Index error when trying to use image loaded with napari-aicsimageio

[Aerendel]

Expected behavior Should be able to load a CZI file into Napari using the napari-aicsimageio reader plugin, select a layer, channel, workflow and run a segmentation.

Actual behavior The Segmenter UI shows the full channel list for the source image, no matter which layer is selected. If user selects anything else than Channel index 0, we see the following error

IndexError: index 3 is out of bounds for axis 2 with size 1

Details

• Root cause is because napari-aicsimageio converts channels into image layers, so effectively we are now dealing with multiple single channel "images". Segmenter plugin reads channel metadata from the original image source if available and presents the full channel list to the user. This behavior does not make sense in this case.
• This will likely be an issue with any other reader plugin that splits an image into multiple layers
• This probably can't just be fixed easily and will require a change in plugin behavior or in user experience. Possible paths:
  • If an image source is available, read everything from the source, including the actual image data (instead of getting it from what's loaded in Napari). This may be slightly confusing but will provide all metadata if available.
  • Forget about channel metadata and only rely on what's available in Napari. This will ensure full compatibility with all situations, but lack of metadata provides a lesser user experience
  • Redesign the user experience / flow for selecting the data to segment, in a way that can netter satisfy all possible scenarios

[Aerendel]

Implemented a temporary solution now to disable loading image data and metadata from the source if a reader plugin is being used. This should ensure the same UX for regular scenarios, and basic compatibility with reader plugins like napari-aicsimageio, until we come up with a better user experience. Opened https://github.com/AllenCell/napari-allencell-segmenter/issues/106 to that effect.