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czbiohub-sf / iohub Public

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Fork 13
Star 52

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0.3.1

Open

No due date

•Last updated Apr 9, 2026

5% complete

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0 issues of 17 selected

Open
(17)
Closed
(1)

Per-frame metadata in UAPI

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

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

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

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.

#33 In czbiohub-sf/iohub;

· mattersoflight opened

on Jan 31, 2023

Universal entry points

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

design discussionNeeds design input before implementationNeeds design input before implementation

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

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.

#209 In czbiohub-sf/iohub;

· d-v-b opened

on Feb 13, 2024

Add TIFF examples

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

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

Status: Open.

#188 In czbiohub-sf/iohub;

· ieivanov opened

on Sep 25, 2023

Nice to have: `repr` functions for ngff nodes

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

good first issueGood for newcomersGood for newcomers

Status: Open.

#265 In czbiohub-sf/iohub;

· ieivanov opened

on Dec 11, 2024

`Position` should be a subclass of `BaseFOV`

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

design discussionNeeds design input before implementationNeeds design input before implementation

Status: Open.

#249 In czbiohub-sf/iohub;

· talonchandler opened

on Sep 26, 2024

CLI to update metadata of zarr stores

area: cliCommand-line interfaceCommand-line interface

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

Status: Open.

#210 In czbiohub-sf/iohub;

· ieivanov opened

on Feb 16, 2024

Fix copying sub-stores

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

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

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.

#266 In czbiohub-sf/iohub;

· ziw-liu opened

on Jan 21, 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.

#338 In czbiohub-sf/iohub;

· ziw-liu opened

on Sep 16, 2025

Compute time scale for ndtiff datasets

Status: Draft (not ready).

czbiohub-sf/iohubnumber 316

#316 In czbiohub-sf/iohub;

· ieivanov opened

on Jul 12, 2025

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.

#335 In czbiohub-sf/iohub;

· ziw-liu opened

on Sep 12, 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.

#327 In czbiohub-sf/iohub;

· srivarra opened

on Sep 8, 2025

Add a quiet option for `iohub convert` / `TiffConverter`

area: cliCommand-line interfaceCommand-line interface

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

Status: Open.

#391 In czbiohub-sf/iohub;

· srivarra opened

on Mar 20, 2026

Implement parallelized zarr conversion

area: cliCommand-line interfaceCommand-line interface

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

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

Status: Open.

#383 In czbiohub-sf/iohub;

· vturonlagot opened

on Mar 5, 2026

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