New OME ZARR Image Reader#200
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Change the ome-zarr dependencies to hopefully work better with the strict package requirements of aicsimageio.
…n test_openslidewsi.py
didn't change index.rst as the support is probably more narrow than any conception of a WSI in the zarr format.
Fix assumption that ngff-multiscales have a strict dimension ordering Format code with black and autopep8 Move imports that are now optional to a try except block Add docstring to _fetch_downsamples Optimise read_region by adding some processing to lazy_initialize
Make imports more robust Expand possible dimnames Fix incorrect OME spec assumption in fetch_mpp Update slice varname for better readability Cache slice involved variables in init rather than read
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Support for locally stored OMEZarr Multiscale specification WSIs. I made changes based on #163 , then changes based on a look at the references to openslide in the repo, then changes based on my testing of the OMEZarr reader. I chose to use ngff-zarr to read OMEZarr Multiscales files, and to recognize files based on
OMEZARR_EXTENSIONS = {'.zarr'}as the code for WSI extension recognition expects a single file suffix.Testing I've done:
Credit to @HarveySouth