Volumetric (3d) images are acquired for many scientific and biomedical purposes using imaging methods such as serial section microscopy, CT scans, and MRI. A frequent step in the analysis and reconstruction of such data is the alignment and registration of images that were acquired in succession along a spatial or temporal dimension. For example, in serial section electron microscopy, individual 2d sections are imaged via electron microscopy and then must be aligned to one another in order to produce a coherent 3d volume. State of the art approaches find image correspondences derived from patch matching and invariant feature detectors, and then solve optimization problems that rigidly or elastically deform series of images into an aligned volume. Here we show how fully convolutional neural networks trained with an adversarial loss function can be used for two tasks: (1) synthesis of missing or damaged image data from adjacent sections, and (2) fine-scale alignment of block-face electron microscopy data. Finally, we show how these two capabilities can be combined in order to produce artificial isotropic volumes from anisotropic image volumes using a super-resolution adversarial alignment and interpolation approach.
Heinrich and colleagues recently introduced neural network architectures that produce impressive results on the task of generating isotropic 3d volumes from anisotropic source data @cite_12 , which is closely related to the experiments we pursue in Section 5. The novel training methods introduce in this work are likely to be complementary to general advances in neural network architectures for 3d image synthesis.
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Recent advances in convolutional neural networks have shown promising results in 3D shape completion. But due to GPU memory limitations, these methods can only produce low-resolution outputs. To inpaint 3D models with semantic plausibility and contextual details, we introduce a hybrid framework that combines a 3D Encoder-Decoder Generative Adversarial Network (3D-ED-GAN) and a Long-term Recurrent Convolutional Network (LRCN). The 3D-ED-GAN is a 3D convolutional neural network trained with a generative adversarial paradigm to fill missing 3D data in low-resolution. LRCN adopts a recurrent neural network architecture to minimize GPU memory usage and incorporates an Encoder-Decoder pair into a Long Short-term Memory Network. By handling the 3D model as a sequence of 2D slices, LRCN transforms a coarse 3D shape into a more complete and higher resolution volume. While 3D-ED-GAN captures global contextual structure of the 3D shape, LRCN localizes the fine-grained details. Experimental results on both real-world and synthetic data show reconstructions from corrupted models result in complete and high-resolution 3D objects. 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. 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. Back-propagation 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. While deep convolutional neural networks (CNN) have been successfully applied for 2D image analysis, it is still challenging to apply them to 3D anisotropic volumes, especially when the within-slice resolution is much higher than the between-slice resolution and when the amount of 3D volumes is relatively small. On one hand, direct learning of CNN with 3D convolution kernels suffers from the lack of data and likely ends up with poor generalization; insufficient GPU memory limits the model size or representational power. On the other hand, applying 2D CNN with generalizable features to 2D slices ignores between-slice information. Coupling 2D network with LSTM to further handle the between-slice information is not optimal due to the difficulty in LSTM learning. To overcome the above challenges, we propose a 3D Anisotropic Hybrid Network (AH-Net) that transfers convolutional features learned from 2D images to 3D anisotropic volumes. Such a transfer inherits the desired strong generalization capability for within-slice information while naturally exploiting between-slice information for more effective modelling. The focal loss is further utilized for more effective end-to-end learning. We experiment with the proposed 3D AH-Net on two different medical image analysis tasks, namely lesion detection from a Digital Breast Tomosynthesis volume, and liver and liver tumor segmentation from a Computed Tomography volume and obtain the state-of-the-art results. The purpose of this study is to determine whether current video datasets have sufficient data for training very deep convolutional neural networks (CNNs) with spatio-temporal three-dimensional (3D) kernels. Recently, the performance levels of 3D CNNs in the field of action recognition have improved significantly. However, to date, conventional research has only explored relatively shallow3Darchitectures. We examine the architectures of various 3D CNNs from relatively shallow to very deep ones on current video datasets. Based on the results of those experiments, the following conclusions could be obtained: (i) ResNet-18 training resulted in significant overfitting for UCF-101, HMDB-51, and ActivityNet but not for Kinetics. (ii) The Kinetics dataset has sufficient data for training of deep 3D CNNs, and enables training of up to 152 ResNets layers, interestingly similar to 2D ResNets on ImageNet. (iii) Kinetics pretrained simple 3D architectures outperforms complex2D architectures, and the pretrained ResNeXt-101 achieved 94.5 and 70.2 on UCF-101 and HMDB-51, respectively. The use of 2D CNNs trained on ImageNet has produced significant progress in various tasks in image. We believe that using deep 3D CNNs together with Kinetics will retrace the successful history of 2D CNNs and ImageNet, and stimulate advances in computer vision for videos. The codes and pretrained models used in this study are publicly available. We introduce a novel neural network architecture for encoding and synthesis of 3D shapes, particularly their structures. Our key insight is that 3D shapes are effectively characterized by their hierarchical organization of parts, which reflects fundamental intra-shape relationships such as adjacency and symmetry. We develop a recursive neural net (RvNN) based autoencoder to map a flat, unlabeled, arbitrary part layout to a compact code. The code effectively captures hierarchical structures of man-made 3D objects of varying structural complexities despite being fixed-dimensional: an associated decoder maps a code back to a full hierarchy. The learned bidirectional mapping is further tuned using an adversarial setup to yield a generative model of plausible structures, from which novel structures can be sampled. Finally, our structure synthesis framework is augmented by a second trained module that produces fine-grained part geometry, conditioned on global and local structural context, leading to a full generative pipeline for 3D shapes. We demonstrate that without supervision, our network learns meaningful structural hierarchies adhering to perceptual grouping principles, produces compact codes which enable applications such as shape classification and partial matching, and supports shape synthesis and interpolation with significant variations in topology and geometry. The purpose of this study is to determine whether current video datasets have sufficient data for training very deep convolutional neural networks (CNNs) with spatio-temporal three-dimensional (3D) kernels. Recently, the performance levels of 3D CNNs in the field of action recognition have improved significantly. However, to date, conventional research has only explored relatively shallow 3D architectures. We examine the architectures of various 3D CNNs from relatively shallow to very deep ones on current video datasets. Based on the results of those experiments, the following conclusions could be obtained: (i) ResNet-18 training resulted in significant overfitting for UCF-101, HMDB-51, and ActivityNet but not for Kinetics. (ii) The Kinetics dataset has sufficient data for training of deep 3D CNNs, and enables training of up to 152 ResNets layers, interestingly similar to 2D ResNets on ImageNet. ResNeXt-101 achieved 78.4 average accuracy on the Kinetics test set. (iii) Kinetics pretrained simple 3D architectures outperforms complex 2D architectures, and the pretrained ResNeXt-101 achieved 94.5 and 70.2 on UCF-101 and HMDB-51, respectively. The use of 2D CNNs trained on ImageNet has produced significant progress in various tasks in image. We believe that using deep 3D CNNs together with Kinetics will retrace the successful history of 2D CNNs and ImageNet, and stimulate advances in computer vision for videos. The codes and pretrained models used in this study are publicly available1. This paper investigates how far a very deep neural network is from attaining close to saturating performance on existing 2D and 3D face alignment datasets. To this end, we make the following 5 contributions: (a) we construct, for the first time, a very strong baseline by combining a state-of-the-art architecture for landmark localization with a state-of-the-art residual block, train it on a very large yet synthetically expanded 2D facial landmark dataset and finally evaluate it on all other 2D facial landmark datasets. (b)We create a guided by 2D landmarks network which converts 2D landmark annotations to 3D and unifies all existing datasets, leading to the creation of LS3D-W, the largest and most challenging 3D facial landmark dataset to date ( 230,000 images). (c) Following that, we train a neural network for 3D face alignment and evaluate it on the newly introduced LS3D-W. (d) We further look into the effect of all “traditional” factors affecting face alignment performance like large pose, initialization and resolution, and introduce a “new” one, namely the size of the network. (e) We show that both 2D and 3D face alignment networks achieve performance of remarkable accuracy which is probably close to saturating the datasets used. Training and testing code as well as the dataset can be downloaded from https: www.adrianbulat.com face-alignment Generative adversarial networks (GANs) are a recent approach to train generative models of data, which have been shown to work particularly well on image data. In the current paper we introduce a new model for texture synthesis based on GAN learning. By extending the input noise distribution space from a single vector to a whole spatial tensor, we create an architecture with properties well suited to the task of texture synthesis, which we call spatial GAN (SGAN). To our knowledge, this is the first successful completely data-driven texture synthesis method based on GANs. Our method has the following features which make it a state of the art algorithm for texture synthesis: high image quality of the generated textures, very high scalability w.r.t. the output texture size, fast real-time forward generation, the ability to fuse multiple diverse source images in complex textures. To illustrate these capabilities we present multiple experiments with different classes of texture images and use cases. We also discuss some limitations of our method with respect to the types of texture images it can synthesize, and compare it to other neural techniques for texture generation. Convolutional Neural Networks (CNNs) have been recently employed to solve problems from both the computer vision and medical image analysis fields. Despite their popularity, most approaches are only able to process 2D images while most medical data used in clinical practice consists of 3D volumes. In this work we propose an approach to 3D image segmentation based on a volumetric, fully convolutional, neural network. Our CNN is trained end-to-end on MRI volumes depicting prostate, and learns to predict segmentation for the whole volume at once. We introduce a novel objective function, that we optimise during training, based on Dice coefficient. In this way we can deal with situations where there is a strong imbalance between the number of foreground and background voxels. To cope with the limited number of annotated volumes available for training, we augment the data applying random non-linear transformations and histogram matching. We show in our experimental evaluation that our approach achieves good performances on challenging test data while requiring only a fraction of the processing time needed by other previous methods. Synthesized medical images have several important applications, e.g., as an intermedium in cross-modality image registration and as supplementary training samples to boost the generalization capability of a classifier. Especially, synthesized computed tomography (CT) data can provide X-ray attenuation map for radiation therapy planning. In this work, we propose a generic cross-modality synthesis approach with the following targets: 1) synthesizing realistic looking 3D images using unpaired training data, 2) ensuring consistent anatomical structures, which could be changed by geometric distortion in cross-modality synthesis and 3) improving volume segmentation by using synthetic data for modalities with limited training samples. We show that these goals can be achieved with an end-to-end 3D convolutional neural network (CNN) composed of mutually-beneficial generators and segmentors for image synthesis and segmentation tasks. The generators are trained with an adversarial loss, a cycle-consistency loss, and also a shape-consistency loss, which is supervised by segmentors, to reduce the geometric distortion. From the segmentation view, the segmentors are boosted by synthetic data from generators in an online manner. Generators and segmentors prompt each other alternatively in an end-to-end training fashion. With extensive experiments on a dataset including a total of 4,496 CT and magnetic resonance imaging (MRI) cardiovascular volumes, we show both tasks are beneficial to each other and coupling these two tasks results in better performance than solving them exclusively. We introduce the concept of unconstrained real-time 3D facial performance capture through explicit semantic segmentation in the RGB input. To ensure robustness, cutting edge supervised learning approaches rely on large training datasets of face images captured in the wild. While impressive tracking quality has been demonstrated for faces that are largely visible, any occlusion due to hair, accessories, or hand-to-face gestures would result in significant visual artifacts and loss of tracking accuracy. The modeling of occlusions has been mostly avoided due to its immense space of appearance variability. To address this curse of high dimensionality, we perform tracking in unconstrained images assuming non-face regions can be fully masked out. Along with recent breakthroughs in deep learning, we demonstrate that pixel-level facial segmentation is possible in real-time by repurposing convolutional neural networks designed originally for general semantic segmentation. We develop an efficient architecture based on a two-stream deconvolution network with complementary characteristics, and introduce carefully designed training samples and data augmentation strategies for improved segmentation accuracy and robustness. We adopt a state-of-the-art regression-based facial tracking framework with segmented face images as training, and demonstrate accurate and uninterrupted facial performance capture in the presence of extreme occlusion and even side views. Furthermore, the resulting segmentation can be directly used to composite partial 3D face models on the input images and enable seamless facial manipulation tasks, such as virtual make-up or face replacement. Recent advances in deep learning, like 3D fully convolutional networks (FCNs), have improved the state-of-the-art in dense semantic segmentation of medical images. However, most network architectures require severely downsampling or cropping the images to meet the memory limitations of today's GPU cards while still considering enough context in the images for accurate segmentation. In this work, we propose a novel approach that utilizes auto-context to perform semantic segmentation at higher resolutions in a multi-scale pyramid of stacked 3D FCNs. We train and validate our models on a dataset of manually annotated abdominal organs and vessels from 377 clinical CT images used in gastric surgery, and achieve promising results with close to 90 Dice score on average. For additional evaluation, we perform separate testing on datasets from different sources and achieve competitive results, illustrating the robustness of the model and approach. We propose an end-to-end deep learning architecture that produces a 3D shape in triangular mesh from a single color image. Limited by the nature of deep neural network, previous methods usually represent a 3D shape in volume or point cloud, and it is non-trivial to convert them to the more ready-to-use mesh model. Unlike the existing methods, our network represents 3D mesh in a graph-based convolutional neural network and produces correct geometry by progressively deforming an ellipsoid, leveraging perceptual features extracted from the input image. We adopt a coarse-to-fine strategy to make the whole deformation procedure stable, and define various of mesh related losses to capture properties of different levels to guarantee visually appealing and physically accurate 3D geometry. Extensive experiments show that our method not only qualitatively produces mesh model with better details, but also achieves higher 3D shape estimation accuracy compared to the state-of-the-art. 3D scene understanding is important for robots to interact with the 3D world in a meaningful way. Most previous works on 3D scene understanding focus on recognizing geometrical or semantic properties of the scene independently. In this work, we introduce Data Associated Recurrent Neural Networks (DA-RNNs), a novel framework for joint 3D scene mapping and semantic labeling. DA-RNNs use a new recurrent neural network architecture for semantic labeling on RGB-D videos. The output of the network is integrated with mapping techniques such as KinectFusion in order to inject semantic information into the reconstructed 3D scene. Experiments conducted on a real world dataset and a synthetic dataset with RGB-D videos demonstrate the ability of our method in semantic 3D scene mapping. We introduce a data-driven approach to complete partial 3D shapes through a combination of volumetric deep neural networks and 3D shape synthesis. From a partially-scanned input shape, our method first infers a low-resolution &#x2013; but complete &#x2013; output. To this end, we introduce a 3D-Encoder-Predictor Network (3D-EPN) which is composed of 3D convolutional layers. The network is trained to predict and fill in missing data, and operates on an implicit surface representation that encodes both known and unknown space. This allows us to predict global structure in unknown areas at high accuracy. We then correlate these intermediary results with 3D geometry from a shape database at test time. In a final pass, we propose a patch-based 3D shape synthesis method that imposes the 3D geometry from these retrieved shapes as constraints on the coarsely-completed mesh. This synthesis process enables us to reconstruct fine-scale detail and generate high-resolution output while respecting the global mesh structure obtained by the 3D-EPN. Although our 3D-EPN outperforms state-of-the-art completion method, the main contribution in our work lies in the combination of a data-driven shape predictor and analytic 3D shape synthesis. In our results, we show extensive evaluations on a newly-introduced shape completion benchmark for both real-world and synthetic data. Inspired by the recent success of methods that employ shape priors to achieve robust 3D reconstructions, we propose a novel recurrent neural network architecture that we call the 3D Recurrent Reconstruction Neural Network (3D-R2N2). The network learns a mapping from images of objects to their underlying 3D shapes from a large collection of synthetic data. Our network takes in one or more images of an object instance from arbitrary viewpoints and outputs a reconstruction of the object in the form of a 3D occupancy grid. Unlike most of the previous works, our network does not require any image annotations or object class labels for training or testing. Our extensive experimental analysis shows that our reconstruction framework i) outperforms the state-of-the-art methods for single view reconstruction, and ii) enables the 3D reconstruction of objects in situations when traditional SFM SLAM methods fail (because of lack of texture and or wide baseline). Inspired by the recent success of methods that employ shape priors to achieve robust 3D reconstructions, we propose a novel recurrent neural network architecture that we call the 3D Recurrent Reconstruction Neural Network (3D-R2N2). The network learns a mapping from images of objects to their underlying 3D shapes from a large collection of synthetic data [13]. Our network takes in one or more images of an object instance from arbitrary viewpoints and outputs a reconstruction of the object in the form of a 3D occupancy grid. Unlike most of the previous works, our network does not require any image annotations or object class labels for training or testing. Our extensive experimental analysis shows that our reconstruction framework (i) outperforms the state-of-the-art methods for single view reconstruction, and (ii) enables the 3D reconstruction of objects in situations when traditional SFM SLAM methods fail (because of lack of texture and or wide baseline). Recent works have shown that exploiting multi-scale representations deeply learned via convolutional neural networks (CNN) is of tremendous importance for accurate contour detection. This paper presents a novel approach for predicting contours which advances the state of the art in two fundamental aspects, i.e. multi-scale feature generation and fusion. Different from previous works directly considering multi-scale feature maps obtained from the inner layers of a primary CNN architecture, we introduce a hierarchical deep model which produces more rich and complementary representations. Furthermore, to refine and robustly fuse the representations learned at different scales, the novel Attention-Gated Conditional Random Fields (AG-CRFs) are proposed. The experiments ran on two publicly available datasets (BSDS500 and NYUDv2) demonstrate the effectiveness of the latent AG-CRF model and of the overall hierarchical framework. Recent advances in camera relocalization use predictions from a regression forest to guide the camera pose optimization procedure. In these methods, each tree associates one pixel with a point in the scene's 3D world coordinate frame. In previous work, these predictions were point estimates and the subsequent camera pose optimization implicitly assumed an isotropic distribution of these estimates. In this paper, we train a regression forest to predict mixtures of anisotropic 3D Gaussians and show how the predicted uncertainties can be taken into account for continuous pose optimization. Experiments show that our proposed method is able to relocalize up to 40 more frames than the state of the art.