MR image reconstruction using deep density priors

Algorithms for Magnetic Resonance (MR) image reconstruction from undersampled measurements exploit prior information to compensate for missing k-space data. Deep learning (DL) provides a powerful framework for extracting such information from existing image datasets, through learning, and then using it for reconstruction. Leveraging this, recent methods employed DL to learn mappings from undersampled to fully sampled images using paired datasets, including undersampled and corresponding fully sampled images, integrating prior knowledge implicitly. In this article, we propose an alternative approach that learns the probability distribution of fully sampled MR images using unsupervised DL, specifically Variational Autoencoders (VAE), and use this as an explicit prior term in reconstruction, completely decoupling the encoding operation from the prior. The resulting reconstruction algorithm enjoys a powerful image prior to compensate for missing k-space data without requiring paired datasets for training nor being prone to associated sensitivities, such as deviations in undersampling patterns used in training and test time or coil settings. We evaluated the proposed method with T1 weighted images from a publicly available dataset, multi-coil complex images acquired from healthy volunteers (N=8) and images with white matter lesions. The proposed algorithm, using the VAE prior, produced visually high quality reconstructions and achieved low RMSE values, outperforming most of the alternative methods on the same dataset. On multi-coil complex data, the algorithm yielded accurate magnitude and phase reconstruction results. In the experiments on images with white matter lesions, the method faithfully reconstructed the lesions. Keywords: Reconstruction, MRI, prior probability, machine learning, deep learning, unsupervised learning, density estimationComment: Published in IEEE TMI. Main text and supplementary material, 19 pages tota

Solving Inverse Problems with Piecewise Linear Estimators: From Gaussian Mixture Models to Structured Sparsity

A general framework for solving image inverse problems is introduced in this paper. The approach is based on Gaussian mixture models, estimated via a computationally efficient MAP-EM algorithm. A dual mathematical interpretation of the proposed framework with structured sparse estimation is described, which shows that the resulting piecewise linear estimate stabilizes the estimation when compared to traditional sparse inverse problem techniques. This interpretation also suggests an effective dictionary motivated initialization for the MAP-EM algorithm. We demonstrate that in a number of image inverse problems, including inpainting, zooming, and deblurring, the same algorithm produces either equal, often significantly better, or very small margin worse results than the best published ones, at a lower computational cost.Comment: 30 page

Automated Visual Fin Identification of Individual Great White Sharks

This paper discusses the automated visual identification of individual great white sharks from dorsal fin imagery. We propose a computer vision photo ID system and report recognition results over a database of thousands of unconstrained fin images. To the best of our knowledge this line of work establishes the first fully automated contour-based visual ID system in the field of animal biometrics. The approach put forward appreciates shark fins as textureless, flexible and partially occluded objects with an individually characteristic shape. In order to recover animal identities from an image we first introduce an open contour stroke model, which extends multi-scale region segmentation to achieve robust fin detection. Secondly, we show that combinatorial, scale-space selective fingerprinting can successfully encode fin individuality. We then measure the species-specific distribution of visual individuality along the fin contour via an embedding into a global `fin space'. Exploiting this domain, we finally propose a non-linear model for individual animal recognition and combine all approaches into a fine-grained multi-instance framework. We provide a system evaluation, compare results to prior work, and report performance and properties in detail.Comment: 17 pages, 16 figures. To be published in IJCV. Article replaced to update first author contact details and to correct a Figure reference on page