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

Improve docs on what the skan measurements actually mean #197

Open
GenevieveBuckley opened this issue Feb 8, 2023 · 1 comment
Open

Comments

@GenevieveBuckley
Copy link
Collaborator

Juan says here that the docs in skan need to be improved, to prevent misunderstanding like the one I made here: https://forum.image.sc/t/how-to-dilate-skeleton-based-on-vessel-diamater/65549/4?

It would be good to improve the docs for all the statistical metrics skan produces.
But the specific measurement I'd confused was:

  • branch-distance: the total length of the branch. Eg: a string laid along the branch, touching it all the way)
  • euclidean-distance: the straight line distance between the start and end points of the branch. Eg: a string pulled taught between the branch start and end. This is (almost) always smaller than the branch-distance (it will be equal to the branch distance in cases where the branch is entirely straight)
@GenevieveBuckley
Copy link
Collaborator Author

I confused euclidean-distance with the thickness of a branch, probably because the name made me think of euclidean distance transforms, and assumed that was used to measure the distance away from the skeleton centreline.

Juan says that actually nothing in skan measures branch thickness at all.

Currently, the branch thickness is not stored anywhere in skan. There are workarounds that I have been meaning to turn into a tutorial and/or build into skan properly, but aren’t there yet.

GenevieveBuckley added a commit to GenevieveBuckley/dask-blog that referenced this issue Feb 8, 2023
Fix factual error related to skan metric interpretation "euclidean-distance". See jni/skan#197
GenevieveBuckley added a commit to dask/dask-blog that referenced this issue Feb 8, 2023
Fix factual error related to skan metric interpretation "euclidean-distance". See jni/skan#197
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

No branches or pull requests

1 participant