SurfDist: Interpretable Three-Dimensional Instance Segmentation Using Curved Surface Patches

We present SurfDist, a convolutional neural network architecture for three-dimensional volumetric instance segmentation. SurfDist is a modification of the popular model architecture StarDist-3D which enables learning instance boundaries as closed piecewise compositions of smooth parametric surfaces. This parameterization breaks StarDist-3D's coupling of instance dimension and instance voxel resolution, and it produces predictions which may be upsampled to arbitrarily high resolutions without introduction of voxelization artifacts. For datasets with blob-shaped instances, common in biomedical imaging, SurfDist can achieve higher segmentation accuracy than StarDist-3D with more compact instance parameterizations.