Deep learning algorithms for connectomics rely upon localized classification, rather than overall morphology. This leads to a high incidence of erroneously merged objects. Humans, by contrast, can easily detect such errors by acquiring intuition for the correct morphology of objects. Biological neurons have complicated and variable shapes, which are challenging to learn, and merge errors take a multitude of different forms. We present an algorithm, MergeNet, that shows 3D ConvNets can, in fact, detect merge errors from high-level neuronal morphology. MergeNet follows unsupervised training and operates across datasets. We demonstrate the performance of MergeNet both on a variety of connectomics data and on a dataset created from merged MNIST images.
There have been numerous recent advances in using neural networks to recognize general three-dimensional objects. Methods include taking 2D projections of the input @cite_4 , combined 2D-3D approaches @cite_8 @cite_7 , and purely 3D networks @cite_33 @cite_36 . Accelerated implementation techniques for 3D networks have been introduced by Budden, et al @cite_15 and Zlateski, Lee, and Seung @cite_6 .
@cite_4 @cite_33 @cite_7 @cite_8 @cite_36 @cite_6 @cite_15
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A longstanding question in computer vision concerns the representation of 3D shapes for recognition: should 3D shapes be represented with descriptors operating on their native 3D formats, such as voxel grid or polygon mesh, or can they be effectively represented with view-based descriptors? We address this question in the context of learning to recognize 3D shapes from a collection of their rendered views on 2D images. We first present a standard CNN architecture trained to recognize the shapes' rendered views independently of each other, and show that a 3D shape can be recognized even from a single view at an accuracy far higher than using state-of-the-art 3D shape descriptors. Recognition rates further increase when multiple views of the shapes are provided. In addition, we present a novel CNN architecture that combines information from multiple views of a 3D shape into a single and compact shape descriptor offering even better recognition performance. The same architecture can be applied to accurately recognize human hand-drawn sketches of shapes. We conclude that a collection of 2D views can be highly informative for 3D shape recognition and is amenable to emerging CNN architectures and their derivatives. Robust object recognition is a crucial skill for robots operating autonomously in real world environments. Range sensors such as LiDAR and RGBD cameras are increasingly found in modern robotic systems, providing a rich source of 3D information that can aid in this task. However, many current systems do not fully utilize this information and have trouble efficiently dealing with large amounts of point cloud data. In this paper, we propose VoxNet, an architecture to tackle this problem by integrating a volumetric Occupancy Grid representation with a supervised 3D Convolutional Neural Network (3D CNN). We evaluate our approach on publicly available benchmarks using LiDAR, RGBD, and CAD data. VoxNet achieves accuracy beyond the state of the art while labeling hundreds of instances per second. Segmentation of 3D images is a fundamental problem in biomedical image analysis. Deep learning (DL) approaches have achieved the state-of-the-art segmentation performance. To exploit the 3D contexts using neural networks, known DL segmentation methods, including 3D convolution, 2D convolution on the planes orthogonal to 2D slices, and LSTM in multiple directions, all suffer incompatibility with the highly anisotropic dimensions in common 3D biomedical images. In this paper, we propose a new DL framework for 3D image segmentation, based on a combination of a fully convolutional network (FCN) and a recurrent neural network (RNN), which are responsible for exploiting the intra-slice and inter-slice contexts, respectively. To our best knowledge, this is the first DL framework for 3D image segmentation that explicitly leverages 3D image anisotropism. Evaluating using a dataset from the ISBI Neuronal Structure Segmentation Challenge and in-house image stacks for 3D fungus segmentation, our approach achieves promising results, comparing to the known DL-based 3D segmentation approaches. Abstract Convolutional networks (ConvNets) have become a popular approach to computer vision. Here we consider the parallelization of ConvNet training, which is computationally costly. Our novel parallel algorithm is based on decomposition into a set of tasks, most of which are convolutions or FFTs. Theoretical analysis suggests that linear speedup with the number of processors is attainable. To attain such performance on real shared-memory machines, our algorithm computes convolutions converging on the same node of the network with temporal locality to reduce cache misses, and sums the convergent convolution outputs via an almost wait-free concurrent method to reduce time spent in critical sections. Benchmarking with multi-core CPUs shows speedup roughly equal to the number of physical cores. We also demonstrate 90x speedup on a many-core CPU (Xeon Phi Knights Corner). Our algorithm can be either faster or slower than certain GPU implementations depending on specifics of the network architecture, kernel sizes, and density and size of the output patch. Deep convolutional neural networks (ConvNets) of 3-dimensional kernels allow joint modeling of spatiotemporal features. These networks have improved performance of video and volumetric image analysis, but have been limited in size due to the low memory ceiling of GPU hardware. Existing CPU implementations overcome this constraint but are impractically slow. Here we extend and optimize the faster Winograd-class of convolutional algorithms to the @math -dimensional case and specifically for CPU hardware. First, we remove the need to manually hand-craft algorithms by exploiting the relaxed constraints and cheap sparse access of CPU memory. Second, we maximize CPU utilization and multicore scalability by transforming data matrices to be cache-aware, integer multiples of AVX vector widths. Treating 2-dimensional ConvNets as a special (and the least beneficial) case of our approach, we demonstrate a 5 to 25-fold improvement in throughput compared to previous state-of-the-art.