Designed after this paper on volumetric segmentation with a 3D U-Net. Currently, the network does not have the B-Spline deformations that are mentioned in the paper. If you figure out a way to apply these to a 3D Keras CNN, let me know! PRs are always welcome!
The code was written to be trained using the BRATS data set for brain tumors, but it can be easily modify to be used in other 3D applications. To adapt the network, you might have to play with the input size to get something that works for your data.
I used Bohdan Pavlyshenko's Kaggle kernel for 2D U-Net segmentation as a base for this 3D U-Net.