Aicsimageio

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 https://github.com/AllenCellModeling/aicsimageio/pull/437
* fix single dimension index when requested as a returned dim by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/438
* admin/citation-update by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/440
* try to handle I the same way as Q coming out of tifffile reading by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/445

**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/v4.9.2...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).

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 https://github.com/AllenCellModeling/aicsimageio/pull/426
* bugfix/czi-scene-selection-for-inconsistent-scenes-regression by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/432
* bugfix/convert-dimension-spec-lists-to-slices-when-possible by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/429
* admin/include-fsspec-dep-for-czi-in-readme by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/433

New Contributors
* colobas made their first contribution in https://github.com/AllenCellModeling/aicsimageio/pull/426

**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/v4.9.1...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 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 https://github.com/AllenCellModeling/aicsimageio/pull/419
* bugfix/czi-scene-indexing by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/417
* admin/add-fsspec-to-upstream-checks by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/422
* bugfix/extract-czi-channel-names-more-safely by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/418
* Fix/czireader float32 dtype by toloudis in https://github.com/AllenCellModeling/aicsimageio/pull/423
* admin/ignore-fsspec-2022.7.0 by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/424
* bugfix/fsspec-local-file-opener-cpp-buffer-for-czi by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/425


**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/v4.9.0...v4.9.1

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.

python
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`](https://allencellmodeling.github.io/aicsimageio/aicsimageio.html#aicsimageio.transforms.generate_stack)

What's Changed
* feature/get-stack by jrussell25 in https://github.com/AllenCellModeling/aicsimageio/pull/403
* feature/lower-log-level-of-OME-TIFF-read-errors by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/414
* feature/image-container by evamaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/415


**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/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](https://github.com/AllenCellModeling/aicsimageio/discussions/372)

The `aicsimageio` v4.8.0 release includes:

* `aicsimageio` now ships with mypy type annotations. If you are using mypy, our types can now be properly imported and type checked against.
* `aicsimageio` image containers and writer functions now have an `fs_kwargs` parameter to pass down any arguments for creating the `fsspec` Filesystem object with. i.e. `AICSImage("s3://some-bucket/some-image.ome.tiff", fs_kwargs=dict(anon=True))` for anonymous / no credential S3 file reading.
* `BioformatsReader` bugfixes for scene management / switching and preparing the reader for the next release of the underlying `bioformats_jar` version.

We have also dropped support for Python 3.7 and added support for Python 3.10

An additional minor package admin change has been added which runs our `aicsimageio` test suite multiple times a week but installs with our upstream dependencies `main` branches instead of released versions. This is so we can help catch bugs earlier in the release process rather than post release.

What's Changed
* admin/ship-mypy-type-annotations-drop-py37-add-py310-manage-test-dependencies-separate-for-each-tox-env by JacksonMaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/397
* bugfix/pass-series-index-in-biofile-init by JacksonMaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/401
* feature-and-admin/create-aicsimage-objects-with-fs-kwargs-and-remove-need-for-creds by JacksonMaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/407
* admin/add-test-upstreams-action by JacksonMaxfield in https://github.com/AllenCellModeling/aicsimageio/pull/406
* admin/prepare-bioformats_reader-to-work-with-new-bioformats_jar-based-on-scyjava by tlambert03 in https://github.com/AllenCellModeling/aicsimageio/pull/402

Contributors
toloudis
AetherUnbound
tlambert03
jrbourbeau
JacksonMaxfield

**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/v4.7.0...v4.8.0

We are pleased to annouce the release of aicsimageio v4.7.0!

This release brings another new reader: [the `OmeTiffTiledReader`](https://allencellmodeling.github.io/aicsimageio/aicsimageio.readers.html#aicsimageio.readers.bfio_reader.OmeTiledTiffReader).

For certain tiled / mosaic OME-TIFFs, this reader massively speedups read performance and you can see all the benchmarks provided by Nicholas-Schaub in the PR which added this reader: https://github.com/AllenCellModeling/aicsimageio/pull/387

The new reader can be installed with `pip install aicsimageio[bfio]`

Changelog
* feature/tiledtiffreader by Nicholas-Schaub in https://github.com/AllenCellModeling/aicsimageio/pull/387

Reviewers
* JacksonMaxfield
* toloudis

**Full Changelog**: https://github.com/AllenCellModeling/aicsimageio/compare/v4.6.4...v4.7.0