Adding binary thinning 3d algorithm

[sychen52]

I recently created this package: https://github.com/sychen52/binary_thinning_3d_cuda
It extracts the skeleton of a 3d binary mask. Do you think it is a good idea to add this functionality to this repo?

[jaykshirsagar05]

Hey!

Thanks for the amazing implementation. It makes much more sense to integrate it https://github.com/vmtk/SlicerExtension-VMTK here. We can also use this to add a clDice custom loss in MONAI for skeleton supervision.

[sychen52]

Using this for a clDice custom loss in MONAI sounds like a great idea. Would you prefer my package to be an external dependency for MONAI (my package has very minimal dependencies), or should I port the CUDA code directly into MONAI's custom C++ extensions?

If it is okay to add my package as an external dependency, I have a PR ready to add it to clDice: #8904

[sychen52]

I think I may be able to add a version of the centerline algorithm with a gradient, similar to the gradient of the soft_skel. Then we can use it during forward as well. Is that worth doing?