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Data standardization to AICSImage #56

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MosGeo opened this issue Aug 21, 2022 · 0 comments
Open

Data standardization to AICSImage #56

MosGeo opened this issue Aug 21, 2022 · 0 comments

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@MosGeo
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MosGeo commented Aug 21, 2022

Use Case

One big advantage of aicsimageio is the standardization of all image types to a common ndarray with known shape. All images would produce the 5 or 6 (CZI) dimensions. This format is easy to handle in plugins and everything works as expected.

Based on info here: #24 (comment), napari-aicsimageio returns the raw data from the reader rather than the aicsimage which breaks the standardization and thus breaks any plugins that rely on the standardization.

Solution

Have a toggle in napari-aicsimageio to choose to return the raw data or the aicsimage.

for example:

import napari
import napari-aicsimageio
napari-aicsimageio.return_aicsimage_data =  True

# Run napari
...

Alternatives

All plugins that want the standard should use the layer.metadata['aicsimage'].

@MosGeo MosGeo changed the title Data Standardization to AICSImage Data standardization to AICSImage Aug 21, 2022
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