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thewtex / ngff-zarr

A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
https://ngff-zarr.readthedocs.io
MIT License
21 stars 4 forks source link

Image data not displayed in napari #45

Closed GFleishman closed 1 year ago

GFleishman commented 1 year ago

Creating an ome-ngff-zarr image with this package, then dragging into napari does not produce the expected result. An image layer does open, but no data is displayed. More details here: https://github.com/ome/napari-ome-zarr/issues/91

This is solved, just submitting here for documentation purposes. Will submit a PR with the fix.

GFleishman commented 1 year ago

After running some more tests on bigger datasets that required the _large_image_serialization method within to_multiscales I found that outputs were still formatted with the '.' separator - I guess because they were inheriting the dimension_separator from the cached arrays. So, now I have added dimension_separator="/" to every dask.array.to_zarr call and every zarr.creation.open_array call within to_multiscales and to_ngfff_zarr. Now outputs are formatted correctly even for huge data. This is a second pull request.