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

Annotation exporting #49

Merged
merged 38 commits into from
Jul 31, 2023
Merged

Annotation exporting #49

merged 38 commits into from
Jul 31, 2023

Conversation

danton267
Copy link
Collaborator

  • Adds Dash UI and callbacks to download annotations
  • Adds figure annotation conversion to a suitable format with all relevant metadata

TODO:

  • finish creating format compatible with napari

@danton267 danton267 self-assigned this Jul 20, 2023
@danton267 danton267 linked an issue Jul 20, 2023 that may be closed by this pull request
@github-actions
Copy link

github-actions bot commented Jul 20, 2023

Staging application has been deployed and is available at: https://dash5-services.plotly.host/ml-exchange-staging
Production app name: ml-exchange
Current branch name: annotation-exporting
Commit: 72e2542

@hannahker
Copy link
Collaborator

@danton267 see #56 for some suggested fixes.

@hannahker
Copy link
Collaborator

@danton267 -- super minor change requested by LBL: Can we update the output .npy files so that there's 1 file per annotated slice? So for example, if the user annotates slices 1 and 34, the outputs should be:

  • mask_001.npy
  • mask_034.npy

@danton267
Copy link
Collaborator Author

danton267 commented Jul 27, 2023

@danton267 -- super minor change requested by LBL: Can we update the output .npy files so that there's 1 file per annotated slice? So for example, if the user annotates slices 1 and 34, the outputs should be:

done! The mask data is now exported as .zip with one .npy (or .sp) file per slice

@danton267 danton267 merged commit 64328da into main Jul 31, 2023
4 checks passed
@danton267 danton267 deleted the annotation-exporting branch July 31, 2023 12:22
@danton267 danton267 linked an issue Jul 31, 2023 that may be closed by this pull request
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.

Export annotations in Napari-compatible format Create pixel mask from annotations
3 participants