hms-dbmi / vizarr

A minimal Zarr image viewer based on Viv.
https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr
MIT License
123 stars 18 forks source link

Display collection using Plate layout #124

Closed will-moore closed 2 years ago

will-moore commented 3 years ago

This is an investigation into viewing Collections - See #123.

NB: very preliminary as it uses Collections spec which is still being discussed: https://github.com/ome/ngff/issues/31

It uses the same display as a Plate, making the assumption that all images are the same shape and can be rendered with the same rendering settings!

To handle very diverse images of different shapes, numbers of resolution levels, pixelTypes etc is going to need a different strategy.

I'll try to create some public data for testing...

cc @dominikl

manzt commented 3 years ago

Thanks for making the PR @will-moore. I can help with adding types -- looking forward to some public data to test with!

will-moore commented 3 years ago

Sample dataset at https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0043/13901.zarr with 529 images exported from http://idr.openmicroscopy.org/webclient/?show=dataset-13901

Screenshot 2021-10-05 at 09 17 33
will-moore commented 3 years ago

Deployed at https://deploy-preview-124--vizarr.netlify.app/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0043/13901.zarr but it took me a few refreshes to work, since if any of the images fail to load then nothing shows.

So I think this has been a useful investigation, but we also need to think about alternatives. I have been looking loading an individual deck.gl canvas for each thumbnail, maybe to display in a lazy-loading list. But it's not working yet...

will-moore commented 3 years ago

Also exported this Dataset http://idr.openmicroscopy.org/webclient/?show=dataset-7754 which has only 11 images but they are different sizes to https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0062/8dc4707/7754.zarr and can't be viewed by this PR

manzt commented 3 years ago

Thanks so much for your work here and in #125 @will-moore. I will be out of town this week, but I'll be able to take a closer look when I get back.

will-moore commented 2 years ago

closing until collections spec is better defined