We present VoxelMorph, a fast learning-based framework for deformable, pairwise medical image registration. Traditional registration methods optimize an objective function for each pair of images, which can be time-consuming for large datasets or rich deformation models. In contrast to this approach, and building on recent learning-based methods, we formulate registration as a function that maps an input image pair to a deformation field that aligns these images. We parameterize the function via a convolutional neural network (CNN), and optimize the parameters of the neural network on a set of images. Given a new pair of scans, VoxelMorph rapidly computes a deformation field by directly evaluating the function. In this work, we explore two different training strategies. In the first (unsupervised) setting, we train the model to maximize standard image matching objective functions that are based on the image intensities. In the second setting, we leverage auxiliary segmentations available in the training data. We demonstrate that the unsupervised model's accuracy is comparable to state-of-the-art methods, while operating orders of magnitude faster. We also show that VoxelMorph trained with auxiliary data improves registration accuracy at test time, and evaluate the effect of training set size on registration. Our method promises to speed up medical image analysis and processing pipelines, while facilitating novel directions in learning-based registration and its applications. Our code is freely available at http://voxelmorph.csail.mit.edu.

We present a fast learning-based algorithm for deformable, pairwise 3D medical image registration. Current registration methods optimize an objective function independently for each pair of images, which can be timeconsuming for large data. We define registration as a parametric function, and optimize its parameters given a set of images from a collection of interest. Given a new pair of scans, we can quickly compute a registration field by directly evaluating the function using the learned parameters. We model this function using a convolutional neural network (CNN), and use a spatial transform layer to reconstruct one image from another while imposing smoothness constraints on the registration field. The proposed method does not require supervised information such as ground truth registration fields or anatomical landmarks. We demonstrate registration accuracy comparable to stateof-the-art 3D image registration, while operating orders of magnitude faster in practice. Our method promises to significantly speed up medical image analysis and processing pipelines, while facilitating novel directions in learningbased registration and its applications. Our code is available at https://github.com/balakg/voxelmorph.

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We address the computational problem of novel human pose synthesis. Given an image of a person and a desired pose, we produce a depiction of that person in that pose, retaining the appearance of both the person and background. We present a modular generative neural network that synthesizes unseen poses using training pairs of images and poses taken from human action videos. Our network separates a scene into different body part and background layers, moves body parts to new locations and refines their appearances, and composites the new foreground with a hole-filled background. These subtasks, implemented with separate modules, are trained jointly using only a single target image as a supervised label. We use an adversarial discriminator to force our network to synthesize realistic details conditioned on pose. We demonstrate image synthesis results on three action classes: golf, yoga/workouts and tennis, and show that our method produces accurate results within action classes as well as across action classes. Given a sequence of desired poses, we also produce coherent videos of actions.

Image segmentation is an important task in many medical applications. Methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling medical images requires significant expertise and time, and typical hand-tuned approaches for data augmentation fail to capture the complex variations in such images.We present an automated data augmentation method for synthesizing labeled medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transformations from the images, and use the model along with the labeled example to synthesize additional labeled examples. Each transformation is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. We show that training a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for oneshot biomedical image segmentation.