Showing multiple FOVs of a HCS plate

[m-albert]

Hi, thanks a lot for your work here! Vizarr is awesome!

I just wanted to quickly report this here: I noticed that for HCS datasets with multiple FOVs, only the first one seems to be displayed for each well. Here's an example of a ngff v4 file in which this happens: https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0056B/7361.zarr.

[will-moore]

The plate overview is really meant as a way to browse the Wells rather than show every image (all fields). Since each Well can have many fields, attempting to show all of them is likely to be too slow. That plate has 384 Wells and is already slow-ish to load. Each Well has 30 fields, so showing them all will be quite a bit slower!

We adopt the same strategy in OMERO e.g. that plate is available at https://idr.openmicroscopy.org/webclient/?show=plate-7361 - OMERO also allows you to choose the field index you want to use for viewing the plate, which isn't available yet for vizarr (or napari-ome-zarr).

One strategy to show more fields is to pre-stitch them into larger images. See ome/ngff#137 for a discussion of this.

[m-albert]

Thank you @will-moore!

I completely agree that loading each FOV is far from optimal and comes with substantial overhead. I was thinking though that it'd be nevertheless useful to visualize an entire well. And actually that's already possible when visualizing a specific well: https://hms-dbmi.github.io/vizarr/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0056B/7361.zarr/A/1. In this case, all FOVs are shown with their respective transform metadata 🎉.

Thanks again! Closing here