Deep learning for fast and robust medical image reconstruction and analysis

Medical imaging is an indispensable component of modern medical research as well as clinical practice. Nevertheless, imaging techniques such as magnetic resonance imaging (MRI) and computational tomography (CT) are costly and are less accessible to the majority of the world. To make medical devices more accessible, affordable and efficient, it is crucial to re-calibrate our current imaging paradigm for smarter imaging. In particular, as medical imaging techniques have highly structured forms in the way they acquire data, they provide us with an opportunity to optimise the imaging techniques holistically by leveraging data. The central theme of this thesis is to explore different opportunities where we can exploit data and deep learning to improve the way we extract information for better, faster and smarter imaging. This thesis explores three distinct problems. The first problem is the time-consuming nature of dynamic MR data acquisition and reconstruction. We propose deep learning methods for accelerated dynamic MR image reconstruction, resulting in up to 10-fold reduction in imaging time. The second problem is the redundancy in our current imaging pipeline. Traditionally, imaging pipeline treated acquisition, reconstruction and analysis as separate steps. However, we argue that one can approach them holistically and optimise the entire pipeline jointly for a specific target goal. To this end, we propose deep learning approaches for obtaining high fidelity cardiac MR segmentation directly from significantly undersampled data, greatly exceeding the undersampling limit for image reconstruction. The final part of this thesis tackles the problem of interpretability of the deep learning algorithms. We propose attention-models that can implicitly focus on salient regions in an image to improve accuracy for ultrasound scan plane detection and CT segmentation. More crucially, these models can provide explainability, which is a crucial stepping stone for the harmonisation of smart imaging and current clinical practice.Open Acces

Sparse and Redundant Representations for Inverse Problems and Recognition

Sparse and redundant representation of data enables the description of signals as linear combinations of a few atoms from a dictionary. In this dissertation, we study applications of sparse and redundant representations in inverse problems and object recognition. Furthermore, we propose two novel imaging modalities based on the recently introduced theory of Compressed Sensing (CS). This dissertation consists of four major parts. In the first part of the dissertation, we study a new type of deconvolution algorithm that is based on estimating the image from a shearlet decomposition. Shearlets provide a multi-directional and multi-scale decomposition that has been mathematically shown to represent distributed discontinuities such as edges better than traditional wavelets. We develop a deconvolution algorithm that allows for the approximation inversion operator to be controlled on a multi-scale and multi-directional basis. Furthermore, we develop a method for the automatic determination of the threshold values for the noise shrinkage for each scale and direction without explicit knowledge of the noise variance using a generalized cross validation method. In the second part of the dissertation, we study a reconstruction method that recovers highly undersampled images assumed to have a sparse representation in a gradient domain by using partial measurement samples that are collected in the Fourier domain. Our method makes use of a robust generalized Poisson solver that greatly aids in achieving a significantly improved performance over similar proposed methods. We will demonstrate by experiments that this new technique is more flexible to work with either random or restricted sampling scenarios better than its competitors. In the third part of the dissertation, we introduce a novel Synthetic Aperture Radar (SAR) imaging modality which can provide a high resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed transmitted and/or received electromagnetic waveforms. We demonstrate that this new imaging scheme, requires no new hardware components and allows the aperture to be compressed. Also, it presents many new applications and advantages which include strong resistance to countermesasures and interception, imaging much wider swaths and reduced on-board storage requirements. The last part of the dissertation deals with object recognition based on learning dictionaries for simultaneous sparse signal approximations and feature extraction. A dictionary is learned for each object class based on given training examples which minimize the representation error with a sparseness constraint. A novel test image is then projected onto the span of the atoms in each learned dictionary. The residual vectors along with the coefficients are then used for recognition. Applications to illumination robust face recognition and automatic target recognition are presented

Video Compressive Sensing for Dynamic MRI

We present a video compressive sensing framework, termed kt-CSLDS, to accelerate the image acquisition process of dynamic magnetic resonance imaging (MRI). We are inspired by a state-of-the-art model for video compressive sensing that utilizes a linear dynamical system (LDS) to model the motion manifold. Given compressive measurements, the state sequence of an LDS can be first estimated using system identification techniques. We then reconstruct the observation matrix using a joint structured sparsity assumption. In particular, we minimize an objective function with a mixture of wavelet sparsity and joint sparsity within the observation matrix. We derive an efficient convex optimization algorithm through alternating direction method of multipliers (ADMM), and provide a theoretical guarantee for global convergence. We demonstrate the performance of our approach for video compressive sensing, in terms of reconstruction accuracy. We also investigate the impact of various sampling strategies. We apply this framework to accelerate the acquisition process of dynamic MRI and show it achieves the best reconstruction accuracy with the least computational time compared with existing algorithms in the literature.Comment: 30 pages, 9 figure

Region-Based Approach for Single Image Super-Resolution

Single image super-resolution (SR) is a technique that generates a high- resolution image from a single low-resolution image [1,2,10,11]. Single image super- resolution can be generally classified into two groups: example-based and self-similarity based SR algorithms. The performance of the example-based SR algorithm depends on the similarity between testing data and the database. Usually, a large database is needed for better performance in general. This would result in heavy computational cost. The self-similarity based SR algorithm can generate a high-resolution (HR) image with sharper edges and fewer ringing artifacts if there is sufficient recurrence within or across scales of the same image [10, 11], but it is hard to generate HR details for an image region with fine texture. Based on the limitation of each type of SR algorithm, we propose to combine these two types of algorithms. We segment each image into regions based on image content, and choose the appropriate SR algorithm to recover the HR image for each region based on the texture feature. Our experimental results show that our proposed method takes advantage of each SR algorithm and can produce natural looking results with sharp edges, while suppressing ringing artifacts. We compute PSNR to qualitatively evaluate the SR results, and our proposed method outperforms the self-similarity based or example-based SR algorithm with higher PSNR (+0.1dB)

Compressive MRI quantification using convex spatiotemporal priors and deep encoder-decoder networks

We propose a dictionary-matching-free pipeline for multi-parametric quantitative MRI image computing. Our approach has two stages based on compressed sensing reconstruction and deep learned quantitative inference. The reconstruction phase is convex and incorporates efficient spatiotemporal regularisations within an accelerated iterative shrinkage algorithm. This minimises the under-sampling (aliasing) artefacts from aggressively short scan times. The learned quantitative inference phase is purely trained on physical simulations (Bloch equations) that are flexible for producing rich training samples. We propose a deep and compact encoder-decoder network with residual blocks in order to embed Bloch manifold projections through multi-scale piecewise affine approximations, and to replace the non-scalable dictionary-matching baseline. Tested on a number of datasets we demonstrate effectiveness of the proposed scheme for recovering accurate and consistent quantitative information from novel and aggressively subsampled 2D/3D quantitative MRI acquisition protocols

Robust Subspace Learning: Robust PCA, Robust Subspace Tracking, and Robust Subspace Recovery

PCA is one of the most widely used dimension reduction techniques. A related easier problem is "subspace learning" or "subspace estimation". Given relatively clean data, both are easily solved via singular value decomposition (SVD). The problem of subspace learning or PCA in the presence of outliers is called robust subspace learning or robust PCA (RPCA). For long data sequences, if one tries to use a single lower dimensional subspace to represent the data, the required subspace dimension may end up being quite large. For such data, a better model is to assume that it lies in a low-dimensional subspace that can change over time, albeit gradually. The problem of tracking such data (and the subspaces) while being robust to outliers is called robust subspace tracking (RST). This article provides a magazine-style overview of the entire field of robust subspace learning and tracking. In particular solutions for three problems are discussed in detail: RPCA via sparse+low-rank matrix decomposition (S+LR), RST via S+LR, and "robust subspace recovery (RSR)". RSR assumes that an entire data vector is either an outlier or an inlier. The S+LR formulation instead assumes that outliers occur on only a few data vector indices and hence are well modeled as sparse corruptions.Comment: To appear, IEEE Signal Processing Magazine, July 201