Support bioformats2raw.layout

[will-moore]

As noted in previous discussion at #21, the data generated with:

$ bioformats2raw image directory.zarr

cannot be opened with:

$ napari directory.zarr.

What should be the expected behaviour in this case?

• Open ALL the images under directory.zarr/ in multiple layers? The user could then turn off or delete the layers that they don't want to use. This should probably be the default behaviour in the case where there is only 1 image. But what if there are 3, or 100?
• In the case of an OME-NGFF plate, we show a grid of thumbnails for the first image in each Well. We could try to do the same for non-plate bioformats2raw.layout, but this doesn't give users an easy way to open the Images themselves.
• Any other way that a napari file-reader plugin can direct users to the images within the directory.zarr?

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/napari-only-displays-certain-ome-zarr-files/73542/4

[joshmoore]

and with #47? (which still needs the hard-coded fixing)

That should lead to opening all as layers, which isn't great. Arguably that could be one specific plugin option.

@jwindhager is working on hierarchical support for napari. (Perhaps he could attach a video demonstration?) That is likely the "more correct" way of doing this, but I guess the question is if we would like to wait on that.

Another option would be the strategy discussed for vizarr, which is show the potential images in some form of clickable manner, but I don't know if that's doable in napari.

[will-moore]

@joshmoore - I just don't see that #47 has the logic to traverse all the images....
Ah - I see you need ome/ome-zarr-py#174 too!
OK, that actually works...

[will-moore]

See discussion / request for this feature at ome/ngff#167 (comment)

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/napari-napari-ome-zarr-plugin-is-not-registered/78482/2

[psobolewskiPhD]

• Any other way that a napari file-reader plugin can direct users to the images within the directory.zarr?

I wonder if something akin to scene handling in napari-aicsimageio would work?
See: AllenCellModeling/napari-aicsimageio#27

[joshmoore]

@psobolewskiPhD: nice! For easy reference for those following along:

https://github.com/AllenCellModeling/napari-aicsimageio/blob/main/images/scene-selection.gif

cc: @jwindhager @will-moore

[yfukai]

Hi, I'm not sure if this is an appropriate place to ask this, but related to ome/ngff#167 (comment), I was wondering if something like scene in AICSImage is planned to be included in the spec. That would be quite helpful to organize images that are shading-corrected but yet-to-be-stitched in a common image processing workflow (I'm currently working on a shading correction program and also developed a simple stitching package, and am trying to find a way to let them work with OME-NGFF). Thanks in advance for any feedback on this!

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/general-zarr-pain-xyc-fluorescence-microscopy-data/105774/7