Recursive Training of 2D-3D Convolutional Networks for Neuronal Boundary Detection

Efforts to automate the reconstruction of neural circuits from 3D electron microscopic (EM) brain images are critical for the field of connectomics. An important computation for reconstruction is the detection of neuronal boundaries. Images acquired by serial section EM, a leading 3D EM technique, are highly anisotropic, with inferior quality along the third dimension. For such images, the 2D max-pooling convolutional network has set the standard for performance at boundary detection. Here we achieve a substantial gain in accuracy through three innovations. Following the trend towards deeper networks for object recognition, we use a much deeper network than previously employed for boundary detection. Second, we incorporate 3D as well as 2D filters, to enable computations that use 3D context. Finally, we adopt a recursively trained architecture in which a first network generates a preliminary boundary map that is provided as input along with the original image to a second network that generates a final boundary map. Backpropagation training is accelerated by ZNN, a new implementation of 3D convolutional networks that uses multicore CPU parallelism for speed. Our hybrid 2D-3D architecture could be more generally applicable to other types of anisotropic 3D images, including video, and our recursive framework for any image labeling problem

Convolutional nets for reconstructing neural circuits from brain images acquired by serial section electron microscopy

Neural circuits can be reconstructed from brain images acquired by serial section electron microscopy. Image analysis has been performed by manual labor for half a century, and efforts at automation date back almost as far. Convolutional nets were first applied to neuronal boundary detection a dozen years ago, and have now achieved impressive accuracy on clean images. Robust handling of image defects is a major outstanding challenge. Convolutional nets are also being employed for other tasks in neural circuit reconstruction: finding synapses and identifying synaptic partners, extending or pruning neuronal reconstructions, and aligning serial section images to create a 3D image stack. Computational systems are being engineered to handle petavoxel images of cubic millimeter brain volumes

Geodesic Distance Histogram Feature for Video Segmentation

This paper proposes a geodesic-distance-based feature that encodes global information for improved video segmentation algorithms. The feature is a joint histogram of intensity and geodesic distances, where the geodesic distances are computed as the shortest paths between superpixels via their boundaries. We also incorporate adaptive voting weights and spatial pyramid configurations to include spatial information into the geodesic histogram feature and show that this further improves results. The feature is generic and can be used as part of various algorithms. In experiments, we test the geodesic histogram feature by incorporating it into two existing video segmentation frameworks. This leads to significantly better performance in 3D video segmentation benchmarks on two datasets

Exploring Object Relation in Mean Teacher for Cross-Domain Detection

Rendering synthetic data (e.g., 3D CAD-rendered images) to generate annotations for learning deep models in vision tasks has attracted increasing attention in recent years. However, simply applying the models learnt on synthetic images may lead to high generalization error on real images due to domain shift. To address this issue, recent progress in cross-domain recognition has featured the Mean Teacher, which directly simulates unsupervised domain adaptation as semi-supervised learning. The domain gap is thus naturally bridged with consistency regularization in a teacher-student scheme. In this work, we advance this Mean Teacher paradigm to be applicable for cross-domain detection. Specifically, we present Mean Teacher with Object Relations (MTOR) that novelly remolds Mean Teacher under the backbone of Faster R-CNN by integrating the object relations into the measure of consistency cost between teacher and student modules. Technically, MTOR firstly learns relational graphs that capture similarities between pairs of regions for teacher and student respectively. The whole architecture is then optimized with three consistency regularizations: 1) region-level consistency to align the region-level predictions between teacher and student, 2) inter-graph consistency for matching the graph structures between teacher and student, and 3) intra-graph consistency to enhance the similarity between regions of same class within the graph of student. Extensive experiments are conducted on the transfers across Cityscapes, Foggy Cityscapes, and SIM10k, and superior results are reported when comparing to state-of-the-art approaches. More remarkably, we obtain a new record of single model: 22.8% of mAP on Syn2Real detection dataset.Comment: CVPR 2019; The codes and model of our MTOR are publicly available at: https://github.com/caiqi/mean-teacher-cross-domain-detectio

Efficient Semidefinite Spectral Clustering via Lagrange Duality

We propose an efficient approach to semidefinite spectral clustering (SSC), which addresses the Frobenius normalization with the positive semidefinite (p.s.d.) constraint for spectral clustering. Compared with the original Frobenius norm approximation based algorithm, the proposed algorithm can more accurately find the closest doubly stochastic approximation to the affinity matrix by considering the p.s.d. constraint. In this paper, SSC is formulated as a semidefinite programming (SDP) problem. In order to solve the high computational complexity of SDP, we present a dual algorithm based on the Lagrange dual formalization. Two versions of the proposed algorithm are proffered: one with less memory usage and the other with faster convergence rate. The proposed algorithm has much lower time complexity than that of the standard interior-point based SDP solvers. Experimental results on both UCI data sets and real-world image data sets demonstrate that 1) compared with the state-of-the-art spectral clustering methods, the proposed algorithm achieves better clustering performance; and 2) our algorithm is much more efficient and can solve larger-scale SSC problems than those standard interior-point SDP solvers.Comment: 13 page