WIP: adding reader contribution to napari for ome-zarr painting - Githubissues

AbigailMcGovern / iterseg

napari plugin for iteratively improving 3D instance segmentation of cells (u-net x watershed)

BSD 3-Clause "New" or "Revised" License

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WIP: adding reader contribution to napari for ome-zarr painting #17

Closed jni closed 9 months ago

jni commented 9 months ago

Unfortunately we can't just rely on the napari-ome-zarr plugin because it opens arrays as dask arrays, which can't be painted on. This PR adds a reader contribution that:

reads images as multiscale dask arrays (this should be pretty much equivalent to napari-ome-zarr)
reads labels as tensorstore arrays if available, zarr arrays otherwise. This allows painting into the labels arrays (tensorstore is currently faster to paint on.)

The data scale, channel axes, and colormaps are set correctly from the input.

jni commented 9 months ago

@AbigailMcGovern this should be ready to merge.