Search results

Downsampling for Labels

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)

design discussionNeeds design input before implementationNeeds design input before implementation

Status: Open.

Enhancement

#423 In czbiohub-sf/iohub;

· srivarra opened on Jun 9, 2026

WARNING:iohub.ngff.nodes:Cannot read first position metadata.

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

Status: Open.

Bug

#421 In czbiohub-sf/iohub;

· ieivanov opened on Jun 4, 2026

Methods in iohub.utils are not displayed in the documentation

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

Task

#420 In czbiohub-sf/iohub;

· srivarra opened on Jun 2, 2026

RuntimeError: the checksum is invalid when writing zarr chunks via zarrs codec on Lustre

Status: Open.

#415 In czbiohub-sf/iohub;

· tayllatheodoro opened on May 8, 2026

Update Position.create_zeros with better defaults for chunks and shards

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

Status: Open.

Enhancement

#409 In czbiohub-sf/iohub;

· ieivanov opened on Apr 24, 2026

Convert to version=0.5 by default

Status: Open.

#402 In czbiohub-sf/iohub;

· ieivanov opened on Apr 22, 2026

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.

Enhancement

#391 In czbiohub-sf/iohub;

· srivarra opened on Mar 20, 2026

·  

0.3.1

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.

Enhancement

#383 In czbiohub-sf/iohub;

· vturonlagot opened on Mar 5, 2026

·  

0.3.1

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

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