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Support reading OME-Zarr 0.5

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 295

#295 In czbiohub-sf/iohub;

· by ziw-liu was closed on Jun 4, 2025

Upgrade zarr-python dependency to 3.0

maintenanceMaintenance workMaintenance work

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 275

#275 In czbiohub-sf/iohub;

· by aliddell was closed on May 19, 2025

Parallel writing to shards

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 311

#311 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 4, 2025

Read MMStack with Zarr v3

upstreamIssues with upstream dependenciesIssues with upstream dependencies

μManagerMicro-Manager files and metadataMicro-Manager files and metadata

Status: Merged (completed).

czbiohub-sf/iohubnumber 293

#293 In czbiohub-sf/iohub;

· by ziw-liu was closed on Apr 4, 2025

adding conversion to tensorstore

enhancementNew feature or requestNew feature or request

Status: Merged (completed).

czbiohub-sf/iohubnumber 242

#242 In czbiohub-sf/iohub;

· by edyoshikun was closed on Jul 2, 2025

Write OME-Zarr 0.5

breakingBreaking changeBreaking change

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 310

#310 In czbiohub-sf/iohub;

· by ziw-liu was closed on Jul 2, 2025

Update acquire-zarr tests

CIContinuous integrationContinuous integration

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 320

#320 In czbiohub-sf/iohub;

· by ziw-liu was closed on Aug 19, 2025

Enable tests with ome-zarr-py

CIContinuous integrationContinuous integration

maintenanceMaintenance workMaintenance work

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 297

#297 In czbiohub-sf/iohub;

· by ziw-liu was closed on Aug 20, 2025

OME-Zarr v0.5 (Zarr v3) support

breakingBreaking changeBreaking change

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 301

#301 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

Use store root instead of URI

Status: Merged (completed).

czbiohub-sf/iohubnumber 331

#331 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

Pass kwargs to tensorstore

breakingBreaking changeBreaking change

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Merged (completed).

czbiohub-sf/iohubnumber 332

#332 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 10, 2025

Docs build missing for 0.2.0

bugSomething isn't workingSomething isn't working

CIContinuous integrationContinuous integration

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Closed (completed).

#309 In czbiohub-sf/iohub;

· by ziw-liu was closed on Jul 14, 2025

OME-NGFF v0.5 (with Zarr v3) implementation plan

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Closed (completed).

#271 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

tensorstore support

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

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

Status: Closed (completed).

#26 In czbiohub-sf/iohub;

· by JoOkuma was closed on Sep 9, 2025

Tensorstore URI conversion is broken on Windows.

bugSomething isn't workingSomething isn't working

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

upstreamIssues with upstream dependenciesIssues with upstream dependencies

Status: Closed (completed).

#312 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

Add iohub to the NGFF tools catalog

documentationImprovements or additions to documentationImprovements or additions to documentation

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Closed (completed).

#334 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 22, 2025

Logging configuration in __init__.py affects all downstream dependencies

bugSomething isn't workingSomething isn't working

Status: Closed (completed).

#317 In czbiohub-sf/iohub;

· by cmalinmayor was closed on Jul 30, 2025

get the zarr dataset size with iohub info verbose

enhancementNew feature or requestNew feature or request

upstreamIssues with upstream dependenciesIssues with upstream dependencies

Status: Closed (completed).

#247 In czbiohub-sf/iohub;

· by edyoshikun was closed on Dec 12, 2025

Use zarr-python 3

maintenanceMaintenance workMaintenance work

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Closed (completed).

#273 In czbiohub-sf/iohub;

· by aliddell was closed on Dec 12, 2025

<code>Plate.rename_well</code> is broken on Windows

bugSomething isn't workingSomething isn't working

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Closed (completed).

#329 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

Update docs to advertise OME-Zarr v0.5 support

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Closed (completed).

#330 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 22, 2025

Implement OME-NGFF v0.5 (Zarr v3)

enhancementNew feature or requestNew feature or request

NGFFOME-NGFF (OME-Zarr format)OME-NGFF (OME-Zarr format)

Status: Closed (completed).

#257 In czbiohub-sf/iohub;

· by ziw-liu was closed on Sep 9, 2025

Reimplement OME-TIFF reading

maintenanceMaintenance workMaintenance work

upstreamIssues with upstream dependenciesIssues with upstream dependencies

μManagerMicro-Manager files and metadataMicro-Manager files and metadata

Status: Closed (completed).

#292 In czbiohub-sf/iohub;

· by ziw-liu was closed on Jan 6, 2026