Issues

• bioformats2raw-converted .nd2 files cannot be opened with iohub>=0.3.0's zarrs-python default

  Bug

  Biohub/iohub#483 · Filter by author talonchandler opened on Oct 1, 2026
  1

  

• Convert a folder of per-well ND2 files (Nikon plate scan) into one HCS plate

  area: cliarea: readers
  Biohub/iohub#482 · Filter by author verajanssen-cz opened on Sep 30, 2026

• ND2 conversion writes garbage for frames past sequenceCount (acquisitions stopped early)

  area: readers
  Biohub/iohub#481 · Filter by author verajanssen-cz opened on Sep 30, 2026
  1

• Support configurable Compression Codecs for writing OME-Zarr

  area: zarr
  Biohub/iohub#480 · Filter by author srivarra opened on Sep 30, 2026
  

• Just use virtual chunks?

  Biohub/iohub#471 · Filter by author TomNicholas opened on Sep 11, 2026
  8

• Copy custom metadata between existing OME-Zarr Positions

  area: cli
  Biohub/iohub#469 · Filter by author srivarra opened on Sep 9, 2026
  

• Add MRC-to-OME-Zarr Conversion

  area: readersarea: zarrdesign discussion
  Biohub/iohub#457 · Filter by author srivarra opened on Aug 7, 2026
  5

  

• Investigate Zarrista

  area: zarr
  Task

  Biohub/iohub#445 · Filter by author srivarra opened on Jul 24, 2026
  1

  

• Consolidated Metadata

  area: zarr
  Biohub/iohub#435 · Filter by author srivarra opened on Jul 6, 2026

• Update CI to use ODIC Trusted Publishing

  ci
  Biohub/iohub#428 · Filter by author srivarra opened on Jun 22, 2026
  

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

  area: ngff
  Bug

  Biohub/iohub#421 · Filter by author ieivanov opened on Jun 4, 2026
  1

• Update Position.create_zeros with better defaults for chunks and shards

  area: zarr
  Biohub/iohub#409 · Filter by author ieivanov opened on Apr 24, 2026
  

• Convert to version=0.5 by default

  Biohub/iohub#402 · Filter by author ieivanov opened on Apr 22, 2026
  3

• Add a quiet option for iohub convert / TiffConverter

  area: cliarea: readers
  Biohub/iohub#391 · Filter by author srivarra opened on Mar 20, 2026 · 0.3.1

• Zarr Precreation O(n) bug

  area: ngffperformance
  Bug

  Biohub/iohub#349 · Filter by author gav-sturm opened on Nov 5, 2025
  2

• Reader type True TypeError

  area: readers
  Bug

  Biohub/iohub#339 · Filter by author ahillsley opened on Sep 18, 2025
  2

• Test against ome-zarr-models-py 1.0

  area: ngffci
  Task

  Biohub/iohub#338 · Filter by author ziw-liu opened on Sep 16, 2025 · 0.3.1

• Zarr-python 3 cannot read old data with empty channels

  area: zarrupstream
  Bug

  Biohub/iohub#335 · Filter by author ziw-liu opened on Sep 12, 2025 · 0.3.1
  

• CI improvements

  ci
  Task

  Biohub/iohub#333 · Filter by author ziw-liu opened on Sep 10, 2025
  

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

  area: ngffarea: zarr
  Task

  Biohub/iohub#327 · Filter by author srivarra opened on Sep 8, 2025 · 0.3.1
  

• Updating Tooling Infrastructure

  maintenance
  Task

  Biohub/iohub#323 · Filter by author srivarra opened on Aug 21, 2025
  5

  

• Add Codecov to CI

  ci
  Biohub/iohub#319 · Filter by author srivarra opened on Aug 18, 2025
  

• capture the time interval between frames and units (min, second) in ome-zarr metadata

  area: ngff
  Biohub/iohub#304 · Filter by author mattersoflight opened on May 27, 2025
  1

  

• Fix copying sub-stores

  area: ngffupstream
  Bug

  Biohub/iohub#300 · Filter by author ziw-liu opened on May 19, 2025 · 0.3.1

• Choose a faster default compressor

  area: ngffperformance
  Task

  Biohub/iohub#266 · Filter by author ziw-liu opened on Jan 21, 2025 · 0.3.1
  3