Limited capture range, and the requirement to provide high quality initialization for optimization-based 2D 3D image registration methods, can significantly degrade the performance of 3D image reconstruction and motion compensation pipelines. Challenging clinical imaging scenarios, which contain significant subject motion such as fet al in-utero imaging, complicate the 3D image and volume reconstruction process. In this paper we present a learning based image registration method capable of predicting 3D rigid transformations of arbitrarily oriented 2D image slices, with respect to a learned canonical atlas co-ordinate system. Only image slice intensity information is used to perform registration and canonical alignment, no spatial transform initialization is required. To find image transformations we utilize a Convolutional Neural Network (CNN) architecture to learn the regression function capable of mapping 2D image slices to a 3D canonical atlas space. We extensively evaluate the effectiveness of our approach quantitatively on simulated Magnetic Resonance Imaging (MRI), fet al brain imagery with synthetic motion and further demonstrate qualitative results on real fet al MRI data where our method is integrated into a full reconstruction and motion compensation pipeline. Our learning based registration achieves an average spatial prediction error of 7 mm on simulated data and produces qualitatively improved reconstructions for heavily moving fetuses with gestational ages of approximately 20 weeks. Our model provides a general and computationally efficient solution to the 2D 3D registration initialization problem and is suitable for real-time scenarios.
Similarly, @cite_25 use CNNs to perform 2D to 3D registration between a target 2D slice and a source 3D reference volume. Instead of regressing on transformation residuals, the authors regress to a scalar that estimates the dissimilarity between two image patches, and leverage the error from back-propagation to update the transformation parameters. To this end, all operations can be efficiently computed on a GPU for high throughput.
@cite_25
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The 2D-3D registration is a cornerstone to align the inter-treatment X-ray images with the available volumetric images. In this paper, we propose a CNN regression based non-rigid 2D-3D registration method. An iterative refinement scheme is introduced to update the reference volumetric image and the digitally-reconstructed-radiograph (DRR) for convergence to the target X-ray image. The CNN-based regressor represents the mapping between an image pair and the in-between deformation parameters. In particular, the short residual connections in the convolution blocks and long jump connections for the multi-scale feature map fusion facilitate the information propagation in training the regressor. The proposed method has been applied to 2D-3D registration of synthetic X-ray and clinically-captured CBCT images. Experimental results demonstrate the proposed method realizes an accurate and efficient 2D-3D registration of craniofacial images. This paper aims to solve a fundamental problem in intensity-based 2D 3D registration, which concerns the limited capture range and need for very good initialization of state-of-the-art image registration methods. We propose a regression approach that learns to predict rotations and translations of arbitrary 2D image slices from 3D volumes, with respect to a learned canonical atlas co-ordinate system. To this end, we utilize Convolutional Neural Networks (CNNs) to learn the highly complex regression function that maps 2D image slices into their correct position and orientation in 3D space. Our approach is attractive in challenging imaging scenarios, where significant subject motion complicates reconstruction performance of 3D volumes from 2D slice data. We extensively evaluate the effectiveness of our approach quantitatively on simulated MRI brain data with extreme random motion. We further demonstrate qualitative results on fet al MRI where our method is integrated into a full reconstruction and motion compensation pipeline. With our CNN regression approach we obtain an average prediction error of 7 mm on simulated data, and convincing reconstruction quality of images of very young fetuses where previous methods fail. We further discuss applications to Computed Tomography (CT) and X-Ray projections. Our approach is a general solution to the 2D 3D initialization problem. It is computationally efficient, with prediction times per slice of a few milliseconds, making it suitable for real-time scenarios. 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. This paper presents a novel and efficient algorithm for the 3D range to 2D image registration problem in urban scene settings. Our input is a set of unregistered 3D range scans and a set of unregistered and uncalibrated 2D images of the scene. The 3D range scans and 2D images capture real scenes in extremely high detail. A new automated algorithm calibrates each 2D image and computes an optimized transformation between the 2D images and 3D range scans. This transformation is based on a match of 3D with 2D features that maximizes an overlap criterion. Our algorithm attacks the hard 3D range to 2D image registration problem in a systematic, efficient, and automatic way. Images captured by a high-resolution 2D camera, that moves and adjusts freely, are mapped on a centimeter-accurate 3D model of the scene providing photorealistic renderings of high quality. We present results from experiments in three different urban settings. Liver cancer is one of the leading causes of cancer death. To assist doctors in hepatocellular carcinoma diagnosis and treatment planning, an accurate and automatic liver and tumor segmentation method is highly demanded in the clinical practice. Recently, fully convolutional neural networks (FCNs), including 2D and 3D FCNs, serve as the back-bone in many volumetric image segmentation. However, 2D convolutions can not fully leverage the spatial information along the third dimension while 3D convolutions suffer from high computational cost and GPU memory consumption. To address these issues, we propose a novel hybrid densely connected UNet (H-DenseUNet), which consists of a 2D DenseUNet for efficiently extracting intra-slice features and a 3D counterpart for hierarchically aggregating volumetric contexts under the spirit of the auto-context algorithm for liver and tumor segmentation. We propose a new training strategy by formulating the learning process of H-DenseUNet in an end-to-end manner, where the intra-slice representations and inter-slice features can be jointly optimized through a hybrid feature fusion (HFF) layer. We extensively evaluated our method on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge. Our method outperformed other state-of-the-arts on the segmentation results of tumors and achieved very competitive performance for liver segmentation even with a single model. Capturing an enclosing volume of moving subjects and organs using fast individual image slice acquisition has shown promise in dealing with motion artefacts. Motion between slice acquisitions results in spatial inconsistencies that can be resolved by slice-to-volume reconstruction (SVR) methods to provide high quality 3D image data. Existing algorithms are, however, typically very slow, specialised to specific applications and rely on approximations, which impedes their potential clinical use. In this paper, we present a fast multi-GPU accelerated framework for slice-to-volume reconstruction. It is based on optimised 2D 3D registration, super-resolution with automatic outlier rejection and an additional (optional) intensity bias correction. We introduce a novel and fully automatic procedure for selecting the image stack with least motion to serve as an initial registration target. We evaluate the proposed method using artificial motion corrupted phantom data as well as clinical data, including tracked freehand ultrasound of the liver and fet al Magnetic Resonance Imaging. We achieve speed-up factors greater than 30 compared to a single CPU system and greater than 10 compared to currently available state-of-the-art multi-core CPU methods. We ensure high reconstruction accuracy by exact computation of the point-spread function for every input data point, which has not previously been possible due to computational limitations. Our framework and its implementation is scalable for available computational infrastructures and tests show a speed-up factor of 1.70 for each additional GPU. This paves the way for the online application of image based reconstruction methods during clinical examinations. The source code for the proposed approach is publicly available. 3D cardiac MR imaging enables accurate analysis of cardiac morphology and physiology. However, due to the requirements for long acquisition and breath-hold, the clinical routine is still dominated by multi-slice 2D imaging, which hamper the visualization of anatomy and quantitative measurements as relatively thick slices are acquired. As a solution, we propose a novel image super-resolution (SR) approach that is based on a residual convolutional neural network (CNN) model. It reconstructs high resolution 3D volumes from 2D image stacks for more accurate image analysis. The proposed model allows the use of multiple input data acquired from different viewing planes for improved performance. Experimental results on 1233 cardiac short and long-axis MR image stacks show that the CNN model outperforms state-of-the-art SR methods in terms of image quality while being computationally efficient. Also, we show that image segmentation and motion tracking benefits more from SR-CNN when it is used as an initial upscaling method than conventional interpolation methods for the subsequent analysis. We propose a simple, yet effective approach for real-time hand pose estimation from single depth images using three-dimensional Convolutional Neural Networks (3D CNNs). Image based features extracted by 2D CNNs are not directly suitable for 3D hand pose estimation due to the lack of 3D spatial information. Our proposed 3D CNN taking a 3D volumetric representation of the hand depth image as input can capture the 3D spatial structure of the input and accurately regress full 3D hand pose in a single pass. In order to make the 3D CNN robust to variations in hand sizes and global orientations, we perform 3D data augmentation on the training data. Experiments show that our proposed 3D CNN based approach outperforms state-of-the-art methods on two challenging hand pose datasets, and is very efficient as our implementation runs at over 215 fps on a standard computer with a single GPU. To enable real-time, person-independent 3D registration from 2D video, we developed a 3D cascade regression approach in which facial landmarks remain invariant across pose over a range of approximately 60. From a single 2D image of a person's face, a dense 3D shape is registered in real time for each frame. The algorithm utilizes a fast cascade regression framework trained on high-resolution 3D face-scans of posed and spontaneous emotion expression. The algorithm first estimates the location of a dense set of landmarks and their visibility, then reconstructs face shapes by fitting a part-based 3D model. Because no assumptions are required about illumination or surface properties, the method can be applied to a wide range of imaging conditions that include 2D video and uncalibrated multi-view video. The method has been validated in a battery of experiments that evaluate its precision of 3D reconstruction, extension to multi-view reconstruction, temporal integration for videos and 3D head-pose estimation. Experimental findings strongly support the validity of real-time, 3D registration and reconstruction from 2D video. The software is available online at http: zface.org. Display Omitted 3D cascade regression approach is proposed in which facial landmarks remain invariant.From a single 2D image of a person's face, a dense 3D shape is registered in real time for each frame.Multi-view reconstruction and temporal integration for videos are presented.Method is robust for 3D head-pose estimation under various conditions. Three-dimensional convolutional neural networks (3D CNNs) are used efficiently in many computer vision applications. Most previous work in this area has concentrated only on designing and optimizing accelerators for 2D CNN, with few attempts made to accelerate 3D CNN on FPGA. We find accelerating 3D CNNs on FPGA to be challenge due to their high computational complexity and storage demands. More importantly, although the computation patterns of 2D and 3D CNNs are analogous, the conventional approaches adopted for accelerating 2D CNNs may be unfit for 3D CNN acceleration. In this paper, in order to accelerate 2D and 3D CNNs using a uniform framework, we propose a uniform template-based architecture that uses templates based on the Winograd algorithm to ensure fast development of 2D and 3D CNN accelerators. Furthermore, we also develop a uniform analytical model to facilitate efficient design space explorations of 2D and 3D CNN accelerators based on our architecture. Finally, we demonstrate the effectiveness of the template-based architecture by implementing accelerators for real-life 2D and 3D CNNs (VGG16 and C3D) on multiple FPGA platforms. On S2C VUS440, we achieve up to 1.13 TOPS and 1.11 TOPS under low resource utilization for VGG16 and C3D, respectively. End-to-end comparisons with CPU and GPU solutions demonstrate that our implementation of C3D achieves gains of up to 13x and 60x in performance and energy relative to a CPU solution, and a 6.4x energy efficiency gain over a GPU solution. Accurate segmentation of the heart is an important step towards evaluating cardiac function. In this paper, we present a fully automated framework for segmentation of the left (LV) and right (RV) ventricular cavities and the myocardium (Myo) on short-axis cardiac MR images. We investigate various 2D and 3D convolutional neural network architectures for this task. We investigate the suitability of various state-of-the art 2D and 3D convolutional neural network architectures, as well as slight modifications thereof, for this task. Experiments were performed on the ACDC 2017 challenge training dataset comprising cardiac MR images of 100 patients, where manual reference segmentations were made available for end-diastolic (ED) and end-systolic (ES) frames. We find that processing the images in a slice-by-slice fashion using 2D networks is beneficial due to a relatively large slice thickness. However, the exact network architecture only plays a minor role. We report mean Dice coefficients of @math (LV), @math (RV), and @math (Myo), respectively with an average evaluation time of 1.1 seconds per volume on a modern GPU. In this work we address the problem of estimating the 3D human pose from a single RGB image, which is a challenging problem since different 3D poses may have similar 2D projections. Following the success of regression forests for 3D pose estimation from depth data or 2D pose estimation from RGB images, we extend regression forests to infer missing depth data of image features and 3D pose simultaneously. Since we do not observe depth for inference or training directly, we hypothesize the depth of the features by sweeping with a plane through the 3D volume of potential joint locations. The regression forests are then combined with a pictorial structure framework, which is extended to 3D. The approach is evaluated on two challenging benchmarks where stateof-the-art performance is achieved. To enable real-time, person-independent 3D registration from 2D video, we developed a 3D cascade regression approach in which facial landmarks remain invariant across pose over a range of approximately 60 degrees. From a single 2D image of a person's face, a dense 3D shape is registered in real time for each frame. The algorithm utilizes a fast cascade regression framework trained on high-resolution 3D face-scans of posed and spontaneous emotion expression. The algorithm first estimates the location of a dense set of markers and their visibility, then reconstructs face shapes by fitting a part-based 3D model. Because no assumptions are required about illumination or surface properties, the method can be applied to a wide range of imaging conditions that include 2D video and uncalibrated multi-view video. The method has been validated in a battery of experiments that evaluate its precision of 3D reconstruction and extension to multi-view reconstruction. Experimental findings strongly support the validity of real-time, 3D registration and reconstruction from 2D video. The software is available online at http: zface.org. We extends the previous 2D cascaded object pose regression work [9] in two aspects so that it works better for 3D articulated objects. Our first contribution is 3D pose-indexed features that generalize the previous 2D parameterized features and achieve better invariance to 3D transformations. Our second contribution is a principled hierarchical regression that is adapted to the articulated object structure. It is therefore more accurate and faster. Comprehensive experiments verify the state-of-the-art accuracy and efficiency of the proposed approach on the challenging 3D hand pose estimation problem, on a public dataset and our new dataset. In this paper, we present a Convolutional Neural Network (CNN) regression approach to address the two major limitations of existing intensity-based 2-D 3-D registration technology: 1) slow computation and 2) small capture range. Different from optimization-based methods, which iteratively optimize the transformation parameters over a scalar-valued metric function representing the quality of the registration, the proposed method exploits the information embedded in the appearances of the digitally reconstructed radiograph and X-ray images, and employs CNN regressors to directly estimate the transformation parameters. An automatic feature extraction step is introduced to calculate 3-D pose-indexed features that are sensitive to the variables to be regressed while robust to other factors. The CNN regressors are then trained for local zones and applied in a hierarchical manner to break down the complex regression task into multiple simpler sub-tasks that can be learned separately. Weight sharing is furthermore employed in the CNN regression model to reduce the memory footprint. The proposed approach has been quantitatively evaluated on 3 potential clinical applications, demonstrating its significant advantage in providing highly accurate real-time 2-D 3-D registration with a significantly enlarged capture range when compared to intensity-based methods. In this paper, we present a novel method for real-time 3D hand pose estimation from single depth images using 3D Convolutional Neural Networks (CNNs). Image-based features extracted by 2D CNNs are not directly suitable for 3D hand pose estimation due to the lack of 3D spatial information. Our proposed 3D CNN-based method, taking a 3D volumetric representation of the hand depth image as input and extracting 3D features from the volumetric input, can capture the 3D spatial structure of the hand and accurately regress full 3D hand pose in a single pass. In order to make the 3D CNN robust to variations in hand sizes and global orientations, we perform 3D data augmentation on the training data. To further improve the estimation accuracy, we propose applying the 3D deep network architectures and leveraging the complete hand surface as intermediate supervision for learning 3D hand pose from depth images. Extensive experiments on three challenging datasets demonstrate that our proposed approach outperforms baselines and state-of-the-art methods. A cross-dataset experiment also shows that our method has good generalization ability. Furthermore, our method is fast as our implementation runs at over 91 frames per second on a standard computer with a single GPU. Most of the existing deep learning-based methods for 3D hand and human pose estimation from a single depth map are based on a common framework that takes a 2D depth map and directly regresses the 3D coordinates of keypoints, such as hand or human body joints, via 2D convolutional neural networks (CNNs). The first weakness of this approach is the presence of perspective distortion in the 2D depth map. While the depth map is intrinsically 3D data, many previous methods treat depth maps as 2D images that can distort the shape of the actual object through projection from 3D to 2D space. This compels the network to perform perspective distortion-invariant estimation. The second weakness of the conventional approach is that directly regressing 3D coordinates from a 2D image is a highly nonlinear mapping, which causes difficulty in the learning procedure. To overcome these weaknesses, we firstly cast the 3D hand and human pose estimation problem from a single depth map into a voxel-to-voxel prediction that uses a 3D voxelized grid and estimates the per-voxel likelihood for each keypoint. We design our model as a 3D CNN that provides accurate estimates while running in real-time. Our system outperforms previous methods in almost all publicly available 3D hand and human pose estimation datasets and placed first in the HANDS 2017 frame-based 3D hand pose estimation challenge. The code is available in1. Convolutional Neural Network (CNN) has shown promising results for 3D hand pose estimation in depth images. Different from existing CNN-based hand pose estimation methods that take either 2D images or 3D volumes as the input, our proposed Hand PointNet directly processes the 3D point cloud that models the visible surface of the hand for pose regression. Taking the normalized point cloud as the input, our proposed hand pose regression network is able to capture complex hand structures and accurately regress a low dimensional representation of the 3D hand pose. In order to further improve the accuracy of fingertips, we design a fingertip refinement network that directly takes the neighboring points of the estimated fingertip location as input to refine the fingertip location. Experiments on three challenging hand pose datasets show that our proposed method outperforms state-of-the-art methods. We present a simple and effective method for 3D hand pose estimation from a single depth frame. As opposed to previous state-of-the-art methods based on holistic 3D regression, our method works on dense pixel-wise estimation. This is achieved by careful design choices in pose parameterization, which leverages both 2D and 3D properties of depth map. Specifically, we decompose the pose parameters into a set of per-pixel estimations, i.e., 2D heat maps, 3D heat maps and unit 3D directional vector fields. The 2D 3D joint heat maps and 3D joint offsets are estimated via multitask network cascades, which is trained end-to-end. The pixel-wise estimations can be directly translated into a vote casting scheme. A variant of mean shift is then used to aggregate local votes while enforcing consensus between the the estimated 3D pose and the pixel-wise 2D and 3D estimations by design. Our method is efficient and highly accurate. On MSRA and NYU hand dataset, our method outperforms all previous state-of-the-art approaches by a large margin. On the ICVL hand dataset, our method achieves similar accuracy compared to the nearly saturated result obtained by [5] and outperforms various other proposed methods. Code is available online1. We propose a novel approach to 3D human pose estimation from a single depth map. Recently, convolutional neural network (CNN) has become a powerful paradigm in computer vision. Many of computer vision tasks have benefited from CNNs, however, the conventional approach to directly regress 3D body joint locations from an image does not yield a noticeably improved performance. In contrast, we formulate the problem as estimating per-voxel likelihood of key body joints from a 3D occupancy grid. We argue that learning a mapping from volumetric input to volumetric output with 3D convolution consistently improves the accuracy when compared to learning a regression from depth map to 3D joint coordinates. We propose a two-stage approach to reduce the computational overhead caused by volumetric representation and 3D convolution: Holistic 2D prediction and Local 3D prediction. In the first stage, Planimetric Network (P-Net) estimates per-pixel likelihood for each body joint in the holistic 2D space. In the second stage, Volumetric Network (V-Net) estimates the per-voxel likelihood of each body joints in the local 3D space around the 2D estimations of the first stage, effectively reducing the computational cost. Our model outperforms existing methods by a large margin in publicly available datasets.