Multi-contrast reconstruction with Bayesian compressed sensing

Clinical imaging with structural MRI routinely relies on multiple acquisitions of the same region of interest under several different contrast preparations. This work presents a reconstruction algorithm based on Bayesian compressed sensing to jointly reconstruct a set of images from undersampled k-space data with higher fidelity than when the images are reconstructed either individually or jointly by a previously proposed algorithm, M-FOCUSS. The joint inference problem is formulated in a hierarchical Bayesian setting, wherein solving each of the inverse problems corresponds to finding the parameters (here, image gradient coefficients) associated with each of the images. The variance of image gradients across contrasts for a single volumetric spatial position is a single hyperparameter. All of the images from the same anatomical region, but with different contrast properties, contribute to the estimation of the hyperparameters, and once they are found, the k-space data belonging to each image are used independently to infer the image gradients. Thus, commonality of image spatial structure across contrasts is exploited without the problematic assumption of correlation across contrasts. Examples demonstrate improved reconstruction quality (up to a factor of 4 in root-mean-square error) compared with previous compressed sensing algorithms and show the benefit of joint inversion under a hierarchical Bayesian model

Improvements in the registration of multimodal medical imaging : application to intensity inhomogeneity and partial volume corrections

Alignment or registration of medical images has a relevant role on clinical diagnostic and treatment decisions as well as in research settings. With the advent of new technologies for multimodal imaging, robust registration of functional and anatomical information is still a challenge, particular in small-animal imaging given the lesser structural content of certain anatomical parts, such as the brain, than in humans. Besides, patient-dependent and acquisition artefacts affecting the images information content further complicate registration, as is the case of intensity inhomogeneities (IIH) showing in MRI and the partial volume effect (PVE) attached to PET imaging. Reference methods exist for accurate image registration but their performance is severely deteriorated in situations involving little images Overlap. While several approaches to IIH and PVE correction exist these methods still do not guarantee or rely on robust registration. This Thesis focuses on overcoming current limitations af registration to enable novel IIH and PVE correction methods.El registre d'imatges mèdiques té un paper rellevant en les decisions de diagnòstic i tractament clíniques així com en la recerca. Amb el desenvolupament de noves tecnologies d'imatge multimodal, el registre robust d'informació funcional i anatòmica és encara avui un repte, en particular, en imatge de petit animal amb un menor contingut estructural que en humans de certes parts anatòmiques com el cervell. A més, els artefactes induïts pel propi pacient i per la tècnica d'adquisició que afecten el contingut d'informació de les imatges complica encara més el procés de registre. És el cas de les inhomogeneïtats d'intensitat (IIH) que apareixen a les RM i de l'efecte de volum parcial (PVE) característic en PET. Tot i que existeixen mètodes de referència pel registre acurat d'imatges la seva eficàcia es veu greument minvada en casos de poc solapament entre les imatges. De la mateixa manera, també existeixen mètodes per la correcció d'IIH i de PVE però que no garanteixen o que requereixen un registre robust. Aquesta tesi es centra en superar aquestes limitacions sobre el registre per habilitar nous mètodes per la correcció d'IIH i de PVE

Correlated Multimodal Imaging in Life Sciences:Expanding the Biomedical Horizon

International audienceThe frontiers of bioimaging are currently being pushed toward the integration and correlation of several modalities to tackle biomedical research questions holistically and across multiple scales. Correlated Multimodal Imaging (CMI) gathers information about exactly the same specimen with two or more complementary modalities that-in combination-create a composite and complementary view of the sample (including insights into structure, function, dynamics and molecular composition). CMI allows to describe biomedical processes within their overall spatio-temporal context and gain a mechanistic understanding of cells, tissues, diseases or organisms by untangling their molecular mechanisms within their native environment. The two best-established CMI implementations for small animals and model organisms are hardware-fused platforms in preclinical imaging (Hybrid Imaging) and Correlated Light and Electron Microscopy (CLEM) in biological imaging. Although the merits of Preclinical Hybrid Imaging (PHI) and CLEM are well-established, both approaches would benefit from standardization of protocols, ontologies and data handling, and the development of optimized and advanced implementations. Specifically, CMI pipelines that aim at bridging preclinical and biological imaging beyond CLEM and PHI are rare but bear great potential to substantially advance both bioimaging and biomedical research. CMI faces three mai

Methods for multi-spectral image fusion: identifying stable and repeatable information across the visible and infrared spectra

Fusion of images captured from different viewpoints is a well-known challenge in computer vision with many established approaches and applications; however, if the observations are captured by sensors also separated by wavelength, this challenge is compounded significantly. This dissertation presents an investigation into the fusion of visible and thermal image information from two front-facing sensors mounted side-by-side. The primary focus of this work is the development of methods that enable us to map and overlay multi-spectral information; the goal is to establish a combined image in which each pixel contains both colour and thermal information. Pixel-level fusion of these distinct modalities is approached using computational stereo methods; the focus is on the viewpoint alignment and correspondence search/matching stages of processing. Frequency domain analysis is performed using a method called phase congruency. An extensive investigation of this method is carried out with two major objectives: to identify predictable relationships between the elements extracted from each modality, and to establish a stable representation of the common information captured by both sensors. Phase congruency is shown to be a stable edge detector and repeatable spatial similarity measure for multi-spectral information; this result forms the basis for the methods developed in the subsequent chapters of this work. The feasibility of automatic alignment with sparse feature-correspondence methods is investigated. It is found that conventional methods fail to match inter-spectrum correspondences, motivating the development of an edge orientation histogram (EOH) descriptor which incorporates elements of the phase congruency process. A cost function, which incorporates the outputs of the phase congruency process and the mutual information similarity measure, is developed for computational stereo correspondence matching. An evaluation of the proposed cost function shows it to be an effective similarity measure for multi-spectral information

Proceedings of the 2009 Joint Workshop of Fraunhofer IOSB and Institute for Anthropomatics, Vision and Fusion Laboratory

The joint workshop of the Fraunhofer Institute of Optronics, System Technologies and Image Exploitation IOSB, Karlsruhe, and the Vision and Fusion Laboratory (Institute for Anthropomatics, Karlsruhe Institute of Technology (KIT)), is organized annually since 2005 with the aim to report on the latest research and development findings of the doctoral students of both institutions. This book provides a collection of 16 technical reports on the research results presented on the 2009 workshop