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hms-dbmi / viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.
http://avivator.gehlenborglab.org
MIT License
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Avivator crashes when specifying OME-Zarr URL without explicit path (i.e. "0") #678

Closed anton-slashm closed 1 year ago

anton-slashm commented 1 year ago

Describe the bug Avivator crashes when opening OME-ZARR URL without explicit path specified

To Reproduce Open OME-ZARR in Avivator without explicit path specified, i.e. http://127.0.0.1:3000/?image_url=http://localhost:8080/test_img_zarr/

Expected behavior Avivator should default to path "0", i.e http://127.0.0.1:3000/?image_url=http://localhost:8080/test_img.zarr/0/

Screenshots If applicable, add screenshots to help explain your problem.

Environment:

ilan-gold commented 1 year ago

What exactly is the problem here? If the image does not have a multiscales key and so we should assume it is not therefore multiscale? Would it be possible to upload and/or share some test data?

anton-slashm commented 1 year ago

@ilan-gold The problem I was trying to solve is more of quality of service improvement. Right now, if you pass just the URL of ome-zarr, it will crash. You need to specifically tell it to go into xxx/0 to get it to work. It was an issue for me when I started using it, because I couldn't figure out why the images weren't opening. As for the multiscales part, I just reused the existing logic.

ilan-gold commented 1 year ago

I'm a little confused @anton-slashm. https://avivator.gehlenborglab.org/?image_url=https://minio-dev.openmicroscopy.org/idr/v0.4/2022-01-05/idr0062/6001240.zarr seems to work fine. Perhaps you are not on v0.4 for your data? Is the image not multiscale? I don't think we are going to backport to v0.3 but if that isn't the issue, I am still not sure I follow. It would be great if you could point me to an example.