Data standardization to AICSImage

[MosGeo]

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: https://github.com/AllenCellModeling/napari-aicsimageio/issues/24#issuecomment-918270038, 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'].