A Dictionary Learning Approach with Overlap for the Low Dose Computed Tomography Reconstruction and Its Vectorial Application to Differential Phase Tomography

X-ray based Phase-Contrast Imaging (PCI) techniques have been demonstrated to enhance the visualization of soft tissues in comparison to conventional imaging methods. Nevertheless the delivered dose as reported in the literature of biomedical PCI applications often equals or exceeds the limits prescribed in clinical diagnostics. The optimization of new computed tomography strategies which include the development and implementation of advanced image reconstruction procedures is thus a key aspect. In this scenario, we implemented a dictionary learning method with a new form of convex functional. This functional contains in addition to the usual sparsity inducing and fidelity terms, a new term which forces similarity between overlapping patches in the superimposed regions. The functional depends on two free regularization parameters: a coefficient multiplying the sparsity-inducing L-1 norm of the patch basis functions coefficients, and a coefficient multiplying the L-2 norm of the differences between patches in the overlapping regions. The solution is found by applying the iterative proximal gradient descent method with FISTA acceleration. The gradient is computed by calculating projection of the solution and its error backprojection at each iterative step. We study the quality of the solution, as a function of the regularization parameters and noise, on synthetic data for which the solution is a-priori known. We apply the method on experimental data in the case of Differential Phase Tomography. For this case we use an original approach which consists in using vectorial patches, each patch having two components: one per each gradient component. The resulting algorithm, implemented in the European Synchrotron Radiation Facility tomography reconstruction code PyHST, has proven to be efficient and well-adapted to strongly reduce the required dose and the number of projections in medical tomography

A Dictionary Learning Approach with Overlap for the Low Dose Computed Tomography Reconstruction and Its Vectorial Application to Differential Phase Tomography

X-ray based Phase-Contrast Imaging (PCI) techniques have been demonstrated to enhance the visualization of soft tissues in comparison to conventional imaging methods. Nevertheless the delivered dose as reported in the literature of biomedical PCI applications often equals or exceeds the limits prescribed in clinical diagnostics. The optimization of new computed tomography strategies which include the development and implementation of advanced image reconstruction procedures is thus a key aspect. In this scenario, we implemented a dictionary learning method with a new form of convex functional. This functional contains in addition to the usual sparsity inducing and fidelity terms, a new term which forces similarity between overlapping patches in the superimposed regions. The functional depends on two free regularization parameters: a coefficient multiplying the sparsity-inducing L-1 norm of the patch basis functions coefficients, and a coefficient multiplying the L-2 norm of the differences between patches in the overlapping regions. The solution is found by applying the iterative proximal gradient descent method with FISTA acceleration. The gradient is computed by calculating projection of the solution and its error backprojection at each iterative step. We study the quality of the solution, as a function of the regularization parameters and noise, on synthetic data for which the solution is a-priori known. We apply the method on experimental data in the case of Differential Phase Tomography. For this case we use an original approach which consists in using vectorial patches, each patch having two components: one per each gradient component. The resulting algorithm, implemented in the European Synchrotron Radiation Facility tomography reconstruction code PyHST, has proven to be efficient and well-adapted to strongly reduce the required dose and the number of projections in medical tomography

Convolutional neuronal networks combined with X-ray phase-contrast imaging for a fast and observer-independent discrimination of cartilage and liver diseases stages

We applied transfer learning using Convolutional Neuronal Networks to high resolution X-ray phase contrast computed tomography datasets and tested the potential of the systems to accurately classify Computed Tomography images of different stages of two diseases, i.e. osteoarthritis and liver fibrosis. The purpose is to identify a time-effective and observer-independent methodology to identify pathological conditions. Propagation-based X-ray phase contrast imaging WAS used with polychromatic X-rays to obtain a 3D visualization of 4 human cartilage plugs and 6 rat liver samples with a voxel size of 0.7x0.7x0.7 mu m(3) and 2.2x2.2x2.2 mu m(3), respectively. Images with a size of 224x224 pixels are used to train three pre-trained convolutional neuronal networks for data classification, which are the VGG16, the Inception V3, and the Xception networks. We evaluated the performance of the three systems in terms of classification accuracy and studied the effect of the variation of the number of inputs, training images and of iterations. The VGG16 network provides the highest classification accuracy when the training and the validation-test of the network are performed using data from the same samples for both the cartilage (99.8%) and the liver (95.5%) datasets. The Inception V3 and Xception networks achieve an accuracy of 84.7% (43.1%) and of 72.6% (53.7%), respectively, for the cartilage (liver) images. By using data from different samples for the training and validation-test processes, the Xception network provided the highest test accuracy for the cartilage dataset (75.7%), while for the liver dataset the VGG16 network gave the best results (75.4%). By using convolutional neuronal networks we show that it is possible to classify large datasets of biomedical images in less than 25 min on a 8 CPU processor machine providing a precise, robust, fast and observer-independent method for the discrimination/classification of different stages of osteoarthritis and liver diseases

Synchrotron-generated microbeams induce hippocampal transections in rats

Synchrotron-generated microplanar beams (microbeams) provide the most stereo-selective irradiation modality known today. This novel irradiation modality has been shown to control seizures originating from eloquent cortex causing no neurological deficit in experimental animals. To test the hypothesis that application of microbeams in the hippocampus, the most common source of refractory seizures, is safe and does not induce severe side effects, we used microbeams to induce transections to the hippocampus of healthy rats. An array of parallel microbeams carrying an incident dose of 600 Gy was delivered to the rat hippocampus. Immunohistochemistry of phosphorylated gamma-H2AX showed cell death along the microbeam irradiation paths in rats 48 hours after irradiation. No evident behavioral or neurological deficits were observed during the 3-month period of observation. MR imaging showed no signs of radio-induced edema or radionecrosis 3 months after irradiation. Histological analysis showed a very well preserved hippocampal cytoarchitecture and confirmed the presence of clear-cut microscopic transections across the hippocampus. These data support the use of synchrotron-generated microbeams as a novel tool to slice the hippocampus of living rats in a minimally invasive way, providing (i) a novel experimental model to study hippocampal function and (ii) a new treatment tool for patients affected by refractory epilepsy induced by mesial temporal sclerosis

High contrast microstructural visualization of natural acellular matrices by means of phase-based x-ray tomography

Acellular scaffolds obtained via decellularization are a key instrument in regenerative medicine both per se and to drive the development of future-generation synthetic scaffolds that could become available off-the-shelf. In this framework, imaging is key to the understanding of the scaffolds\u2019 internal structure as well as their interaction with cells and other organs, including ideally post-implantation. Scaffolds of a wide range of intricate organs (esophagus, lung, liver and small intestine) were imaged with x-ray phase contrast computed tomography (PC-CT). Image quality was sufficiently high to visualize scaffold microarchitecture and to detect major anatomical features, such as the esophageal mucosal-submucosal separation, pulmonary alveoli and intestinal villi. These results are a long-sought step for the field of regenerative medicine; until now, histology and scanning electron microscopy have been the gold standard to study the scaffold structure. However, they are both destructive: hence, they are not suitable for imaging scaffolds prior to transplantation, and have no prospect for post-transplantation use. PC-CT, on the other hand, is non-destructive, 3D and fully quantitative. Importantly, not only do we demonstrate achievement of high image quality at two different synchrotron facilities, but also with commercial x-ray equipment, which makes the method available to any research laboratory

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

DEVELOPPEMENT ET APPLICATION D'UNE TECHNIQUE D'IMAGERIE PAR RAYONNEMENT SYNCHROTRON BASÉE SUR L'UTILISATION D'UN CRISTAL ANALYSEUR

THE OBJECTIVE OF THIS THESIS IS TWOFOLD: FROM ONE SIDE THE APPLICATION OF THE ANALYSER-BASED X-RAY PHASE CONTRAST IMAGING TO STUDY CARTILAGE, BONE AND BONE IMPLANTS USING THE ID17 AND ID19 ESRF SYNCHROTRON RADIATION SOURCES AND ON THE OTHER TO CONTRIBUTE TO THE DEVELOPMENT OF THE PHASE CONTRAST TECHNIQUES FROM THE THEORETICAL AND EXPERIMENTAL POINT OF VIEW. SEVERAL HUMAN SAMPLES HAVE BEEN STUDIED IN VITRO USING THE ANALYSER BASED IMAGING (ABI) TECHNIQUE. EXAMINATION INCLUDED PROJECTION AND COMPUTED TOMOGRAPHY IMAGING AND 3D VOLUME RENDERING OF HIP, BIG TOE AND ANKLE ARTICULAR JOINTS. X-RAY ABI IMAGES HAVE BEEN CRITICALLY COMPARED WITH THOSE OBTAINED WITH THE CONVENTIONAL TECHNIQUES, INCLUDING RADIOGRAPHY, COMPUTED TOMOGRAPHY, ULTRASOUND, MAGNETIC RESONANCE AND HISTOLOGY, THE LATTER TAKEN AS GOLD STANDARD. RESULTS SHOW THAT ONLY ABI IMAGING WAS ABLE TO EITHER VISUALIZE OR CORRECTLY ESTIMATE THE EARLY PATHOLOGICAL STATUS OF THE CARTILAGE. THE STATUS OF THE BONE INGROWTH IN SHEEP IMPLANTS HAVE ALSO BEEN EXAMINED IN VITRO: ABI IMAGES PERMITTED TO CORRECTLY DISTINGUISH BETWEEN GOOD AND INCOMPLETE BONE HEALING. PIONEERING IN-VIVO ABI ON GUINEA PIGS WERE ALSO SUCCESSFULLY PERFORMED, CONFIRMING THE POSSIBLE USE OF THE TECHNIQUE TO FOLLOW UP THE PROGRESSION OF JOINT DISEASES, THE BONE/METAL INGROWTH AND THE EFFICACY OF DRUGS TREATMENTS.AS PART OF THE DEVELOPMENT OF THE PHASE CONTRAST TECHNIQUES, TWO OBJECTIVES HAVE BEEN REACHED. FIRSTLY, IT HAS BEEN EXPERIMENTALLY DEMONSTRATED FOR THE FIRST TIME THAT THE ABI AND THE PROPAGATION BASED IMAGING (PBI) CAN BE COMBINED TO CREATE IMAGES WITH ORIGINAL FEATURES (HYBRID IMAGING, HI). SECONDLY, IT HAS BEEN PROPOSED AND EXPERIMENTALLY TESTED A NEW SIMPLIFIED SET-UP CAPABLE TO PRODUCE IMAGES WITH PROPERTIES SIMILAR TO THOSE OBTAINED WITH THE ABI TECHNIQUE OR HI. FINALLY, BOTH THE ABI AND THE HI HAVE BEEN THEORETICAL STUDIED WITH AN INNOVATIVE, WAVE-BASED SIMULATION PROGRAM, WHICH WAS ABLE TO CORRECTLY REPRODUCE EXPERIMENTAL RESULTS.CETTE THESE A UN DOUBLE OBJECTIF: D'UNE PART IL S'AGIT DE L'APPLICATION DE L'IMAGERIE X PAR CONTRASTE DE PHASE (AVEC CRISTAL ANALYSEUR) POUR L'ETUDE DES CARTILAGES, OS ET IMPLANTS A L'AIDE DU RAYONNEMENT SYNCHROTRON ET D'AUTRE PART CE TRAVAIL CONTRIBUE AU DEVELOPPEMENT, THEORIQUE ET EXPERIMENTAL, DES TECHNIQUES D'IMAGERIE PAR CONTRASTE DE PHASE.PLUSIEURS ECHANTILLONS HUMAINS POST MORTEM ONT ETE IMAGES PAR UNE TECHNIQUE DE CONTRASTE DE PHASE UTILISANT UN CRISTAL ANALYSEUR (ABI). L'ETUDE COMPREND L'IMAGERIE PAR PROJECTION ET TOMOGRAPHIQUE D'ARTICULATIONS DE HANCHE, ORTEIL ET CHEVILLE. LES IMAGES PAR ABI ONT ETE CONFRONTEES A CELLES OBTENUES PAR DES TECHNIQUES CONVENTIONNELLES : RADIOGRAPHIE, TOMODENSITOMETRIE, ECHOGRAPHIE, IMAGERIE PAR RESONANCE MAGNETIQUE ET A DE L'HISTOLOGIE, QUI SERT DE REFERENCE. LES RESULTATS MONTRENT QUE SEULE L'IMAGERIE PAR ABI PERMET DE VISUALISER OU ESTIMER CORRECTEMENT LE STATUT PATHOLOGIQUE PRECOCE DU CARTILAGE. LA CROISSANCE DE L'OS APRES IMPLANTS A AUSSI ETE ETUDIEE SUR LES ECHANTILLONS POST MORTEM DE MOUTON : LA TECHNIQUE D'IMAGERIE PAR ABI PERMET DE FAIRE LA DIFFERENCE ENTRE UNE BONNE GUERISON ET UN RECUPERATION INCOMPLETE DE L'OS. DES EXPERIENCES PIONNIERES, IN VIVO, REALISEES AVEC DES COCHONS DE GUINEE ONT EGALEMENT ETE MENEES AVEC SUCCES, CONFIRMANT AINSI L'UTILISATION POSSIBLE DE LA TECHNIQUE POUR LE SUIVI DES MALADIES AFFECTANT LES ARTICULATIONS, L'ASSIMILATION DES IMPLANTS OU ENCORE L'ETUDE DE L'EFFICACITE DE MEDICAMENTS.EN CE QUI CONCERNE LE DEVELOPPEMENT DES TECHNIQUES PAR CONTRASTE DE PHASE, DEUX OBJECTIFS ONT ETE ATTEINTS. POUR LA PREMIERE FOIS, IL A ETE DEMONTRE EXPERIMENTALEMENT QUE LES TECHNIQUES D'IMAGERIE UTILISANT LE CONTRASTE DE PHASE PAR ABI ET PAR PROPAGATION (PPI) PEUVENT ETRE COMBINEES POUR CREER DES IMAGES AYANT DES CARACTERISTIQUES PROPRES (IMAGERIE HYBRIDE HI). DEUXIEMEMENT, UNE NOUVELLE CONFIGURATION EXPERIMENTALE SIMPLIFIEE, POUR L'ACQUISITION D'IMAGES PROCHES DE CELLES OBTENUES PAR ABI OU HI, EST PROPOSEE ET TESTEE. ENFIN, LES DEUX TECHNIQUES D'IMAGERIE PAR ABI OU HI ONT ETE ETUDIEES D'UN POINT DE VUE THEORIQUE AVEC UN CODE DE SIMULATION ORIGINAL QUI EST CAPABLE DE REPRODUIRE LES RESULTATS EXPERIMENTAUX