Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Display collection using Plate layout #124

Closed
wants to merge 3 commits into from

Conversation

will-moore
Copy link
Collaborator

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

NB: very preliminary as it uses Collections spec which is still being discussed: ome/ngff#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
Copy link
Member

manzt commented Oct 4, 2021

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

@will-moore
Copy link
Collaborator Author

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

This was only a TEMP format and never made it to the HCS spec. HCS images are now
/plate/A/1/0/ and the acquisition is not included in the URL
@will-moore
Copy link
Collaborator Author

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
Copy link
Collaborator Author

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

This was referenced Oct 5, 2021
@manzt
Copy link
Member

manzt commented Oct 10, 2021

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
Copy link
Collaborator Author

closing until collections spec is better defined

@will-moore will-moore closed this Jan 5, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants