Image alignment by mesh warps, such as meshflow, is a fundamental task which has been widely applied in various vision applications(e.g., multi-frame HDR/denoising, video stabilization). Traditional mesh warp methods detect and match image features, where the quality of alignment highly depends on the quality of image features. However, the image features are not robust in occurrence of low-texture and low-light scenes. Deep homography methods, on the other hand, are free from such problem by learning deep features for robust performance. However, a homography is limited to plane motions. In this work, we present a deep meshflow motion model, which takes two images as input and output a sparse motion field with motions located at mesh vertexes. The deep meshflow enjoys the merics of meshflow that can describe nonlinear motions while also shares advantage of deep homography that is robust against challenging textureless scenarios. In particular, a new unsupervised network structure is presented with content-adaptive capability. On one hand, the image content that cannot be aligned under mesh representation are rejected by our learned mask, similar to the RANSAC procedure. On the other hand, we learn multiple mesh resolutions, combining to a non-uniform mesh division. Moreover, a comprehensive dataset is presented, covering various scenes for training and testing. The comparison between both traditional mesh warp methods and deep based methods show the effectiveness of our deep meshflow motion model.

With this work, we release CLAIRE, a distributed-memory implementation of an effective solver for constrained large deformation diffeomorphic image registration problems in three dimensions. We consider an optimal control formulation. We invert for a stationary velocity field that parameterizes the deformation map. Our solver is based on a globalized, preconditioned, inexact reduced space Gauss--Newton--Krylov scheme. We exploit state-of-the-art techniques in scientific computing to develop an effective solver that scales to thousands of distributed memory nodes on high-end clusters. We present the formulation, discuss algorithmic features, describe the software package, and introduce an improved preconditioner for the reduced space Hessian to speed up the convergence of our solver. We test registration performance on synthetic and real data. We demonstrate registration accuracy on several neuroimaging datasets. We compare the performance of our scheme against different flavors of the Demons algorithm for diffeomorphic image registration. We study convergence of our preconditioner and our overall algorithm. We report scalability results on state-of-the-art supercomputing platforms. We demonstrate that we can solve registration problems for clinically relevant data sizes in two to four minutes on a standard compute node with 20 cores, attaining excellent data fidelity. With the present work we achieve a speedup of (on average) 5$\times$ with a peak performance of up to 17$\times$ compared to our former work.

The use of Convolutional neural networks (ConvNets) in medical imaging research has become widespread in recent years. However, a major drawback of these methods is that they require a large number of annotated training images. Data augmentation has been proposed to alleviate this. One data augmentation strategy is to apply random deformation to existing image data, but the deformed images often will not follow exhibit realistic shape or intensity patterns. In this paper, we present a novel, ConvNet based image registration method for creating patient-like digital phantoms from the existing computerized phantoms. Unlike existing learning-based registration techniques, for which the performance predominantly depends on the domain-specific training images, the proposed method is fully unsupervised, meaning that it optimizes an objective function independently of training data for a given image pair. While classical methods registration also do not require training data, they work in lower-dimensional parameter space; the proposed approach operates directly in the high-dimensional parameter space without any training beforehand. In this paper, we show that the resulting deformed phantom competently matches the anatomy model of a real human while providing the "gold-standard" for the anatomies. Combined with simulation programs, the generated phantoms could potentially serve as a data augmentation tool in today's deep learning studies.

Medical image segmentation is a fundamental task in medical image analysis. Despite that deep convolutional neural networks have gained stellar performance in this challenging task, they typically rely on large labeled datasets, which have limited their extension to customized applications. By revisiting the superiority of atlas based segmentation methods, we present a new framework of One-pass aligned Atlas Set for Images Segmentation (OASIS). To address the problem of time-consuming iterative image registration used for atlas warping, the proposed method takes advantage of the power of deep learning to achieve one-pass image registration. In addition, by applying label constraint, OASIS also makes the registration process to be focused on the regions to be segmented for improving the performance of segmentation. Furthermore, instead of using image based similarity for label fusion, which can be distracted by the large background areas, we propose a novel strategy to compute the label similarity based weights for label fusion. Our experimental results on the challenging task of prostate MR image segmentation demonstrate that OASIS is able to significantly increase the segmentation performance compared to other state-of-the-art methods.

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