Data

Tools

Indexes

Applications

Experiments

Open Source Science

Recent Releases of iohub

iohub - v0.2.2

Patch release that adds an experimental tensorstore handle for Zarr arrays, along with bug fixes.

0.2.x be the last minor version to support zarr-python v2. Zarr-python v3 will be required for 0.3 to support Zarr format v3.

What's Changed

  • adding conversion to tensorstore by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/242
  • Update flake8-typing-imports version by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/314
  • Fix docs build for new versions by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/313
  • More robust conversion by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/315
  • Contain logger configuration by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/318

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.1...v0.2.2

- Python
Published by ziw-liu 5 months ago

iohub - v0.2.2rc1

Release candidate testing for 0.2.2 patches.

What's Changed

  • adding conversion to tensorstore by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/242
  • Update flake8-typing-imports version by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/314
  • Fix docs build for new versions by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/313
  • More robust conversion by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/315
  • Contain logger configuration by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/318

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.1...v0.2.2rc1

- Python
Published by ziw-liu 5 months ago

iohub - v0.2.2rc0

Release candidate testing for 0.2.2 patches.

What's Changed

  • adding conversion to tensorstore by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/242
  • Update flake8-typing-imports version by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/314
  • Fix docs build for new versions by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/313
  • More robust conversion by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/315

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.1...v0.2.2rc0

- Python
Published by ziw-liu 5 months ago

iohub - v0.2.1

This a patch release with compatibility fixes for various Micro-Manager configurations as well as some maintenance updates.

0.2.x be the last minor version to support zarr-python v2. Zarr-python v3 will be required for 0.3 to support Zarr format v3.

What's Changed

  • Catch json decoding error from incomplete NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/298
  • Update packaging metadata for 0.2.0 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/288
  • Catch truncated unicode error in NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/302
  • Add logo by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/299
  • Pin tifffile for zarr-python 2 compatibility by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/303
  • Convert micro-manager acquired line acquisitions by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/306
  • Convert time scale for OME-TIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/308

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.0...v0.2.1

- Python
Published by ziw-liu 6 months ago

iohub - v0.2.1rc1

Release candidate testing for 0.2.1 patches.

What's Changed

  • Catch json decoding error from incomplete NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/298
  • Update packaging metadata for 0.2.0 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/288
  • Catch truncated unicode error in NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/302
  • Add logo by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/299
  • Pin tifffile for zarr-python 2 compatibility by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/303
  • Convert micro-manager acquired line acquisitions by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/306
  • Convert time scale for OME-TIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/308

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.0...v0.2.1rc1

- Python
Published by ziw-liu 6 months ago

iohub - v0.2.1rc0

Release candidate testing for 0.2.1 patches.

What's Changed

  • Catch json decoding error from incomplete NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/298
  • Update packaging metadata for 0.2.0 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/288
  • Catch truncated unicode error in NDTIFF by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/302
  • Add logo by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/299
  • Pin tifffile for zarr-python 2 compatibility by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/303

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.0...v0.2.1rc0

- Python
Published by ziw-liu 7 months ago

iohub - v0.2.0

Major changes:

  • The Micro-Manager OME-TIFF/NDTIFF and ClearControl readers have been migrated to use the unified FOV-mapping API.
  • The single-page TIFF and PTI readers has been deprecated.
  • OME-Zarr nodes and models have been moved into the ngff module.

0.2 be the last minor version to support zarr-python v2. Zarr-python v3 will be required for 0.3 to support Zarr format v3.

What's Changed

  • Inheriting BaseFOV on ClearControlFOV by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/148
  • Universal API implementations for Micro-Manager OME-TIFF and NDTiff by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/185
  • Fix bug determining number of rows and cols by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/214
  • Fix bug reading dragonfly acquisitions by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/215
  • Sort keys in metadata .json files by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/211
  • Add CITATION.cff by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/219
  • Modify warning by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/220
  • Add Y5 to orange display color group by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/224
  • Fix README examples link by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/225
  • UAPI docs update by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/223
  • Unified API for Micro-manager readers by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/222
  • Fix docs switcher path by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/227
  • Refactor NGFF module and migrate to Pydantic v2 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/233
  • Fixing pyramid scaling factor by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/238
  • Use annotation instead of field for tagged union by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/244
  • Export ImageArray from the ngff module by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/245
  • set-scale utility by @aaronalvarezcz in https://github.com/czbiohub-sf/iohub/pull/228
  • Porting create_empty_zarr to iohub by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/234
  • Fix well naming case mismatch bug by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/254
  • Fixing tests for processsingleposition_setup() by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/252
  • rename-wells CLI utility by @josephschull in https://github.com/czbiohub-sf/iohub/pull/232
  • Limit action runners by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/246
  • Add decompressed OME-Zarr dataset size to iohub info by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/248
  • Support falcon datasets with latest micromanager by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/237
  • Remove BOM from well name by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/259
  • Add conversion of ImageArray to dask by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/262
  • More robust calculation of "z-step_um" for ndtiff datasets by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/263
  • add support for the get_transform analog to set_transform by @pattonw in https://github.com/czbiohub-sf/iohub/pull/264
  • Make sure converter output dir ends in .zarr by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/269
  • Fix reading Dragonfly non-OpenCell datasets with incomplete metadata by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/268
  • Compare MM FOVs by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/276
  • Set contrast limits method by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/279
  • Check overwrite path by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/280
  • Authenticate NDTIFF download in CI by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/281
  • Fix test combine FOVs by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/283
  • make nodes.Position.metadata.omero an optional attribute by @yuriyzubov in https://github.com/czbiohub-sf/iohub/pull/284
  • Bump supported python range to 3.11-3.13 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/277
  • Correctly name copied Position in Plate.from_positions by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/256
  • Support metadata for .zarr converted from .nd2 using bioformats2raw conversion by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/272
  • Set default pixel size for old NDTiff format by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/285
  • Filter test file names on windows by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/286
  • Use sphinx-polyversion by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/274
  • Remove fetching step in build docs action by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/289
  • Set scale for any coordinate transform by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/287
  • Update deploy pages action by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/290
  • Handle case-insensitive platforms in Zarr hierarchy by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/291

New Contributors

  • @aaronalvarezcz made their first contribution in https://github.com/czbiohub-sf/iohub/pull/228
  • @josephschull made their first contribution in https://github.com/czbiohub-sf/iohub/pull/232
  • @pattonw made their first contribution in https://github.com/czbiohub-sf/iohub/pull/264
  • @yuriyzubov made their first contribution in https://github.com/czbiohub-sf/iohub/pull/284

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.1.0...v0.2.0

- Python
Published by ziw-liu 8 months ago

iohub - v0.2.0rc0

Release candidate testing for 0.2.0.

What's Changed

  • Compare MM FOVs by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/276
  • Set contrast limits method by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/279
  • Check overwrite path by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/280
  • Authenticate NDTIFF download in CI by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/281
  • Fix test combine FOVs by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/283
  • make nodes.Position.metadata.omero an optional attribute by @yuriyzubov in https://github.com/czbiohub-sf/iohub/pull/284
  • Bump supported python range to 3.11-3.13 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/277
  • Correctly name copied Position in Plate.from_positions by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/256
  • Support metadata for .zarr converted from .nd2 using bioformats2raw conversion by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/272
  • Set default pixel size for old NDTiff format by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/285
  • Filter test file names on windows by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/286
  • Use sphinx-polyversion by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/274
  • Remove fetching step in build docs action by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/289
  • Set scale for any coordinate transform by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/287
  • Update deploy pages action by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/290
  • Handle case-insensitive platforms in Zarr hierarchy by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/291

New Contributors

  • @yuriyzubov made their first contribution in https://github.com/czbiohub-sf/iohub/pull/284

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.0b0...v0.2.0rc0

- Python
Published by ziw-liu 9 months ago

iohub - v0.2.0b0

Beta testing for 0.2.0.

What's Changed

  • set-scale utility by @aaronalvarezcz in https://github.com/czbiohub-sf/iohub/pull/228
  • Porting create_empty_zarr to iohub by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/234
  • Fix well naming case mismatch bug by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/254
  • Fixing tests for processsingleposition_setup() by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/252
  • rename-wells CLI utility by @josephschull in https://github.com/czbiohub-sf/iohub/pull/232
  • Limit action runners by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/246
  • Add decompressed OME-Zarr dataset size to iohub info by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/248
  • Support falcon datasets with latest micromanager by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/237
  • Remove BOM from well name by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/259
  • Add conversion of ImageArray to dask by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/262
  • More robust calculation of "z-step_um" for ndtiff datasets by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/263
  • add support for the get_transform analog to set_transform by @pattonw in https://github.com/czbiohub-sf/iohub/pull/264
  • Make sure converter output dir ends in .zarr by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/269
  • Fix reading Dragonfly non-OpenCell datasets with incomplete metadata by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/268

New Contributors

  • @aaronalvarezcz made their first contribution in https://github.com/czbiohub-sf/iohub/pull/228
  • @josephschull made their first contribution in https://github.com/czbiohub-sf/iohub/pull/232
  • @pattonw made their first contribution in https://github.com/czbiohub-sf/iohub/pull/264

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.2.0a1...v0.2.0b0

- Python
Published by ziw-liu 10 months ago

iohub - v0.2.0a1

Alpha testing for 0.2.0.

What's Changed

  • Inheriting BaseFOV on ClearControlFOV by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/148
  • Universal API implementations for Micro-Manager OME-TIFF and NDTiff by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/185
  • Fix bug determining number of rows and cols by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/214
  • Fix bug reading dragonfly acquisitions by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/215
  • Sort keys in metadata .json files by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/211
  • Add CITATION.cff by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/219
  • Modify warning by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/220
  • Add Y5 to orange display color group by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/224
  • Fix README examples link by @talonchandler in https://github.com/czbiohub-sf/iohub/pull/225
  • UAPI docs update by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/223
  • Unified API for Micro-manager readers by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/222
  • Fix docs switcher path by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/227
  • Refactor NGFF module and migrate to Pydantic v2 by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/233
  • Fixing pyramid scaling factor by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/238
  • Use annotation instead of field for tagged union by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/244
  • Export ImageArray from the ngff module by @edyoshikun in https://github.com/czbiohub-sf/iohub/pull/245

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.1.0...v0.2.0a1

- Python
Published by ziw-liu over 1 year ago

iohub - v0.1.0

The first stable release of iohub. We only include source code download on GitHub since iohub is pure Python.

This release supports API and CLI for the following formats:

Read

  • OME-Zarr (OME-NGFF v0.4)
  • Micro-Manager TIFF sequence, OME-TIFF (MMStack), and NDTiff datasets
  • Custom data formats generated by Biohub microscopes
    • Falcon (PTI)
    • Dorado (ClearControl)
    • Dragonfly (OpenCell OME-TIFF)
    • Mantis (NDTiff)
    • DaXi (OME-TIFF)

Write - OME-Zarr

Note: With v0.2.0 we plan to include breaking API changes as proposed in https://github.com/czbiohub-sf/iohub/pull/132.

- Python
Published by ziw-liu almost 2 years ago

iohub - 0.1.0rc0

Release candidate for 0.1.0.

What's Changed

  • Support MM 2.0.1 for single page TIFFs by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/179
  • Enable XYZ chunking at conversion by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/178
  • Better NDTiff reading when the first position is missing by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/190
  • Fix for when ChNames key is not available by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/191
  • Added option to not check copied data by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/192
  • Fix product integer overflow by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/193
  • OpenCell reader extension by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/197
  • Extend HCS label parsing by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/189
  • Scaling chunk size according to pyramid factors by @JoOkuma in https://github.com/czbiohub-sf/iohub/pull/201
  • Modified fluorophore color code by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/202
  • Update documentation and metadata by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/203
  • Save ndtiff image plane metadata per position by @ieivanov in https://github.com/czbiohub-sf/iohub/pull/204
  • Bump supported Python versions by @ziw-liu in https://github.com/czbiohub-sf/iohub/pull/200

Full Changelog: https://github.com/czbiohub-sf/iohub/compare/v0.1.0dev5...v0.1.0rc0

- Python
Published by ziw-liu about 2 years ago