TorchIO
Pytorch, seems to have nice tools for 3D medical imaging especially, e.g. for elastic deformations via b-spline
MIC-DKFZ/batchgenerators
numpy based data augmentations
Neurite
Great toolset for DL especially with large volume support
VoxelMorph
Great toolset for all things related to Registration/Alignment/Deformations
Nobrainer
Deep Learning Framework for 3D processing implementing existing models from recent literature
NiTorch
NeuroImaging in PyTorch
fast.ai
A Layered API for Deep Learning