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.

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The innate immune cell compartment is highly diverse in the healthy central nervous system (CNS), including parenchymal and non-parenchymal macrophages. However, this complexity is increased in inflammatory settings by the recruitment of circulating myeloid cells. It is unclear which disease-specific myeloid subsets exist and what their transcriptional profiles and dynamics during CNS pathology are. Combining deep single-cell transcriptome analysis, fate mapping, in vivo imaging, clonal analysis, and transgenic mouse lines, we comprehensively characterized unappreciated myeloid subsets in several CNS compartments during neuroinflammation. During inflammation, CNS macrophage subsets undergo self-renewal, and random proliferation shifts toward clonal expansion. Last, functional studies demonstrated that endogenous CNS tissue macrophages are redundant for antigen presentation. Our results highlight myeloid cell diversity and provide insights into the brain’s innate immune system.

Optical flow estimation can be formulated as an end-toend supervised learning problem, which yields estimates with a superior accuracy-runtime tradeoff compared to alternative methodology. In this paper, we make such networks estimate their local uncertainty about the correctness of their prediction, which is vital information when building decisions on top of the estimations. For the first time we compare several strategies and techniques to estimate uncertainty in a large-scale computer vision task like optical flow estimation. Moreover, we introduce a new network architecture utilizing the Winner-Takes-All loss and show that this can provide complementary hypotheses and uncertainty estimates efficiently with a single forward pass and without the need for sampling or ensembles. Finally, we demonstrate the quality of the different uncertainty estimates, which is clearly above previous confidence measures on optical flow and allows for interactive frame rates. * equal contribution

Future prediction is a fundamental principle of intelligence that helps plan actions and avoid possible dangers. As the future is uncertain to a large extent, modeling the uncertainty and multimodality of the future states is of great relevance. Existing approaches are rather limited in this regard and mostly yield a single hypothesis of the future or, at the best, strongly constrained mixture components that suffer from instabilities in training and mode collapse. In this work, we present an approach that involves the prediction of several samples of the future with a winner-takes-all loss and iterative grouping of samples to multiple modes. Moreover, we discuss how to evaluate predicted multimodal distributions, including the common real scenario, where only a single sample from the ground-truth distribution is available for evaluation. We show on synthetic and real data that the proposed approach triggers good estimates of multimodal distributions and avoids mode collapse.