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

Investigate replacing custom connected-component labelling with 3rd party library #287

Open
dstansby opened this issue Apr 17, 2023 · 3 comments
Labels
cellfinder-core Issue concerns the core backend enhancement New feature or request

Comments

@dstansby
Copy link
Member

I've come across https://github.com/seung-lab/connected-components-3d, which seems like a mature and well used (~250 stars) library for connected component labelling. It would be good to investigate whether we can replace the custom connected component labelling with this library, to reduce the maintenance burden in cellfinder-core.

@dstansby dstansby added the enhancement New feature or request label Apr 17, 2023
@adamltyson
Copy link
Member

Fine by me. It would be great to use an existing dependency like scikit-image if possible though.

@dstansby
Copy link
Member Author

I've realised that one issue of using an external library is it might require loading all the planes in memory at once, which we don't want to do. So perhaps best to close this?

@adamltyson
Copy link
Member

Would it? Could we not just call it only the planes currently in memory?

@willGraham01 willGraham01 added the cellfinder-core Issue concerns the core backend label Jan 3, 2024
@willGraham01 willGraham01 transferred this issue from brainglobe/cellfinder-core Jan 3, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
cellfinder-core Issue concerns the core backend enhancement New feature or request
Projects
Status: Backlog
Development

No branches or pull requests

3 participants