Example of an open source OME-Zarr being used with Avivator

[d33bs]

Hello, awesome stuff with this project! I'm interested in exploring how to use Avivator with OME-Zarr's. Are there any examples of open source OME-Zarr's being used with Avivator? I noticed the randomly loaded examples appear to all be OME-Tiff's (or at least not OME-Zarr's)(I could just be having bad luck here!). If there are truly no examples for OME-Zarr I'd suggest adding at least one example to help users observe the way those data are loaded within Avivator (I can create an issue to this effect if useful).

I ask as when I currently attempt to open an OME-Zarr locally (I supply it through the dev server site and pnpm dev) I see an error with seemingly no traceback or troubleshooting details. I plan to reference a working OME-Zarr to make sure the data are formatted appropriately to what Avivator expects.

[ilan-gold]

Hmmm @d33bs yes we should support it at some level, but I don't remember exactly how. @manzt would probably be able to give more specifics. For example https://avivator.gehlenborglab.org/?image_url=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr loads (from https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr&viewState={%22zoom%22:1.41438157972179,%22target%22:[135.5,137.5]}) modulo its ability to set the correct colors (I also don't think it pulls channel values from the metadata, but our auto-settings function is quite good so the image should look fine)

[ilan-gold]

It's possible we only support certain versions of ome-zarr, or a subset (we definitely don't support plates/wells here), but I don't remember exactly what.

[d33bs]

Thanks @ilan-gold ! I was able to pull up that example you shared and will take a look at the files to make sure I'm aligning with the files I'm using.