsStatus: Open.Methods in
iohub.utilsare not displayed in the documentationdocumentationImprovements or additions to documentationImprovements or additions to documentationStatus: Open.RuntimeError: the checksum is invalid when writing zarr chunks via zarrs codec on Lustre
area: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)Status: Open.#415 In czbiohub-sf/iohub;Update
Position.create_zeroswith better defaults for chunks and shardsarea: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)Status: Open.#409 In czbiohub-sf/iohub;- Status: Open.#402 In czbiohub-sf/iohub;
Add a quiet option for
iohub convert/TiffConverterarea: cliCommand-line interfaceCommand-line interfacearea: readersFormat readers, converters, data ingestFormat readers, converters, data ingestStatus: Open.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.