Self-Tuned Deep Super Resolution

Deep learning has been successfully applied to image super resolution (SR). In this paper, we propose a deep joint super resolution (DJSR) model to exploit both external and self similarities for SR. A Stacked Denoising Convolutional Auto Encoder (SDCAE) is first pre-trained on external examples with proper data augmentations. It is then fine-tuned with multi-scale self examples from each input, where the reliability of self examples is explicitly taken into account. We also enhance the model performance by sub-model training and selection. The DJSR model is extensively evaluated and compared with state-of-the-arts, and show noticeable performance improvements both quantitatively and perceptually on a wide range of images

An Optimized PatchMatch for multi-scale and multi-feature label fusion

Automatic segmentation methods are important tools for quantitative analysis of Magnetic Resonance Images (MRI). Recently, patch-based label fusion approaches have demonstrated state-of-the-art segmentation accuracy. In this paper, we introduce a new patch-based label fusion framework to perform segmentation of anatomical structures. The proposed approach uses an Optimized PAtchMatch Label fusion (OPAL) strategy that drastically reduces the computation time required for the search of similar patches. The reduced computation time of OPAL opens the way for new strategies and facilitates processing on large databases. In this paper, we investigate new perspectives offered by OPAL, by introducing a new multi-scale and multi-feature framework. During our validation on hippocampus segmentation we use two datasets: young adults in the ICBM cohort and elderly adults in the EADC-ADNI dataset. For both, OPAL is compared to state-of-the-art methods. Results show that OPAL obtained the highest median Dice coefficient (89.9% for ICBM and 90.1% for EADC-ADNI). Moreover, in both cases, OPAL produced a segmentation accuracy similar to inter-expert variability. On the EADC-ADNI dataset, we compare the hippocampal volumes obtained by manual and automatic segmentation. The volumes appear to be highly correlated that enables to perform more accurate separation of pathological populations. (C) 2015 Elsevier Inc. All rights reserved.This study has been carried out with financial support from the French State, managed by the French National Research Agency (ANR) in the frame of the Investments for the future Program IdEx Bordeaux (ANR-10-IDEX-03-02), Cluster of excellence CPU and TRAIL (HR-DTI ANR-10-LABX-57). We also thank Tong Tong and Daniel Rueckert for providing us complete results of the methods proposed in Tong et al. (2013), Sonia Tangaro and Marina Boccardi for providing us complete results of the method proposed in Tangaro et al. (2014), and Katherine Gray and Robin Wolz for providing us complete results of the LEAP method proposed in Gray et al. (2014). Data collection and sharing for this project were funded by the Alzheimer's Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904). The ADNI is funded by the National Institute on Aging and the National Institute of Biomedical Imaging and Bioengineering and through generous contributions from the following: Abbott, AstraZeneca AB, Bayer Schering Pharma AG, Bristol-Myers Squibb, Eisai Global Clinical Development, Elan Corporation, Genentech, GE Healthcare, GlaxoSmithKline, Innogenetics NV, Johnson and Johnson, Eli Lilly and Co., Medpace, Inc., Merck and Co., Inc., Novartis AG, Pfizer Inc., F. Hoffmann-La Roche, Schering-Plough, Synarc Inc., as well as nonprofit partners, the Alzheimer's Association and Alzheimer's Drug Discovery Foundation, with participation from the U.S. Food and Drug Administration. Private sector contributions to the ADNI are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study was coordinated by the Alzheimer's Disease Cooperative Study at the University of California, San Diego. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of California, Los Angeles. This research was also supported by the Spanish grant TIN2013-43457-R from the Ministerio de Economia y competitividad, NIH grants P30AG010129, K01 AG030514 and the Dana Foundation.Giraud, R.; Ta, V.; Papadakis, N.; Manjón Herrera, JV.; Collins, L.; Coupé Pierrick; Alzheimers Dis Neuroimaging Initia (2016). An Optimized PatchMatch for multi-scale and multi-feature label fusion. NeuroImage. 124(1):770-782. https://doi.org/10.1016/j.neuroimage.2015.07.076S770782124

Algorithms for super-resolution of images based on Sparse Representation and Manifolds

lmage super-resolution is defined as a class of techniques that enhance the spatial resolution of images. Super-resolution methods can be subdivided in single and multi image methods. This thesis focuses on developing algorithms based on mathematical theories for single image super­ resolution problems. lndeed, in arder to estimate an output image, we adopta mixed approach: i.e., we use both a dictionary of patches with sparsity constraints (typical of learning-based methods) and regularization terms (typical of reconstruction-based methods). Although the existing methods already per- form well, they do not take into account the geometry of the data to: regularize the solution, cluster data samples (samples are often clustered using algorithms with the Euclidean distance as a dissimilarity metric), learn dictionaries (they are often learned using PCA or K-SVD). Thus, state-of-the-art methods still suffer from shortcomings. In this work, we proposed three new methods to overcome these deficiencies. First, we developed SE-ASDS (a structure tensor based regularization term) in arder to improve the sharpness of edges. SE-ASDS achieves much better results than many state-of-the- art algorithms. Then, we proposed AGNN and GOC algorithms for determining a local subset of training samples from which a good local model can be computed for recon- structing a given input test sample, where we take into account the underlying geometry of the data. AGNN and GOC methods outperform spectral clustering, soft clustering, and geodesic distance based subset selection in most settings. Next, we proposed aSOB strategy which takes into account the geometry of the data and the dictionary size. The aSOB strategy outperforms both PCA and PGA methods. Finally, we combine all our methods in a unique algorithm, named G2SR. Our proposed G2SR algorithm shows better visual and quantitative results when compared to the results of state-of-the-art methods.Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorTese (Doutorado)Super-resolução de imagens é definido como urna classe de técnicas que melhora a resolução espacial de imagens. Métodos de super-resolução podem ser subdivididos em métodos para urna única imagens e métodos para múltiplas imagens. Esta tese foca no desenvolvimento de algoritmos baseados em teorias matemáticas para problemas de super-resolução de urna única imagem. Com o propósito de estimar urna imagem de saída, nós adotamos urna abordagem mista, ou seja: nós usamos dicionários de patches com restrição de esparsidade (método baseado em aprendizagem) e termos de regularização (método baseado em reconstrução). Embora os métodos existentes sejam eficientes, eles nao levam em consideração a geometria dos dados para: regularizar a solução, clusterizar os dados (dados sao frequentemente clusterizados usando algoritmos com a distancia Euclideana como métrica de dissimilaridade), aprendizado de dicionários (eles sao frequentemente treinados usando PCA ou K-SVD). Portante, os métodos do estado da arte ainda tem algumas deficiencias. Neste trabalho, nós propomos tres métodos originais para superar estas deficiencias. Primeiro, nós desenvolvemos SE-ASDS (um termo de regularização baseado em structure tensor) afim de melhorar a nitidez das bordas das imagens. SE-ASDS alcança resultados muito melhores que os algoritmos do estado da arte. Em seguida, nós propomos os algoritmos AGNN e GOC para determinar um subconjunto de amostras de treinamento a partir das quais um bom modelo local pode ser calculado para reconstruir urna dada amostra de entrada considerando a geometria dos dados. Os métodos AGNN e GOC superamos métodos spectral clustering, soft clustering e os métodos baseados em distancia geodésica na maioria dos casos. Depois, nós propomos o método aSOB que leva em consideração a geometria dos dados e o tamanho do dicionário. O método aSOB supera os métodos PCA e PGA. Finalmente, nós combinamos todos os métodos que propomos em um único algoritmo, a saber, G2SR. Nosso algoritmo G2SR mostra resultados melhores que os métodos do estado da arte em termos de PSRN, SSIM, FSIM e qualidade visual

Bayesian fusion of multi-band images : A powerful tool for super-resolution

Hyperspectral (HS) imaging, which consists of acquiring a same scene in several hundreds of contiguous spectral bands (a three dimensional data cube), has opened a new range of relevant applications, such as target detection [MS02], classification [C.-03] and spectral unmixing [BDPD+12]. However, while HS sensors provide abundant spectral information, their spatial resolution is generally more limited. Thus, fusing the HS image with other highly resolved images of the same scene, such as multispectral (MS) or panchromatic (PAN) images is an interesting problem. The problem of fusing a high spectral and low spatial resolution image with an auxiliary image of higher spatial but lower spectral resolution, also known as multi-resolution image fusion, has been explored for many years [AMV+11]. From an application point of view, this problem is also important as motivated by recent national programs, e.g., the Japanese next-generation space-borne hyperspectral image suite (HISUI), which fuses co-registered MS and HS images acquired over the same scene under the same conditions [YI13]. Bayesian fusion allows for an intuitive interpretation of the fusion process via the posterior distribution. Since the fusion problem is usually ill-posed, the Bayesian methodology offers a convenient way to regularize the problem by defining appropriate prior distribution for the scene of interest. The aim of this thesis is to study new multi-band image fusion algorithms to enhance the resolution of hyperspectral image. In the first chapter, a hierarchical Bayesian framework is proposed for multi-band image fusion by incorporating forward model, statistical assumptions and Gaussian prior for the target image to be restored. To derive Bayesian estimators associated with the resulting posterior distribution, two algorithms based on Monte Carlo sampling and optimization strategy have been developed. In the second chapter, a sparse regularization using dictionaries learned from the observed images is introduced as an alternative of the naive Gaussian prior proposed in Chapter 1. instead of Gaussian prior is introduced to regularize the ill-posed problem. Identifying the supports jointly with the dictionaries circumvented the difficulty inherent to sparse coding. To minimize the target function, an alternate optimization algorithm has been designed, which accelerates the fusion process magnificently comparing with the simulation-based method. In the third chapter, by exploiting intrinsic properties of the blurring and downsampling matrices, a much more efficient fusion method is proposed thanks to a closed-form solution for the Sylvester matrix equation associated with maximizing the likelihood. The proposed solution can be embedded into an alternating direction method of multipliers or a block coordinate descent method to incorporate different priors or hyper-priors for the fusion problem, allowing for Bayesian estimators. In the last chapter, a joint multi-band image fusion and unmixing scheme is proposed by combining the well admitted linear spectral mixture model and the forward model. The joint fusion and unmixing problem is solved in an alternating optimization framework, mainly consisting of solving a Sylvester equation and projecting onto a simplex resulting from the non-negativity and sum-to-one constraints. The simulation results conducted on synthetic and semi-synthetic images illustrate the advantages of the developed Bayesian estimators, both qualitatively and quantitatively

Machine Learning for Beamforming in Audio, Ultrasound, and Radar

Multi-sensor signal processing plays a crucial role in the working of several everyday technologies, from correctly understanding speech on smart home devices to ensuring aircraft fly safely. A specific type of multi-sensor signal processing called beamforming forms a central part of this thesis. Beamforming works by combining the information from several spatially distributed sensors to directionally filter information, boosting the signal from a certain direction but suppressing others. The idea of beamforming is key to the domains of audio, ultrasound, and radar. Machine learning is the other central part of this thesis. Machine learning, and especially its sub-field of deep learning, has enabled breakneck progress in tackling several problems that were previously thought intractable. Today, machine learning powers many of the cutting edge systems we see on the internet for image classification, speech recognition, language translation, and more. In this dissertation, we look at beamforming pipelines in audio, ultrasound, and radar from a machine learning lens and endeavor to improve different parts of the pipelines using ideas from machine learning. We start off in the audio domain and derive a machine learning inspired beamformer to tackle the problem of ensuring the audio captured by a camera matches its visual content, a problem we term audiovisual zooming. Staying in the audio domain, we then demonstrate how deep learning can be used to improve the perceptual qualities of speech by denoising speech clipping, codec distortions, and gaps in speech. Transitioning to the ultrasound domain, we improve the performance of short-lag spatial coherence ultrasound imaging by exploiting the differences in tissue texture at each short lag value by applying robust principal component analysis. Next, we use deep learning as an alternative to beamforming in ultrasound and improve the information extraction pipeline by simultaneously generating both a segmentation map and B-mode image of high quality directly from raw received ultrasound data. Finally, we move to the radar domain and study how deep learning can be used to improve signal quality in ultra-wideband synthetic aperture radar by suppressing radio frequency interference, random spectral gaps, and contiguous block spectral gaps. By training and applying the networks on raw single-aperture data prior to beamforming, it can work with myriad sensor geometries and different beamforming equations, a crucial requirement in synthetic aperture radar

Compressing Positive Semidefinite Operators with Sparse/Localized Bases

Given a positive semidefinite (PSD) operator, such as a PSD matrix, an elliptic operator with rough coefficients, a covariance operator of a random field, or the Hamiltonian of a quantum system, we would like to find its best finite rank approximation with a given rank. One way to achieve this objective is to project the operator to its eigenspace that corresponds to the smallest or largest eigenvalues, depending on the setting. The eigenfunctions are typically global, i.e. nonzero almost everywhere, but our interest is to find the sparsest or most localized bases for these subspaces. The sparse/localized basis functions lead to better physical interpretation and preserve some sparsity structure in the original operator. Moreover, sparse/localized basis functions also enable us to develop more efficient numerical algorithms to solve these problems. In this thesis, we present two methods for this purpose, namely the sparse operator compression (Sparse OC) and the intrinsic sparse mode decomposition (ISMD). The Sparse OC is a general strategy to construct finite rank approximations to PSD operators, for which the range space of the finite rank approximation is spanned by a set of sparse/localized basis functions. The basis functions are energy minimizing functions on local patches. When applied to approximate the solution operator of elliptic operators with rough coefficients and various homogeneous boundary conditions, the Sparse OC achieves the optimal convergence rate with nearly optimally localized basis functions. Our localized basis functions can be used as multiscale basis functions to solve elliptic equations with multiscale coefficients and provide the optimal convergence rate O(hk) for 2k'th order elliptic problems in the energy norm. From the perspective of operator compression, these localized basis functions provide an efficient and optimal way to approximate the principal eigen-space of the elliptic operators. From the perspective of the Sparse PCA, we can approximate a large set of covariance functions by a rank-n operator with a localized basis and with the optimal accuracy. While the Sparse OC works well on the solution operator of elliptic operators, we also propose the ISMD that works well on low rank or nearly low rank PSD operators. Given a rank-n PSD operator, say a N-by-N PSD matrix A (n ≤ N), the ISMD decomposes it into n rank-one matrices Σni=1gigTi where the mode {gi}ni=1 are required to be as sparse as possible. Under the regular-sparse assumption (see Definition 1.3.2), we have proved that the ISMD gives the optimal patchwise sparse decomposition, and is stable to small perturbations in the matrix to be decomposed. We provide several applications in both the physical and data sciences to demonstrate the effectiveness of the proposed strategies.</p