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Register a new userLearning and Segmenting Dense Voxel Embeddings for 3D Neuron Reconstruction
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Added by
Kisuk Lee
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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We show dense voxel embeddings learned via deep metric learning can be employed to produce a highly accurate segmentation of neurons from 3D electron microscopy images. A metric graph on a set of edges between voxels is constructed from the dense voxel embeddings generated by a convolutional network. Partitioning the metric graph with long-range edges as repulsive constraints yields an initial segmentation with high precision, with substantial accuracy gain for very thin objects. The convolutional embedding net is reused without any modification to agglomerate the systematic splits caused by complex self-contact motifs. Our proposed method achieves state-of-the-art accuracy on the challenging problem of 3D neuron reconstruction from the brain images acquired by serial section electron microscopy. Our alternative, object-centered representation could be more generally useful for other computational tasks in automated neural circuit reconstruction.
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Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a series of deep learning based segmentation methods have been proposed to improve the quality of raw 3D optical image stacks by removing noises and restoring neuronal structures from low-contrast background. Due to the variety of neuron morphology and the lack of large neuron datasets, most of current neuron segmentation models rely on introducing complex and specially-designed submodules to a base architecture with the aim of encoding better feature representations. Though successful, extra burden would be put on computation during inference. Therefore, rather than modifying the base network, we shift our focus to the dataset itself. The encoder-decoder backbone used in most neuron segmentation models attends only intra-volume voxel points to learn structural features of neurons but neglect the shared intrinsic semantic features of voxels belonging to the same category among different volumes, which is also important for expressive representation learning. Hence, to better utilise the scarce dataset, we propose to explicitly exploit such intrinsic features of voxels through a novel voxel-level cross-volume representation learning paradigm on the basis of an encoder-decoder segmentation model. Our method introduces no extra cost during inference. Evaluated on 42 3D neuron images from BigNeuron project, our proposed method is demonstrated to improve the learning ability of the original segmentation model and further enhancing the reconstruction performance.
Conventional methods of 3D object generative modeling learn volumetric predictions using deep networks with 3D convolutional operations, which are direct analogies to classical 2D ones. However, these methods are computationally wasteful in attempt to predict 3D shapes, where information is rich only on the surfaces. In this paper, we propose a novel 3D generative modeling framework to efficiently generate object shapes in the form of dense point clouds. We use 2D convolutional operations to predict the 3D structure from multiple viewpoints and jointly apply geometric reasoning with 2D projection optimization. We introduce the pseudo-renderer, a differentiable module to approximate the true rendering operation, to synthesize novel depth maps for optimization. Experimental results for single-image 3D object reconstruction tasks show that we outperforms state-of-the-art methods in terms of shape similarity and prediction density.
We present Point-Voxel CNN (PVCNN) for efficient, fast 3D deep learning. Previous work processes 3D data using either voxel-based or point-based NN models. However, both approaches are computationally inefficient. The computation cost and memory footprints of the voxel-based models grow cubically with the input resolution, making it memory-prohibitive to scale up the resolution. As for point-based networks, up to 80% of the time is wasted on structuring the sparse data which have rather poor memory locality, not on the actual feature extraction. In this paper, we propose PVCNN that represents the 3D input data in points to reduce the memory consumption, while performing the convolutions in voxels to reduce the irregular, sparse data access and improve the locality. Our PVCNN model is both memory and computation efficient. Evaluated on semantic and part segmentation datasets, it achieves much higher accuracy than the voxel-based baseline with 10x GPU memory reduction; it also outperforms the state-of-the-art point-based models with 7x measured speedup on average. Remarkably, the narrower version of PVCNN achieves 2x speedup over PointNet (an extremely efficient model) on part and scene segmentation benchmarks with much higher accuracy. We validate the general effectiveness of PVCNN on 3D object detection: by replacing the primitives in Frustrum PointNet with PVConv, it outperforms Frustrum PointNet++ by 2.4% mAP on average with 1.5x measured speedup and GPU memory reduction.
This work is to tackle the problem of point cloud semantic segmentation for 3D hybrid scenes under the framework of zero-shot learning. Here by hybrid, we mean the scene consists of both seen-class and unseen-class 3D objects, a more general and realistic setting in application. To our knowledge, this problem has not been explored in the literature. To this end, we propose a network to synthesize point features for various classes of objects by leveraging the semantic features of both seen and unseen object classes, called PFNet. The proposed PFNet employs a GAN architecture to synthesize point features, where the semantic relationship between seen-class and unseen-class features is consolidated by adapting a new semantic regularizer, and the synthesized features are used to train a classifier for predicting the labels of the testing 3D scene points. Besides we also introduce two benchmarks for algorithmic evaluation by re-organizing the public S3DIS and ScanNet datasets under six different data splits. Experimental results on the two benchmarks validate our proposed method, and we hope our introduced two benchmarks and methodology could be of help for more research on this new direction.
We present Voxel Transformer (VoTr), a novel and effective voxel-based Transformer backbone for 3D object detection from point clouds. Conventional 3D convolutional backbones in voxel-based 3D detectors cannot efficiently capture large context information, which is crucial for object recognition and localization, owing to the limited receptive fields. In this paper, we resolve the problem by introducing a Transformer-based architecture that enables long-range relationships between voxels by self-attention. Given the fact that non-empty voxels are naturally sparse but numerous, directly applying standard Transformer on voxels is non-trivial. To this end, we propose the sparse voxel module and the submanifold voxel module, which can operate on the empty and non-empty voxel positions effectively. To further enlarge the attention range while maintaining comparable computational overhead to the convolutional counterparts, we propose two attention mechanisms for multi-head attention in those two modules: Local Attention and Dilated Attention, and we further propose Fast Voxel Query to accelerate the querying process in multi-head attention. VoTr contains a series of sparse and submanifold voxel modules and can be applied in most voxel-based detectors. Our proposed VoTr shows consistent improvement over the convolutional baselines while maintaining computational efficiency on the KITTI dataset and the Waymo Open dataset.
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