To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deep learning” approach has since become accepted as a standard for segmentation of EM images. The challenge has continued to accept submissions, and the best so far has resulted from cooperation between two teams. The challenge has probably saturated, as algorithms cannot progress beyond limits set by ambiguities inherent in 2D scoring and the size of the test dataset. Retrospective evaluation of the challenge scoring system reveals that it was not sufficiently robust to variations in the widths of neurite borders. We propose a solution to this problem, which should be useful for a future 3D segmentation challenge.
Harvesting dense pixel-level annotations to train deep neural networks for semantic segmentation is extremely expensive and unwieldy at scale. While learning from synthetic data where labels are readily available sounds promising, performance degrades significantly when testing on novel realistic data due to domain discrepancies. We present Dual Channel-wise Alignment Networks (DCAN), a simple yet effective approach to reduce domain shift at both pixel-level and feature-level. Exploring statistics in each channel of CNN feature maps, our framework performs channel-wise feature alignment, which preserves spatial structures and semantic information, in both an image generator and a segmentation network. In particular, given an image from the source domain and unlabeled samples from the target domain, the generator synthesizes new images on-the-fly to resemble samples from the target domain in appearance and the segmentation network further refines highlevel features before predicting semantic maps, both of which leverage feature statistics of sampled images from the target domain. Unlike much recent and concurrent work relying on adversarial training, our framework is lightweight and easy to train. Extensive experiments on adapting models trained on synthetic segmentation benchmarks to real urban scenes demonstrate the effectiveness of the proposed framework.
We present a Reinforcement Learning (RL) solution to the view planning problem (VPP), which generates a sequence of view points that are capable of sensing all accessible area of a given object represented as a 3D model. In doing so, the goal is to minimize the number of view points, making the VPP a class of set covering optimization problem (SCOP). The SCOP is N P -hard, and the inapproximability results tell us that the greedy algorithm provides the best approximation that runs in polynomial time. In order to find a solution that is better than the greedy algorithm, (i) we introduce a novel score function by exploiting the geometry of the 3D model, (ii) we model an intuitive human approach to VPP using this score function, and (iii) we cast VPP as a Markovian Decision Process (MDP), and solve the MDP in RL framework using well-known RL algorithms. In particular, we use SARSA, Watkins-Q and TD with function approximation to solve the MDP. We compare the results of our method with the baseline greedy algorithm in an extensive set of test objects, and show that we can outperform the baseline in almost all cases.
This paper presents a new active contour-based, statistical method for simultaneous volumetric segmentation of multiple subcortical structures in the brain. In biological tissues, such as the human brain, neighboring structures exhibit co-dependencies which can aid in segmentation, if properly analyzed and modeled. Motivated by this observation, we formulate the segmentation problem as a maximum a posteriori estimation problem, in which we incorporate statistical prior models on the shapes and intershape (relative) poses of the structures of interest. This provides a principled mechanism to bring high level information about the shapes and the relationships of anatomical structures into the segmentation problem. For learning the prior densities we use a nonparametric multivariate kernel density estimation framework. We combine these priors with data in a variational framework and develop an active contour-based iterative segmentation algorithm. We test our method on the problem of volumetric segmentation of basal ganglia structures in magnetic resonance images. We present a set of 2-D and 3-D experiments as well as a quantitative performance analysis. In addition, we perform a comparison to several existent segmentation methods and demonstrate the improvements provided by our approach in terms of segmentation accuracy.
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