University Medical Center Freiburg

About: University Medical Center Freiburg is a healthcare organization based out in Freiburg, Germany. It is known for research contribution in the topics: Transplantation & Population. The organization has 5627 authors who have published 8143 publications receiving 219865 citations. The organization is also known as: Division of Rheumatology and Clinical Immunology, University Medical Center Freiburg, Freiburg, Germany. & Universitätsklinikum Freiburg.

3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation

Abstract: This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.