A Theoretically Guaranteed Deep Optimization Framework for Robust Compressive Sensing MRI

Magnetic Resonance Imaging (MRI) is one of the most dynamic and safe imaging techniques available for clinical applications. However, the rather slow speed of MRI acquisitions limits the patient throughput and potential indi cations. Compressive Sensing (CS) has proven to be an efficient technique for accelerating MRI acquisition. The most widely used CS-MRI model, founded on the premise of reconstructing an image from an incompletely filled k-space, leads to an ill-posed inverse problem. In the past years, lots of efforts have been made to efficiently optimize the CS-MRI model. Inspired by deep learning techniques, some preliminary works have tried to incorporate deep architectures into CS-MRI process. Unfortunately, the convergence issues (due to the experience-based networks) and the robustness (i.e., lack real-world noise modeling) of these deeply trained optimization methods are still missing. In this work, we develop a new paradigm to integrate designed numerical solvers and the data-driven architectures for CS-MRI. By introducing an optimal condition checking mechanism, we can successfully prove the convergence of our established deep CS-MRI optimization scheme. Furthermore, we explicitly formulate the Rician noise distributions within our framework and obtain an extended CS-MRI network to handle the real-world nosies in the MRI process. Extensive experimental results verify that the proposed paradigm outperforms the existing state-of-the-art techniques both in reconstruction accuracy and efficiency as well as robustness to noises in real scene

Adaptive Nonlocal Signal Restoration and Enhancement Techniques for High-Dimensional Data

The large number of practical applications involving digital images has motivated a significant interest towards restoration solutions that improve the visual quality of the data under the presence of various acquisition and compression artifacts. Digital images are the results of an acquisition process based on the measurement of a physical quantity of interest incident upon an imaging sensor over a specified period of time. The quantity of interest depends on the targeted imaging application. Common imaging sensors measure the number of photons impinging over a dense grid of photodetectors in order to produce an image similar to what is perceived by the human visual system. Different applications focus on the part of the electromagnetic spectrum not visible by the human visual system, and thus require different sensing technologies to form the image. In all cases, even with the advance of technology, raw data is invariably affected by a variety of inherent and external disturbing factors, such as the stochastic nature of the measurement processes or challenging sensing conditions, which may cause, e.g., noise, blur, geometrical distortion and color aberration. In this thesis we introduce two filtering frameworks for video and volumetric data restoration based on the BM3D grouping and collaborative filtering paradigm. In its general form, the BM3D paradigm leverages the correlation present within a nonlocal emph{group} composed of mutually similar basic filtering elements, e.g., patches, to attain an enhanced sparse representation of the group in a suitable transform domain where the energy of the meaningful part of the signal can be thus separated from that of the noise through coefficient shrinkage. We argue that the success of this approach largely depends on the form of the used basic filtering elements, which in turn define the subsequent spectral representation of the nonlocal group. Thus, the main contribution of this thesis consists in tailoring specific basic filtering elements to the the inherent characteristics of the processed data at hand. Specifically, we embed the local spatial correlation present in volumetric data through 3-D cubes, and the local spatial and temporal correlation present in videos through 3-D spatiotemporal volumes, i.e. sequences of 2-D blocks following a motion trajectory. The foundational aspect of this work is the analysis of the particular spectral representation of these elements. Specifically, our frameworks stack mutually similar 3-D patches along an additional fourth dimension, thus forming a 4-D data structure. By doing so, an effective group spectral description can be formed, as the phenomena acting along different dimensions in the data can be precisely localized along different spectral hyperplanes, and thus different filtering shrinkage strategies can be applied to different spectral coefficients to achieve the desired filtering results. This constitutes a decisive difference with the shrinkage traditionally employed in BM3D-algorithms, where different hyperplanes of the group spectrum are shrunk subject to the same degradation model. Different image processing problems rely on different observation models and typically require specific algorithms to filter the corrupted data. As a consequent contribution of this thesis, we show that our high-dimensional filtering model allows to target heterogeneous noise models, e.g., characterized by spatial and temporal correlation, signal-dependent distributions, spatially varying statistics, and non-white power spectral densities, without essential modifications to the algorithm structure. As a result, we develop state-of-the-art methods for a variety of fundamental image processing problems, such as denoising, deblocking, enhancement, deflickering, and reconstruction, which also find practical applications in consumer, medical, and thermal imaging

Models and Methods for Estimation and Filtering of Signal-Dependent Noise in Imaging

The work presented in this thesis focuses on Image Processing, that is the branch of Signal Processing that centers its interest on images, sequences of images, and videos. It has various applications: imaging for traditional cameras, medical imaging, e.g., X-ray and magnetic resonance imaging (MRI), infrared imaging (thermography), e.g., for security purposes, astronomical imaging for space exploration, three-dimensional (video+depth) signal processing, and many more.This thesis covers a small but relevant slice that is transversal to this vast pool of applications: noise estimation and denoising. To appreciate the relevance of this thesis it is essential to understand why noise is such an important part of Image Processing. Every acquisition device, and every measurement is subject to interferences that causes random fluctuations in the acquired signals. If not taken into consideration with a suitable mathematical approach, these fluctuations might invalidate any use of the acquired signal. Consider, for example, an MRI used to detect a possible condition; if not suitably processed and filtered, the image could lead to a wrong diagnosis. Therefore, before any acquired image is sent to an end-user (machine or human), it undergoes several processing steps. Noise estimation and denoising are usually parts of these fundamental steps.Some sources of noise can be removed by suitably modeling the acquisition process of the camera, and developing hardware based on that model. Other sources of noise are instead inevitable: high/low light conditions of the acquired scene, hardware imperfections, temperature of the device, etc. To remove noise from an image, the noise characteristics have to be first estimated. The branch of image processing that fulfills this role is called noise estimation. Then, it is possible to remove the noise artifacts from the acquired image. This process is referred to as denoising.For practical reasons, it is convenient to model noise as random variables. In this way, we assume that the noise fluctuations take values whose probabilities follow specific distributions characterized only by few parameters. These are the parameters that we estimate. We focus our attention on noise modeled by Gaussian distributions, Poisson distributions, or a combination of these. These distributions are adopted for modeling noise affecting images from digital cameras, microscopes, telescopes, radiography systems, thermal cameras, depth-sensing cameras, etc. The parameters that define a Gaussian distribution are its mean and its variance, while a Poisson distribution depends only on its mean, since its variance is equal to the mean (signal-dependent variance). Consequently, the parameters of a Poisson-Gaussian distribution describe the relation between the intensity of the noise-free signal and the variance of the noise affecting it. Degradation models of this kind are referred to as signal-dependent noise.Estimation of signal-dependent noise is commonly performed by processing, individually, groups of pixels with equal intensity in order to sample the aforementioned relation between signal mean and noise variance. Such sampling is often subject to outliers; we propose a robust estimation model where the noise parameters are estimated optimizing a likelihood function that models the local variance estimates from each group of pixels as mixtures of Gaussian and Cauchy distributions. The proposed model is general and applicable to a variety of signal-dependent noise models, including also possible clipping of the data. We also show that, under certain hypotheses, the relation between signal mean and noise variance can also be effectively sampled from groups of pixels of possibly different intensities.Then, we propose a spatially adaptive transform to improve the denoising performance of a specific class of filters, namely nonlocal transformdomain collaborative filters. In particular, the proposed transform exploits the spatial coordinates of nonlocal similar features from an image to better decorrelate the data, and consequently to improve the filtering. Unlike non-adaptive transforms, the proposed spatially adaptive transform is capable of representing spatially smooth coarse-scale variations in the similar features of the image. Further, based on the same paradigm, we propose a method that adaptively enhances the local image features depending on their orientation with respect to the relative coordinates of other similar features at other locations in the image.An established approach for removing Poisson noise utilizes so-called variance-stabilizing transformations (VST) to make the noise variance independent of the mean of the signal, hence enabling denoising by a standard denoiser for additive Gaussian noise. Within this framework, we propose an iterative method where at each iteration the previous estimate is summed back to the noisy image in order to improve the stabilizing performance of the transformation, and consequently to improve the denoising results. The proposed iterative procedure allows to circumvent the typical drawbacks that VSTs experience at very low intensities, and thus allows us to apply the standard denoiser effectively even at extremely low counts.The developed methods achieve state-of-the-art results in their respective field of application

A Better Looking Brain: Image Pre-Processing Approaches for fMRI Data

Researchers in the field of functional neuroimaging have faced a long standing problem in pre-processing low spatial resolution data without losing meaningful details within. Commonly, the brain function is recorded by a technique known as echo-planar imaging that represents the measure of blood flow (BOLD signal) through a particular location in the brain as an array of intensity values changing over time. This approach to record a movie of blood flow in the brain is known as fMRI. The neural activity is then studied from the temporal correlation patterns existing within the fMRI time series. However, the resulting images are noisy and contain low spatial detail, thus making it imperative to pre-process them appropriately to derive meaningful activation patterns. Two of the several standard preprocessing steps employed just before the analysis stage are denoising and normalization. Fundamentally, it is difficult to perfectly remove noise from an image without making assumptions about signal and noise distributions. A convenient and commonly used alternative is to smooth the image with a Gaussian filter, but this method suffers from various obvious drawbacks, primarily loss of spatial detail. A greater challenge arises when we attempt to derive average activation patterns from fMRI images acquired from a group of individuals. The brain of one individual differs from others in a structural sense as well as in a functional sense. Commonly, the inter-individual differences in anatomical structures are compensated for by co-registering each subject\u27s data to a common normalization space, known as spatial normalization. However, there are no existing methods to compensate for the differences in functional organization of the brain. This work presents first steps towards data-driven robust algorithms for fMRI image denoising and multi-subject image normalization by utilizing inherent information within fMRI data. In addition, a new validation approach based on spatial shape of the activation regions is presented to quantify the effects of preprocessing and also as a tool to record the differences in activation patterns between individual subjects or within two groups such as healthy controls and patients with mental illness. Qualititative and quantitative results of the proposed framework compare favorably against existing and widely used model-driven approaches such as Gaussian smoothing and structure-based spatial normalization. This work is intended to provide neuroscience researchers tools to derive more meaningful activation patterns to accurately identify imaging biomarkers for various neurodevelopmental diseases and also maximize the specificity of a diagnosis

Compressed Sensing in Resource-Constrained Environments: From Sensing Mechanism Design to Recovery Algorithms

Compressed Sensing (CS) is an emerging field based on the revelation that a small collection of linear projections of a sparse signal contains enough information for reconstruction. It is promising that CS can be utilized in environments where the signal acquisition process is extremely difficult or costly, e.g., a resource-constrained environment like the smartphone platform, or a band-limited environment like visual sensor network (VSNs). There are several challenges to perform sensing due to the characteristic of these platforms, including, for example, needing active user involvement, computational and storage limitations and lower transmission capabilities. This dissertation focuses on the study of CS in resource-constrained environments. First, we try to solve the problem on how to design sensing mechanisms that could better adapt to the resource-limited smartphone platform. We propose the compressed phone sensing (CPS) framework where two challenging issues are studied, the energy drainage issue due to continuous sensing which may impede the normal functionality of the smartphones and the requirement of active user inputs for data collection that may place a high burden on the user. Second, we propose a CS reconstruction algorithm to be used in VSNs for recovery of frames/images. An efficient algorithm, NonLocal Douglas-Rachford (NLDR), is developed. NLDR takes advantage of self-similarity in images using nonlocal means (NL) filtering. We further formulate the nonlocal estimation as the low-rank matrix approximation problem and solve the constrained optimization problem using Douglas-Rachford splitting method. Third, we extend the NLDR algorithm to surveillance video processing in VSNs and propose recursive Low-rank and Sparse estimation through Douglas-Rachford splitting (rLSDR) method for recovery of the video frame into a low-rank background component and sparse component that corresponds to the moving object. The spatial and temporal low-rank features of the video frame, e.g., the nonlocal similar patches within the single video frame and the low-rank background component residing in multiple frames, are successfully exploited

Robust density modelling using the student's t-distribution for human action recognition

The extraction of human features from videos is often inaccurate and prone to outliers. Such outliers can severely affect density modelling when the Gaussian distribution is used as the model since it is highly sensitive to outliers. The Gaussian distribution is also often used as base component of graphical models for recognising human actions in the videos (hidden Markov model and others) and the presence of outliers can significantly affect the recognition accuracy. In contrast, the Student's t-distribution is more robust to outliers and can be exploited to improve the recognition rate in the presence of abnormal data. In this paper, we present an HMM which uses mixtures of t-distributions as observation probabilities and show how experiments over two well-known datasets (Weizmann, MuHAVi) reported a remarkable improvement in classification accuracy. © 2011 IEEE

Tight-frame-like Sparse Recovery Using Non-tight Sensing Matrices

The choice of the sensing matrix is crucial in compressed sensing (CS). Gaussian sensing matrices possess the desirable restricted isometry property (RIP), which is crucial for providing performance guarantees on sparse recovery. Further, sensing matrices that constitute a Parseval tight frame result in minimum mean-squared-error (MSE) reconstruction given oracle knowledge of the support of the sparse vector. However, if the sensing matrix is not tight, could one achieve the reconstruction performance assured by a tight frame by suitably designing the reconstruction strategy? This is the key question that we address in this paper. We develop a novel formulation that relies on a generalized l2-norm-based data-fidelity loss that tightens the sensing matrix, along with the standard l1 penalty for enforcing sparsity. The optimization is performed using proximal gradient method, resulting in the tight-frame iterative shrinkage thresholding algorithm (TF-ISTA). We show that the objective convergence of TF-ISTA is linear akin to that of ISTA. Incorporating Nesterovs momentum into TF-ISTA results in a faster variant, namely, TF-FISTA, whose objective convergence is quadratic, akin to that of FISTA. We provide performance guarantees on the l2-error for the proposed formulation. Experimental results show that the proposed algorithms offer superior sparse recovery performance and faster convergence. Proceeding further, we develop the network variants of TF-ISTA and TF-FISTA, wherein a convolutional neural network is used as the sparsifying operator. On the application front, we consider compressed sensing image recovery (CSIR). Experimental results on Set11, BSD68, Urban100, and DIV2K datasets show that the proposed models outperform state-of-the-art sparse recovery methods, with performance measured in terms of peak signal-to-noise ratio (PSNR) and structural similarity index metric (SSIM).Comment: 33 pages, 12 figure

Robust Algorithms for Low-Rank and Sparse Matrix Models

Data in statistical signal processing problems is often inherently matrix-valued, and a natural first step in working with such data is to impose a model with structure that captures the distinctive features of the underlying data. Under the right model, one can design algorithms that can reliably tease weak signals out of highly corrupted data. In this thesis, we study two important classes of matrix structure: low-rankness and sparsity. In particular, we focus on robust principal component analysis (PCA) models that decompose data into the sum of low-rank and sparse (in an appropriate sense) components. Robust PCA models are popular because they are useful models for data in practice and because efficient algorithms exist for solving them. This thesis focuses on developing new robust PCA algorithms that advance the state-of-the-art in several key respects. First, we develop a theoretical understanding of the effect of outliers on PCA and the extent to which one can reliably reject outliers from corrupted data using thresholding schemes. We apply these insights and other recent results from low-rank matrix estimation to design robust PCA algorithms with improved low-rank models that are well-suited for processing highly corrupted data. On the sparse modeling front, we use sparse signal models like spatial continuity and dictionary learning to develop new methods with important adaptive representational capabilities. We also propose efficient algorithms for implementing our methods, including an extension of our dictionary learning algorithms to the online or sequential data setting. The underlying theme of our work is to combine ideas from low-rank and sparse modeling in novel ways to design robust algorithms that produce accurate reconstructions from highly undersampled or corrupted data. We consider a variety of application domains for our methods, including foreground-background separation, photometric stereo, and inverse problems such as video inpainting and dynamic magnetic resonance imaging.PHDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/143925/1/brimoor_1.pd