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We introduce a new machine learning approach for image segmentation that uses a neural network to model the conditional energy of a segmentation given an image. Our approach, combinatorial energy learning for image segmentation (CELIS) places a particular emphasis on modeling the inherent combinatorial nature of dense image segmentation problems. We propose efficient algorithms for learning deep neural networks to model the energy function, and for local optimization of this energy in the space of supervoxel agglomerations. We extensively evaluate our method on a publicly available 3-D microscopy dataset with 25 billion voxels of ground truth data. On an 11 billion voxel test set, we find that our method improves volumetric reconstruction accuracy by more than 20% as compared to two state-of-the-art baseline methods: graph-based segmentation of the output of a 3-D convolutional neural network trained to predict boundaries, as well as a random forest classifier trained to agglomerate supervoxels that were generated by a 3-D convolutional neural network.
Learning-based approaches for semantic segmentation have two inherent challenges. First, acquiring pixel-wise labels is expensive and time-consuming. Second, realistic segmentation datasets are highly unbalanced: some categories are much more abundan
The success of deep learning heavily depends on the availability of large labeled training sets. However, it is hard to get large labeled datasets in medical image domain because of the strict privacy concern and costly labeling efforts. Contrastive
Semantic segmentation is pixel-wise classification which retains critical spatial information. The feature map reuse has been commonly adopted in CNN based approaches to take advantage of feature maps in the early layers for the later spatial reconst
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths an
Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this