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

Hierarchy browser #53

Merged
merged 90 commits into from
Oct 22, 2024
Merged

Hierarchy browser #53

merged 90 commits into from
Oct 22, 2024

Conversation

will-moore
Copy link
Member

@will-moore will-moore commented Oct 7, 2024

Deployed at https://will-moore.github.io/ome2024-ngff-challenge/
and also at https://deploy-preview-53--ngff-challenge.netlify.app/

We are now loading ALL zarr samples from the csv files into the page, so we can sort and filter by various attributes.
This requires that extra data is added to the csv files (via the updated load_zarr_stats.py).
We can currently filter by source institution (and then by sub institution or collection), imaging modality, organism and number of dimensions.
Can also sort by various attributes.

TODOs:

  • Show image.zarr name for each item
  • Show T: 1, Z: 10, Y: 400, X: 500 instead of in table
  • When showing ?csv=... page, page should say that in the Header.. and show Home link
  • Remove .csv from collection link.
  • Move Filter by Shards/Chunks etc under "Advanced" options. Add more filtering choices.
  • Add tooltips to sort controls
  • Filter by Name, Description
  • Improve display of samples: - show 'origin', name, etc
  • Fix or remove vizarr link: Mismatch between Validator and Vizarr viewer #60
  • Improve thumbnails - try to pick optimal size based on image size and number of datasets (assume that downsampling is 2x for each resolution without loading array shape for each resolution).
Screenshot 2024-10-13 at 08 30 38

Copy link

netlify bot commented Oct 7, 2024

Deploy Preview for ngff-challenge ready!

Name Link
🔨 Latest commit 21f480f
🔍 Latest deploy log https://app.netlify.com/sites/ngff-challenge/deploys/67178bfc479e4c00089d7c2c
😎 Deploy Preview https://deploy-preview-53--ngff-challenge.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify site configuration.

will-moore added a commit to will-moore/jax-ngff-challenge-2024 that referenced this pull request Oct 8, 2024
Testing an updated NGFF samples viewer that benefits from having more metadata "consolidated" in the csv.
See ome/ome2024-ngff-challenge#53
@will-moore
Copy link
Member Author

Bunch more testing, looking good. No blockers reported or remaining on https://docs.google.com/document/d/107XnRIcHhhJW2lUeFqJF3_mEiOMEMvLgzsIJL73YP9o/edit

Merging...

@will-moore will-moore merged commit bc41e93 into ome:main Oct 22, 2024
9 checks passed
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.

1 participant