L'étude non destructive du bois à partir de scanners à rayons X nécessite d’imaginer de nouvelles solutions adaptées à l'analyse des images. Préoccupation à la fois de la recherche agronomique et du milieu industriel des scieries, la segmentation des nœuds de bois est un défi majeur en termes de robustesse aux spécificités de chaque espèce et aux conditions d'acquisition des images. Les travaux menés dans cette thèse permettent de proposer un processus de segmentation en deux phases. Il isole d'abord chaque nœud dans une zone réduite puis segmente le nœud unique de chaque zone. Les solutions proposées pour chaque phase permettent d'intégrer les connaissances sur l'organisation interne du tronc et les mécanismes inhérents à sa croissance, à travers des outils classiques du traitement et de l'analyse d'image. La première phase repose en grande partie sur un principe de détection du mouvement emprunté à l'analyse vidéo et revisité. Deux approches de segmentation sont ensuite proposées, considérant pour l'une les coupes tomographiques initiales, et pour l'autre de nouvelles coupes ré-échantillonnées pour chaque nœud, orthogonalement à sa trajectoire. L'intégralité du processus a été implémenté dans un logiciel dédié aussi bien à l'expérimentation et la validation de l'approche qu'aux échanges interdisciplinaires. Le support applicatif du bois souligne la capacité de spécialisation des algorithmes génériques du traitement et de l'analyse d'image, et la pertinence de l'intégration de connaissances a priori dans cette optique / The non-destructive study of wood from X-Ray CT scanners requires to imagine new solutions adapted to analysis of images. Relating both agronomic research and industrial sector of sawmills, segmentation of wood knots is a major challenge in terms of robustness to specificities of each species and to image acquisition conditions. The works carried out in this thesis allow to propose a segmentation process in two phases. It first isolates each knot in a reduced area then it segments the unique knot of each area. Proposed solutions for each phase allow to integrate knowledges about internal organization of trunk and mechanisms inherent to its growth, through classical tools of image analysis and processing. The first phase is essentially based on a movement detection principle borrowed from video analysis and revisited. Two segmentation approaches are then proposed, considering for one the initial CT slices and for the other news slices resampled for each knot orthogonally to its trajectory. The complete process has been implemented in a software dedicated both for experimentation and validation of approach, and to interdisciplinary dialogs. The applicative support of wood emphasizes the specialization abilities of generic image analysis and processing algorithms, and the relevance to integrate priori knowledges in this perspective

L'ostéoporose est une maladie caractérisée par la perte de la masse osseuse et la dégradation de la micro-architecture osseuse. Bien que l'ostéoporose ne soit pas une maladie mortelle, les fractures qu'elle provoque peuvent entraîner de graves complications (lésions des vaisseaux et des nerfs, infections, raideur), parfois accompagnées de menaces de mort. La micro-architecture osseuse joue un rôle important dans le diagnostic de l'ostéoporose. Deux appareils de tomodensitométrie courants pour scanner la micro-architecture osseuse sont la tomodensitométrie quantitative périphérique à haute résolution et la tomodensitométrie microscopique. Le premier dispositif donne accès à l'investigation in vivo, mais sa résolution spatiale est inférieure. Le micro tomodensitomètre donne une meilleure résolution spatiale, mais il est contraint à une mesure ex vivo. Dans cette thèse, notre but est d'améliorer la résolution spatiale des images de tomodensitométrie périphérique à haute résolution afin que l'analyse quantitative des images résolues soit proche de celle donnée par les images de tomodensitométrie Micro. Nous sommes partis de la régularisation de la variation totale, à une combinaison de la variation totale et du potentiel de double puits pour améliorer le contraste des résultats. Ensuite, nous envisageons d'utiliser la méthode d'apprentissage par dictionnaire pour récupérer plus de détails sur la structure. Par la suite, une méthode d'apprentissage approfondi a été proposée pour résoudre un problème de super résolution et de segmentation joint. Les résultats montrent que la méthode d'apprentissage profond est très prometteuse pour les applications futures. / Osteoporosis is a disease characterized by loss of bone mass and degradation of bone microarchitecture. Although osteoporosis is not a fatal disease, the fractures it causes can lead to serious complications (damage to vessels and nerves, infections, stiffness), sometimes accompanied with risk of death. The bone micro-architecture plays an important role for the diagnosis of osteoporosis. Two common CT devices to scan bone micro architecture is High resolution-peripheral Quantitative CT and Micro CT. The former device gives access to in vivo investigation, but its spatial resolution is inferior. Micro CT gives better spatial resolution, but it is constrained to ex vivo measurement. In this thesis, we attempt to improve the spatial resolution of high resolution peripheral CT images so that the quantitative analysis of the resolved images is close to the one given by Micro CT images. We started from the total variation regularization, to a combination of total variation and double-well potential to enhance the contrast of results. Then we consider to use dictionary learning method to recover more structure details. Afterward, a deep learning method has been proposed to solve a joint super resolution and segmentation problem. The results show that the deep learning method is very promising for future applications.

[Truncated abstract] Rocks, as the host to natural chains of coupled thermal, hydraulic and mechanical processes, are heterogeneous at a variety of length scales, and in their mechanical properties, as well as in the hydraulic and thermal transport properties. Rock heterogeneity affects the ultimate hydro-carbon recovery or geothermal energy production. This heterogeneity has been considered one important and difficult problem that needs to be taken into account for its effect on the coupled processes. The aim of this thesis is to investigate the effect of rock heterogeneity on multi-physical processes. A fully coupled finite element model, hereinafter referred to as a porosity-based model (PBM) was developed to characterise the thermal-hydraulic-mechanical (THM) coupling processes. The development of the PBM consists of a two-staged workflow. First, based on poromechanics, porosity, one of the inherent rock properties, was derived as a variant function of the thermal, hydraulic and mechanical effects. Then, empirical relations or experimental results, correlating porosity with the mechanical, hydraulic and thermal properties, were incorporated as the coupling effects. In the PBM, the bulk volume of the model is assumed to be changeable. The rate of the volumetric strain was derived as the difference of two parts: the first part is the change in volume per unit of volume and per unit of time (this part was traditionally considered the rate of volumetric strain); and the second is the product of the first part and the volumetric strain. The second part makes the PBM a significant advancement of the models reported in the literature. ... impact of the rock heterogeneity on the hydro-mechanical responses because of the requirement of large memory and long central processing unit (CPU) time for the 3D applications. In the 2D PBM applications, as the thermal boundary condition applied to the rock samples containing some fractures, the pore pressure is generated by the thermal gradient. Some pore pressure islands can be generated as the statistical model and the digital image model are applied to characterise the initial porosity distribution. However, by using the homogeneous model, this phenomenon cannot be produced. In the 3D PBM applications, the existing fractures become the preferential paths for the fluid flowing inside the numerical model. The numerical results show that the PBM is sufficiently reliable to account for the rock mineral distribution in the hydro-mechanical coupling processes. The applications of the statistical method and the digital image processing technique make it possible to visualise the rock heterogeneity effect on the pore pressure distribution and the heat dissipation inside the rock model. Monitoring the fluid flux demonstrates the impact of the rock heterogeneity on the fluid product, which concerns petroleum engineering. The overall fluid flux (OFF) is mostly overestimated when the rock and fluid properties are assumed to be homogeneous. The 3D PBM application is an example. As the rock is heterogeneous, the OFF by the digital core is almost the same as that by the homogeneous model (this is due to that some fractures running through the digital core become the preferential path for the fluid flow), and around 1.5 times of that by the statistical model.

This diploma thesis deals with reduction of metal artifacts in CT data with submicron resolution. The first part of this thesis briefly describes x-ray computed tomography followed by the description of artifacts of tomographic images and existing approaches of the reduction of metal artifacts. In the second part proposed methods of reduction of metal artifacts and their implementation in Matlab programming environment are described. Finally functionality of algorithms is tested on a newly created database and the results are compared, evaluated and discussed.

The objective of the Dissertation was to describe, quantify and interpret to which degree the shape and size of the facial skeleton of people living in the territory of today's Czech Republic in the period from the Early Middle Ages to the present day, i.e. in the course of the approx. last 1200 years, have changed. In this time period, morphological differences between populations, changes in the sexual dimorphism, modularity and allometry of the facial skeleton were examined. The evaluation was based on CT-images of skulls from three historical populations, specifically from the Early Middle Ages, High Middle Ages and the early modern period. The current population was represented by CT-images of living people. We studied the facial skeletons of a total of 329 individuals, of which 183 were men and 146 women. The CT- images were used as a base for the creation of virtual 3D surface models. The facial skeleton was divided into three morphological units, which were further examined. These were the skeleton of the upper face, lower jaw and palate. The statistical processing was carried out applying methods of geometric morphometrics allowing the separate studying of the shape and size variability of the examined units. When comparing the size and shape differences between studied populations it is...

A presença da Medicina Nuclear como modalidade de obtenção de imagens médicas é um dos principais procedimentos utilizados hoje nos centros de saúde, tendo como grande vantagem a capacidade de analisar o comportamento metabólico do paciente, traduzindo-se em diagnósticos precoces. Entretanto, sabe-se que a quantificação em Medicina Nuclear é dificultada por diversos fatores, entre os quais estão a correção de atenuação, espalhamento, algoritmos de reconstrução e modelos assumidos. Neste contexto, o principal objetivo deste projeto foi melhorar a acurácia e a precisão na análise de imagens de PET/CT via processos realísticos e bem controlados. Para esse fim, foi proposta a elaboração de uma estrutura modular, a qual está composta por um conjunto de passos consecutivamente interligados começando com a simulação de phantoms antropomórficos 3D para posteriormente gerar as projeções realísticas PET/CT usando a plataforma GATE (com simulação de Monte Carlo), em seguida é aplicada uma etapa de reconstrução de imagens 3D, na sequência as imagens são filtradas (por meio do filtro de Anscombe/Wiener para a redução de ruído Poisson caraterístico deste tipo de imagens) e, segmentadas (baseados na teoria Fuzzy Connectedness). Uma vez definida a região de interesse (ROI) foram produzidas as Curvas de Atividade de Entrada e Resultante requeridas no processo de análise da dinâmica de compartimentos com o qual foi obtida a quantificação do metabolismo do órgão ou estrutura de estudo. Finalmente, de uma maneira semelhante imagens PET/CT reais fornecidas pelo Instituto do Coração (InCor) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP) foram analisadas. Portanto, concluiu-se que a etapa de filtragem tridimensional usando o filtro Anscombe/Wiener foi relevante e de alto impacto no processo de quantificação metabólica e em outras etapas importantes do projeto em geral. / The presence of Nuclear Medicine as a medical imaging modality is one of the main procedures utilized nowadays in medical centers, and the great advantage of that procedure is its capacity to analyze the metabolic behavior of the patient, resulting in early diagnoses. However, the quantification in Nuclear Medicine is known to be complicated by many factors, such as degradations due to attenuation, scattering, reconstruction algorithms and assumed models. In this context, the goal of this project is to improve the accuracy and the precision of quantification in PET/CT images by means of realistic and well-controlled processes. For this purpose, we proposed to develop a framework, which consists in a set of consecutively interlinked steps that is initiated with the simulation of 3D anthropomorphic phantoms. These phantoms were used to generate realistic PET/CT projections by applying the GATE platform (with Monte Carlo simulation). Then a 3D image reconstruction was executed, followed by a filtering process (using the Anscombe/Wiener filter to reduce Poisson noise characteristic of this type of images) and, a segmentation process (based on the Fuzzy Connectedness theory). After defining the region of interest (ROI), input activity and output response curves are required for the compartment analysis in order to obtain the Metabolic Quantification of the selected organ or structure. Finally, in the same manner real images provided from the Heart Institute (InCor) of Hospital das Clínicas, Faculty of Medicine, University of São Paulo (HC-FMUSP) were analysed. Therefore, it is concluded that the three-dimensional filtering step using the Ascombe/Wiener filter was preponderant and had a high impact on the metabolic quantification process and on other important stages of the whole project.

A presença da Medicina Nuclear como modalidade de obtenção de imagens médicas é um dos principais procedimentos utilizados hoje nos centros de saúde, tendo como grande vantagem a capacidade de analisar o comportamento metabólico do paciente, traduzindo-se em diagnósticos precoces. Entretanto, sabe-se que a quantificação em Medicina Nuclear é dificultada por diversos fatores, entre os quais estão a correção de atenuação, espalhamento, algoritmos de reconstrução e modelos assumidos. Neste contexto, o principal objetivo deste projeto foi melhorar a acurácia e a precisão na análise de imagens de PET/CT via processos realísticos e bem controlados. Para esse fim, foi proposta a elaboração de uma estrutura modular, a qual está composta por um conjunto de passos consecutivamente interligados começando com a simulação de phantoms antropomórficos 3D para posteriormente gerar as projeções realísticas PET/CT usando a plataforma GATE (com simulação de Monte Carlo), em seguida é aplicada uma etapa de reconstrução de imagens 3D, na sequência as imagens são filtradas (por meio do filtro de Anscombe/Wiener para a redução de ruído Poisson caraterístico deste tipo de imagens) e, segmentadas (baseados na teoria Fuzzy Connectedness). Uma vez definida a região de interesse (ROI) foram produzidas as Curvas de Atividade de Entrada e Resultante requeridas no processo de análise da dinâmica de compartimentos com o qual foi obtida a quantificação do metabolismo do órgão ou estrutura de estudo. Finalmente, de uma maneira semelhante imagens PET/CT reais fornecidas pelo Instituto do Coração (InCor) do Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo (HC-FMUSP) foram analisadas. Portanto, concluiu-se que a etapa de filtragem tridimensional usando o filtro Anscombe/Wiener foi relevante e de alto impacto no processo de quantificação metabólica e em outras etapas importantes do projeto em geral. / The presence of Nuclear Medicine as a medical imaging modality is one of the main procedures utilized nowadays in medical centers, and the great advantage of that procedure is its capacity to analyze the metabolic behavior of the patient, resulting in early diagnoses. However, the quantification in Nuclear Medicine is known to be complicated by many factors, such as degradations due to attenuation, scattering, reconstruction algorithms and assumed models. In this context, the goal of this project is to improve the accuracy and the precision of quantification in PET/CT images by means of realistic and well-controlled processes. For this purpose, we proposed to develop a framework, which consists in a set of consecutively interlinked steps that is initiated with the simulation of 3D anthropomorphic phantoms. These phantoms were used to generate realistic PET/CT projections by applying the GATE platform (with Monte Carlo simulation). Then a 3D image reconstruction was executed, followed by a filtering process (using the Anscombe/Wiener filter to reduce Poisson noise characteristic of this type of images) and, a segmentation process (based on the Fuzzy Connectedness theory). After defining the region of interest (ROI), input activity and output response curves are required for the compartment analysis in order to obtain the Metabolic Quantification of the selected organ or structure. Finally, in the same manner real images provided from the Heart Institute (InCor) of Hospital das Clínicas, Faculty of Medicine, University of São Paulo (HC-FMUSP) were analysed. Therefore, it is concluded that the three-dimensional filtering step using the Ascombe/Wiener filter was preponderant and had a high impact on the metabolic quantification process and on other important stages of the whole project.