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Implement parallelized zarr conversion

Status: Open.

#383 In czbiohub-sf/iohub;

· vturonlagot opened on Mar 5, 2026

Add more <code>ruff</code> rules

maintenanceProject tooling, config, dependencies, build systemProject tooling, config, dependencies, build system

Status: Open.

Task

#382 In czbiohub-sf/iohub;

· srivarra opened on Mar 4, 2026

·  

0.3.0

Reconsider how chunk sizes should be computed

area: 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 implementation

performanceSpeed and memory usage of the codeSpeed and memory usage of the code

Status: Open.

Task

#374 In czbiohub-sf/iohub;

· ieivanov opened on Feb 13, 2026

·  

0.3.0

Keep track of original MM position name in zarr metadata

area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collections

area: readersFormat readers, converters, data ingestFormat readers, converters, data ingest

Status: Open.

Enhancement

#354 In czbiohub-sf/iohub;

· ieivanov opened on Nov 26, 2025

Define how omero["name"] should be used

area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collections

design discussionNeeds design input before implementationNeeds design input before implementation

Status: Open.

Task

#353 In czbiohub-sf/iohub;

· ieivanov opened on Nov 26, 2025

Zarr Precreation O(n) bug

area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collections

performanceSpeed and memory usage of the codeSpeed and memory usage of the code

Status: Open.

Bug

#349 In czbiohub-sf/iohub;

· gav-sturm opened on Nov 5, 2025

Bump supported python ranges

ciContinuous integrationContinuous integration

maintenanceProject tooling, config, dependencies, build systemProject tooling, config, dependencies, build system

Status: Open.

Enhancement

#342 In czbiohub-sf/iohub;

· ziw-liu opened on Oct 11, 2025

Reader type True TypeError

area: readersFormat readers, converters, data ingestFormat readers, converters, data ingest

Status: Open.

Bug

#339 In czbiohub-sf/iohub;

· ahillsley opened on Sep 18, 2025

Test against ome-zarr-models-py 1.0

area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collections

ciContinuous integrationContinuous integration

Status: Open.

Task

#338 In czbiohub-sf/iohub;

· ziw-liu opened on Sep 16, 2025

·  

0.3.1

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 dependencies

Status: Open.

Bug

#335 In czbiohub-sf/iohub;

· ziw-liu opened on Sep 12, 2025

·  

0.3.0

CI improvements

ciContinuous integrationContinuous integration

Status: Open.

Task

#333 In czbiohub-sf/iohub;

· ziw-liu opened on Sep 10, 2025

OME-Zarr v0.5 (Zarr v3) Review Updates

area: ngffOME-NGFF metadata, spec compliance, collectionsOME-NGFF metadata, spec compliance, collections

area: zarrZarr integration, storage backends (zarr-python/tensorstore/zarrs)Zarr integration, storage backends (zarr-python/tensorstore/zarrs)

Status: Open.

Task

#327 In czbiohub-sf/iohub;

· srivarra opened on Sep 8, 2025

·  

0.3.0