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ome / napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images
https://www.napari-hub.org/plugins/napari-ome-zarr
BSD 3-Clause "New" or "Revised" License
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Write ome-zarr images (feature request) #67

Open haesleinhuepf opened 2 years ago

haesleinhuepf commented 2 years ago

Hi all,

I'm just wondering how complicated it might be to provide a writer for napari. I just tried to save a dataset in napari as "test.zarr" and it was written to disc as "test.zarr.tif".

If you say writing zarr files from napari makes sense, e.g. using this code, I'd be happy to provide a pull-request.

Thanks!

Best, Robert

joshmoore commented 2 years ago

Hi @haesleinhuepf.

I'm just wondering how complicated it might be to provide a writer for napari.

Definitely doable. There's recently been a bunch of work in https://github.com/ome/ome-zarr-py/pull/192 to improve support for this (overall speed and the types of data that you can pass in like dask or not dask). It's not released but help testing is very welcome.

I just tried to save a dataset in napari as "test.zarr" and it was written to disc as "test.zarr.tif".

Don't know why that would happen. You clicked on "save" in the UI?

If you say writing zarr files from napari makes sense, e.g. using this code, I'd be happy to provide a pull-request.

Hmmm.... that looks to be "just a zarr" and not an "OME-Zarr" and so I'll defer to you if you want that. If you are interested in writing an NGFF, I'd suggest we use the helper functions from ome-zarr-py.

~Josh