Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python
This is the last version that will support Python3.8
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.12.1...v4.13.0
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.12.0...v4.12.1
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.11.0...v4.12.0
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.10.0...v4.11.0
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.9.4...v4.10.0
UnboundLocalError in TiffGlobReader by @ianhi in https://github.com/AllenCellModeling/aicsimageio/pull/449
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.9.3...v4.9.4
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).
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).
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).
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.
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
Full Changelog: https://github.com/AllenCellModeling/aicsimageio/compare/v4.8.0...v4.9.0
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