Support reading OME-Zarr 0.5#295
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* use fsspec as a wrapper for ZarrTiffStore * update deprecated readers and tests * document the helper function * add back the binary check after a flag * use kwarg for file mode in reader * restore dtype attribute * restore opening zarr with dask * stringify path name * remove redundant dtype
it doesn't matter what the order is
ziw-liu
commented
Apr 15, 2025
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| # SHOULD | ||
| version: Literal["0.1", "0.2", "0.3", "0.4"] = "0.4" | ||
| version: Literal["0.1", "0.2", "0.3", "0.4", "0.5"] | None = Field( |
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zarr-python 3.0.8 breakage
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@aliddell recent zarr-python and numcodec updates broke many things – they shipped multiple breaking changes in patch versions! Also in the news, all zarr-python versions in [3.0.0, 3.0.7] got yanked from PyPI so I'm bumping the requirement. |
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@aliddell is it easy(-ish) to write a test case using acquire-zarr's python bindings to write and using iohub to read? |
This reverts commit 77146dd.
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After manually adding metadata omitted by ome/ome2024-ngff-challenge#95. This branch can be used with napari-iohub to visualize v0.5 HCS plates: 
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ziw-liu
commented
Jun 2, 2025
aliddell
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Jun 2, 2025
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LGTM I just have a couple of questions and a suggestion you can take or leave.
Co-authored-by: Alan Liddell <alan.c.liddell@gmail.com>
edyoshikun
reviewed
Jun 3, 2025
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iohub infoworks on single-FOV acquire-zarr outputNext step (for another PR): support writing OME-Zarr v0.5 datasets.