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brainglobe / cellfinder

Automated 3D cell detection in very large images
https://brainglobe.info/documentation/cellfinder/index.html
BSD 3-Clause "New" or "Revised" License
181 stars 39 forks source link

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

Open dstansby opened 1 year ago

dstansby commented 1 year ago

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.

adamltyson commented 1 year ago

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

dstansby commented 1 year ago

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 commented 1 year ago

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