ND2 xarray OME metadata update (last Python3.8 supported version)

Special Note

This is the last version that will support Python3.8

What's Changed

• Revert to pre-2023.3.15 tifffile to avoid mm_stack issue by @SeanLeRoy in #529
• Adjust pydantic import by @SeanLeRoy in #535
• Feature/nd2reader-xarray-ome-metadata by @yichechang in #533
• Adjust bfio & fsspec versions to avoid bugs by @SeanLeRoy in #537

New Contributors

• @yichechang made their first contribution in #533

Full Changelog: v4.12.1...v4.13.0

OME metadata for ND2 reader and ome-types upgrade

What's Changed

• Feature/ome_metadata-for-nd2 by @tlambert03 in #521
• DependencyFix/Upgrade ome-types to 0.3.4 by @Armavica in #522

New Contributors

• @Armavica made their first contribution in #522

Full Changelog: v4.12.0...v4.12.1

zarr and sldy reader and other improvements

What's Changed

• Admin: Update deploy process by @SeanLeRoy in #494
• Feature/sldy reader by @SeanLeRoy in #496
• OmeZarrReader by @BrianWhitneyAI in #493
• Admin/OmeZarrReader redundant test by @BrianWhitneyAI in #507
• OmeZarrReader physical_pixel_sizes support by @BrianWhitneyAI in #509
• Admin/OmeZarrReader variable dimension unit tests by @BrianWhitneyAI in #510
• Guess dims for missing field 'axes' by @BrianWhitneyAI in #514
• Ignore missing Position dimension by @SeanLeRoy in #498
• Feature/OmeZarr Chunk Dims by @BrianWhitneyAI in #519
• Limit numpy and dask by @SeanLeRoy in #527

Full Changelog: v4.11.0...v4.12.0

mosaic tile improvements and other bugfixes

AICSImageIO 4.11.0

What's Changed

• Extract S dim from OME data by @SeanLeRoy in #483
• admin/support-py311 by @evamaxfield in #446
• Bugfix/mosaic lif merge error by @SeanLeRoy in #480
• Bugfix/slow tile retrieval by @SeanLeRoy in #486
• store frame metadata when reading a specific scene by @joshua-gould in #492
• Adjusting tiffile versioning by @BrianWhitneyAI in #487

New Contributors

• @joshua-gould made their first contribution in #492

Full Changelog: v4.10.0...v4.11.0

bug fixes and OME-Zarr Writer

AICSImageIO 4.10.0

What's Changed

• fix/fix_future_warnings by @JasonYu1 in #453
• More descriptive scene index error message. by @pgarrison in #458
• Fix/build fix ometypes validation by @toloudis in #461
• feature/zarrwriter by @toloudis in #381
• Bugfix/Docs-README-Mention-mvn/maven-requirement-for-bioformats_jar by @psobolewskiPhD in #463
• Quality of Life: Make pip install platform independent by @SeanLeRoy in #466
• Bugfix: Fix tests not asserting error expected by @SeanLeRoy in #464
• Bugfix: Restrict tifffile version for now by @SeanLeRoy in #472
• Bugfix: Upgrade minimum fsspec version by @SeanLeRoy in #473
• Bugfix: unclear warning for missing 'bfio' install. by @BrianWhitneyAI in #471
• feature/add-physical-pixel-size-to-tiff-reader by @tlambert03 in #456
• feature/github-action-stale by @BrianWhitneyAI in #474
• bugfix: removing 2.11.0 threshold by @BrianWhitneyAI in #470
• Bugfix/empty scene name by @BrianWhitneyAI in #477
• try to use optimized codepath through ome-types by @toloudis in #478
• Restrict xarray version to support py3.8 by @SeanLeRoy in #481

New Contributors

• @JasonYu1 made their first contribution in #453
• @pgarrison made their first contribution in #458

Full Changelog: v4.9.4...v4.10.0

Bugfixes for TiffGlobReader

What's Changed

• bugfix/Fix UnboundLocalError in TiffGlobReader by @ianhi in #449

Full Changelog: v4.9.3...v4.9.4

Dimension Handling Fixes

AICSImageIO v4.9.3

AICSImageIO is a library for image reading, writing, and metadata conversion in pure Python with readers for many Bio and Microscopy related formats (TIFF, CZI, ND2, DV, LIF).

What's Changed

• fix/position-names-in-nd2-tests by @tlambert03 in #437
• fix single dimension index when requested as a returned dim by @toloudis in #438
• admin/citation-update by @evamaxfield in #440
• try to handle I the same way as Q coming out of tifffile reading by @toloudis in #445

Full Changelog: v4.9.2...v4.9.3

A Mixed Bag of Bugfixes

AICSImageIO v4.9.2

AICSImageIO is a library for image reading, writing, and metadata conversion in pure Python with readers for many Bio and Microscopy related formats (TIFF, CZI, ND2, DV, LIF).

This release include the option to add physical pixel sizes to the ArrayLikeReader (#426), a bugfix related to non-naturally indexed CZI scenes (#432), a hopeful patch to catch some edge cases regarding passing specific indices as a list or tuple to our get_image_data (and related) calls (#429), and finally, some documentation improvements regarding the installation of CZI support (#433).

What's Changed

• feature/add-physical-pixel-sizes-param-to-array-like by @colobas in #426
• bugfix/czi-scene-selection-for-inconsistent-scenes-regression by @toloudis in #432
• bugfix/convert-dimension-spec-lists-to-slices-when-possible by @toloudis in #429
• admin/include-fsspec-dep-for-czi-in-readme by @evamaxfield in #433

New Contributors

• @colobas made their first contribution in #426

Full Changelog: v4.9.1...v4.9.2

A Bug Fix Here, A Bug Fix There, Bug Fixes Everywhere

AICSImageIO v4.9.1

AICSImageIO is a library for image reading, writing, and metadata conversion in pure Python with readers for many Bio and Microscopy related formats (TIFF, CZI, ND2, DV, LIF).

This release has a suite of bugfixes for the Dimensions object typing, CZI file formats scene indexing, CZI file formats channel names extraction, CZI file formats pixel type, and then finally a couple of changes related to a breaking change in the upstream filesystem handler (fsspec).

What's Changed

• bugfix/dynamic-dimension-typing by @evamaxfield in #419
• bugfix/czi-scene-indexing by @toloudis in #417
• admin/add-fsspec-to-upstream-checks by @evamaxfield in #422
• bugfix/extract-czi-channel-names-more-safely by @toloudis in #418
• Fix/czireader float32 dtype by @toloudis in #423
• admin/ignore-fsspec-2022.7.0 by @evamaxfield in #424
• bugfix/fsspec-local-file-opener-cpp-buffer-for-czi by @evamaxfield in #425

Full Changelog: v4.9.0...v4.9.1

Scene Stacking!

This release introduces a new feature, scene stacking!

The original issue that spawned this entire feature can be seen here: #335
We currently have a decent number of users that loop over all scenes and stack them into a single array manually. This release adds a function to both the AICSImage and all Reader objects that will do that for you, with some additional options as to how to stack.

many_scene_image = AICSImage("many-scenes.czi")
all_scenes_np = many_scene_image.get_stack()
all_scenes_da = many_scene_image.get_dask_stack()
all_scenes_xarray_np = many_scene_image.get_xarray_stack()
all_scenes_xarray_da = many_scene_image.get_xarray_dask_stack()

All of these have a few extra parameters which can be seen in our documentation for generate_stack

What's Changed

• feature/get-stack by @jrussell25 in #403
• feature/lower-log-level-of-OME-TIFF-read-errors by @evamaxfield in #414
• feature/image-container by @evamaxfield in #415

Full Changelog: v4.8.0...v4.9.0

Other News

We finally started working on a version 5, or "the plugin revamp" of this library! You can track our progress in the version 5 discussion post