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Per-frame metadata in UAPI

enhancementNew feature or requestNew feature or request

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

μManagerMicro-Manager files and metadataMicro-Manager files and metadata

Status: Open.

#155 In czbiohub-sf/iohub;

· ziw-liu opened on Jun 22, 2023

identify optimal chunk size for computational imaging, DL, and visualization workflows

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

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

Status: Open.

#33 In czbiohub-sf/iohub;

· mattersoflight opened on Jan 31, 2023

Universal entry points

enhancementNew feature or requestNew feature or request

help wantedExtra attention is neededExtra attention is needed

Status: Open.

#40 In czbiohub-sf/iohub;

· AhmetCanSolak opened on Feb 6, 2023

support ome-ngff on s3

enhancementNew feature or requestNew feature or request

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

Status: Open.

#209 In czbiohub-sf/iohub;

· d-v-b opened on Feb 13, 2024

Add TIFF examples

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#212 In czbiohub-sf/iohub;

· ziw-liu opened on Feb 22, 2024

better logging

enhancementNew feature or requestNew feature or request

Status: Open.

#188 In czbiohub-sf/iohub;

· ieivanov opened on Sep 25, 2023

Nice to have: <code>__repr__</code> functions for ngff nodes

enhancementNew feature or requestNew feature or request

good first issueGood for newcomersGood for newcomers

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

Status: Open.

#265 In czbiohub-sf/iohub;

· ieivanov opened on Dec 11, 2024

<code>Position</code> should be a subclass of <code>BaseFOV</code>

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

Status: Open.

#249 In czbiohub-sf/iohub;

· talonchandler opened on Sep 26, 2024

Save grayscale data and binary masks in the OME-zarr store

enhancementNew feature or requestNew feature or request

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

Status: Open.

#156 In czbiohub-sf/iohub;

· nbathreya opened on Jun 28, 2023

CLI to update metadata of zarr stores

enhancementNew feature or requestNew feature or request

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

Status: Open.

#210 In czbiohub-sf/iohub;

· ieivanov opened on Feb 16, 2024

TIFF UAPI TODOs

documentationImprovements or additions to documentationImprovements or additions to documentation

μManagerMicro-Manager files and metadataMicro-Manager files and metadata

Status: Open.

#213 In czbiohub-sf/iohub;

· ziw-liu opened on Mar 4, 2024

Fix copying sub-stores

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

upstreamIssues with upstream dependenciesIssues with upstream dependencies

Status: Open.

#300 In czbiohub-sf/iohub;

· ziw-liu opened on May 19, 2025

Choose a faster default compressor

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

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

Status: Open.

#266 In czbiohub-sf/iohub;

· ziw-liu opened on Jan 21, 2025

Add Codecov to CI

CIContinuous integrationContinuous integration

Status: Open.

#319 In czbiohub-sf/iohub;

· srivarra opened on Aug 18, 2025

Compute time scale for ndtiff datasets

μManagerMicro-Manager files and metadataMicro-Manager files and metadata

Status: Draft (not ready).

czbiohub-sf/iohubnumber 316

#316 In czbiohub-sf/iohub;

· ieivanov opened on Jul 12, 2025

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

Status: Open.

#327 In czbiohub-sf/iohub;

· srivarra opened on Sep 8, 2025

Zarr-python 3 cannot read old data with empty channels

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: Open.

#335 In czbiohub-sf/iohub;

· ziw-liu opened on Sep 12, 2025

Test against ome-zarr-models-py 1.0

CIContinuous integrationContinuous integration

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

Status: Open.

#338 In czbiohub-sf/iohub;

· ziw-liu opened on Sep 16, 2025