v0.2.1

This is 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 #298
• Update packaging metadata for 0.2.0 by @ziw-liu in #288
• Catch truncated unicode error in NDTIFF by @ziw-liu in #302
• Add logo by @ziw-liu in #299
• Pin tifffile for zarr-python 2 compatibility by @ziw-liu in #303
• Convert micro-manager acquired line acquisitions by @talonchandler in #306
• Convert time scale for OME-TIFF by @ziw-liu in #308

Full Changelog: v0.2.0...v0.2.1

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 #298
• Update packaging metadata for 0.2.0 by @ziw-liu in #288
• Catch truncated unicode error in NDTIFF by @ziw-liu in #302
• Add logo by @ziw-liu in #299
• Pin tifffile for zarr-python 2 compatibility by @ziw-liu in #303
• Convert micro-manager acquired line acquisitions by @talonchandler in #306
• Convert time scale for OME-TIFF by @ziw-liu in #308

Full Changelog: v0.2.0...v0.2.1rc1

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 #298
• Update packaging metadata for 0.2.0 by @ziw-liu in #288
• Catch truncated unicode error in NDTIFF by @ziw-liu in #302
• Add logo by @ziw-liu in #299
• Pin tifffile for zarr-python 2 compatibility by @ziw-liu in #303

Full Changelog: v0.2.0...v0.2.1rc0

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

New Contributors

• @aaronalvarezcz made their first contribution in #228
• @josephschull made their first contribution in #232
• @pattonw made their first contribution in #264
• @yuriyzubov made their first contribution in #284

Full Changelog: v0.1.0...v0.2.0

v0.2.0rc0

Release candidate testing for 0.2.0.

What's Changed

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

New Contributors

• @yuriyzubov made their first contribution in #284

Full Changelog: v0.2.0b0...v0.2.0rc0

v0.2.0b0

Beta testing for 0.2.0.

What's Changed

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

New Contributors

• @aaronalvarezcz made their first contribution in #228
• @josephschull made their first contribution in #232
• @pattonw made their first contribution in #264

Full Changelog: v0.2.0a1...v0.2.0b0

v0.2.0a1

Alpha testing for 0.2.0.

What's Changed

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

Full Changelog: v0.1.0...v0.2.0a1

v0.1.0

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

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 #132.

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

Full Changelog: v0.1.0dev5...v0.1.0rc0