Successful management of hydrocarbon reservoirs, geothermal energy extraction sites, radioactive waste and CO2 storage sites depends on a detailed knowledge of fluid transport properties, porosity and permeability. Amongst deformation processes, fluid-rock interaction plays an important role in controlling the petrophysical properties of a rock. The presence of fluids in the rocks induce chemical and physical changes in compositions and texture, affecting porosity and permeability, hence influencing dynamic transport properties and fluid flow. Fluid-rock interaction processes have been deeply investigated in nature and in numerous experimental and numerical modelling studies. However, these studies lack a spatio-temporal characterization of the dynamic evolution of porosity and reaction microfabrics. There is no clear understanding of the spatio-temporal evolution of these properties in three dimensions, and how this evolution affects fluid percolation in the rock. Computed X-ray micro-Tomography (μCT) was applied to investigate these processes in three dimensions and observe their evolution in time (4DμCT). The combination of μCT with 2D analytical techniques (e.g. scanning electron microscope, SEM, electron microcrobe, EMPA, electron backscatter diffraction, EBSD) furthermore enables the extrapolation of the information gained from 2D analyses to the 3rd an 4th dimension (4D μCT). The thesis investigates two different categories of fluid-rock interaction processes, by using 4DμCT to monitor the evolution of mineral reactions (in the first case) and porosity (second case) in relation to strain and time. In the first case study, natural rock samples were analysed. The samples show a compositional change along a strain gradient from olivinic metagabbros to omphacite-garnet bearing eclogites in a ductile shear zone. Synchroton-based x-ray microtomography (sμCT) was applied to document the 3D evolution of garnets along the strain gradient (which represent the 4th dimension). The 3D spatial arrangement of garnet microfabrics can help determine the deformation history and the extent of fluid-rock interaction active during deformation. Results from the sμCT show that in the low strain domain, garnets form a large and well interconnected cluster that develops throughout the entire sample and garnet coronas never completely encapsulate olivine grains. In the most highly deformed eclogites, the oblate shapes of garnets reflect a deformational origin of the microfabrics. EBSD analyses reveal that garnets do not show evidence for crystal plasticity, but rather they highlight evidence for minor fracturing, neo-nucleation and overgrowth, which points to a mechanical disintegration of the garnet coronas during strain localisation. In the second case study, pressure-solution processes were investigated using NaCl as rock-analogue, to monitor the evolution of porosity and pore connectivity in four dimensions, providing a time-resolved characterization of the processes. NaCl samples were uniaxially compacted and μCT scans were taken at regular interval times to characterize the evolution of grain morphologies, pore space and macro-connectivity of the samples. Different uniaxial loads, as well as different bulk sample compositions (phyllosilicates and/or glass beads) were used to investigate their effect on the process. Greater uniaxial loads, and the presence of phyllosilicates within the deforming NaCl columns were found to enhance pressure-solution processes. The pore space becomes highly disconnected in the presence of phyllosilicates, with important implications for fluid percolation and dynamic transport properties. Mean strain rates, calculated from volumetric Digital Image Correlation (3D-DIC) analyses, were found to be higher where phyllosilicates were located. The combination of μCT with volumetric DIC and SEM imaging proved to be an efficient analytical method for investigating the dynamic behaviour of porosity and permeability during ongoing pressure-solution processes. The results showed that fluid-rock interaction critically modifies the rocks at the pore/grain scale, with important consequences on dynamic fluid transport properties. The combination of μCT with classical 2D techniques provided a better understanding on the dynamic evolution of transport properties and fluid percolation during fluid-rock interaction processes, allowing the characterization in three dimensions of reaction microfabrics and porosity.

Submitted by Emanuel Varela Cardoso (emanuel.varela@ufcg.edu.br) on 2018-08-30T23:05:10Z No. of bitstreams: 1 CARLOS HENRICKSON BARBALHO DE MOURA – DISSERTAÇÃO (PPGEPM) 2018.pdf: 10493787 bytes, checksum: 063013097342f1433f86bc8ac8434722 (MD5) / Made available in DSpace on 2018-08-30T23:05:10Z (GMT). No. of bitstreams: 1 CARLOS HENRICKSON BARBALHO DE MOURA – DISSERTAÇÃO (PPGEPM) 2018.pdf: 10493787 bytes, checksum: 063013097342f1433f86bc8ac8434722 (MD5) Previous issue date: 2018-03-28 / Capes / A petrofísica computacional é uma técnica que vem sendo utilizada cada vez mais na indústria do petróleo para caracterizar reservatórios e simular computacionalmente o seu comportamento físico. Através dessa técnica é possível caracterizar um elevado número de amostras, sob diferentes condições ambientais, em um tempo relativamente curto. Este trabalho propõe um modelo de estimativa de permeabilidade que utiliza parâmetros petrofísicos retirados de imagens de microtomografia de raios x (µCT) e os compara com parâmetros petrofísicos medidos em laboratório. Foi analisado um conjunto de 19 amostras com características deposicionais, diagenéticas e texturais diferentes entre si, pertencentes às bacias do Araripe, Potiguar e Sergipe-Alagoas. Delas, 14 são de calcário, 2 de tufa calcária, 2 de caliche e 1 de dolomito. Em laboratório foi utilizado um permoporosímetro a gás para medir os parâmetros porosidade e permeabilidade. As amostras de µCT foram adquiridas com resolução em torno de 2,0 µm. O conjunto de imagens criado foi tratado no software Avizo Fire e foram extraídos os parâmetros porosidade, permeabilidade, conectividade e diâmetro equivalente de poros. Um modelo estatístico foi estabelecido para predição da permeabilidade a partir dos parâmetros do espaço poroso extraídos das imagens de µCT. Os resultados indicam que a conectividade dos microporos, inferida a partir do cálculo do Número de Euler em imagens 3D, é o parâmetro que exerce maior influência na estimativa da permeabilidade, seguida pela porosidade dos macroporos e pela conectividade dos macroporos. O modelo preditivo proposto apresentou um coeficiente de determinação de 0,994, mostrando-se bastante confiável para o grupo de amostras investigado. / Computational petrophysics is a technique that has been increasingly used in the petroleum industry to characterize reservoirs and to simulate computationally its physical behavior. Through this technique it is possible to characterize a big number of samples, under different environmental conditions, in a relatively short time. This work proposes a model of permeability estimation that uses petrophysical parameters taken from x - ray microtomography images (µCT) and compare them with petrophysical parameters measured in the laboratory. It was analyzed a set of 19 samples with different depositional, diagenetic and textural characteristics, belonging to the Araripe, Potiguar and Sergipe - Alagoas basins. Of these, 14 are limestones, 2 of tufa limestone, 2 of caliche and 1 of dolomite. In the laboratory a gas permoporosimeter was used to measure the porosity and permeability parameters. µCT samples were obtained with a resolution of about 2.0 μm. The set of images created was treated in Avizo Fire software and the porosity, permeability, connectivity and pore diameter parameters were extracted. A statistical model was established to predict permeability from pore space parameters extracted from µCT images. The results indicate that the connectivity of micropores, inferred from the calculation of the Euler Number in 3D images, is the parameter that exerts the greatest influence in the estimation of permeability, followed by the porosity of the macropores and the connectivity of the macropores. The proposed predictive model presented a coefficient of determination of 0.994, being very reliable for the group of samples investigated.

No description available.

No / Age estimations based on conventional multifactorial methods were compared with trends observed in the internal morphology of bones obtained from high-resolution µCT. Specifically, average trabecular thickness and number of trabeculae/mm transect were determined in the non-load-bearing capitate (hand) and the load-bearing navicular (foot). The µCT findings reveal age-related trends but - surprisingly - these correspond only loosely with the ages assigned by conventional ageing methods, and are also not in accordance with what would be predicted from biomechanical considerations: trabeculae tend to be thinner in the (habitually) load-bearing navicular than in the (habitually) non-load-bearing capitate. While the statistically significant correlation between trabecular thickness and number of trabeculae would suggest a compensatory mechanism between these two aspects of microanatomy, they are not correlated with the assigned ages and, importantly, may differ between sexes. Only in females is there an unequivocal trend towards trabecular thickness increase with age. These findings, although unexpected, can be reconciled with recent histological evidence and assumed average activity levels in historical populations. Conversely, changes in trabecular number are less clear-cut and may be due to the lack of very old individuals in the sample. Nevertheless, the trends observed for trabecular thickness, as well as for trabecular number, seem to imply that the higher incidence of osteoporosis in women could be explained from a structural point of view alone.

La caractérisation du micro-endommagement et la compréhension de son rôle dans le métabolisme ou dans la fragilisation osseuse restent des challenges, tout particulièrement en raison de l'absence de techniques de mesures bien adaptées à son étude. Il apparaît donc nécessaire de développer de nouvelles techniques non-invasives pour détecter et suivre l'accumulation de micro-endommagement osseux, en particulier celui qui se manifeste par la présence de microfissures. L'objectif de la thèse est d'évaluer la sensibilité de la spectroscopie ultrasonore non-linéaire (NRUS) à l'accumulation du micro-endommagement osseux. La sensibilité et la reproductibilité de la technique NRUS ont tout d'abord été optimisées. Puis, deux groupes d'échantillons d'os cortical ont été prélevés sur des diaphyses fémorales humaines. Les spécimens du premier groupe ont été endommagés progressivement par fatigue en flexion 4-points. Le second groupe a subi un test de ténacité pour initier et propager de manière contrôlée une fissure unique. Nos résultats montrent que la non-linéarité mesurée des échantillons fatigués et fissurés augmente de manière significative après les étapes de fatigue ou le test de ténacité. De plus, nous observons une corrélation significative entre la variation relative du paramètre non-linéaire et l'augmentation de la densité de petites fissures (évaluée par microtomographie par rayonnement synchrotron). Enfin, le niveau de non-linéarité des spécimens fissurés est significativement corrélé à la longueur totale de la fissure. Ces résultats suggèrent que la technique NRUS optimisée est sensible à l'accumulation du micro-endommagement osseux.

Le succès écologique des organismes dépend principalement de leur phénotype. Une composante important du phénotype est la morphologie fonctionnelle car elle influence la performance d’un organisme donné dans un milieu donné et donc reflète son écologie. Des disparités dans la morphologie fonctionnelle ou dans le développement entre espèces peuvent donc mener à des différences écologiques. Ce projet évalue le rôle des mécanismes de variation morphologique dans la production de différences écologiques entre espèces au sein des poissons hybrides du complexe Chrosomus eos-neogaeus. En utilisant la microtomodensitométrie à rayons X et la morphométrie géométrique 3D, la forme des éléments des mâchoires est décrite pour comparer la variation morphologique et les différences développementales entre les membres du complexe C. eos neogaeus. Les hybrides présentent autant de variation phénotypique que les espèces parentales et présentent des phénotypes nouveaux, dit transgressifs. Les hybrides présentent aussi des différences marquées avec les espèces parentales dans leur allométrie et dans leur intégration phénotypique. Finalement, ceux-ci semblent être plastiques et en mesure de modifier leur phénotype pour occuper plusieurs environnements. L’entièreté de ces résultats suggère que des changements dans le développement des hybrides entraînent une différenciation phénotypique et écologique avec les espèces parentales. / An organism’s success is highly dependent on its phenotype. A major component of the phenotype is functional morphology because of its role in determining performance in a given environment clues as to their ecology. Morphological disparity and developmental differences between species can thus lead to ecological differences. This project assesses the role that mechanisms capable of generating morphological variation have in producing ecological differences between species within the hybrid fishes of the Chrosomus eos-neogaeus complex. Using X-ray based computer-aided micro-tomography and 3D geometric morphometrics, the shape of bones composing the jaws was described to measure morphological variation and developmental differences in the C. eos-neogaeus complex. Chrosomus eos-neogaeus hybrids displayed as much variation as parental species and novel, deemed transgressive, phenotypes. Hybrids were also markedly different from parental species in their patterns of allometric scaling and phenotypic integration. Finally, hybrids appeared to be plastic and able to acclimate to different environments. The results of this study indicate that changes in the development of hybrids could lead to phenotypic and, in turn, ecological differences with parental species.

Des charges cycliques élevées induisent la formation de microfissures dans l'os, déclenchant un processus de remodelage ciblé, mené par les ostéoclastes et suivi par les ostéoblastes, visant à réparer et à prévenir l'accumulation des dommages. L'os de cheval de course est un modèle idéal pour étudier les effets d'une charge de haute intensité, car il est sujet à une accumulation focale de microfissures et à la résorption qui s'ensuit dans les articulations. Les ostéoclastes équins ont rarement été étudiés in vitro. Le volume de résorption des ostéoclastes est considéré comme un paramètre direct de l'activité des ostéoclastes, mais des méthodes indirectes de quantification en 2D de la résorption osseuse sont plus souvent utilisées. L'objectif de cette étude était de développer une méthode précise, à haut débit et assistée par l'apprentissage profond pour quantifier le volume de résorption des ostéoclastes équins dans les images micro tomodensitométrie (µCT) 3D. Des ostéoclastes équins ont été cultivés sur des tranches d'os équins, imagés par μCT avant et après la culture. Le volume, le ratio de forme et la profondeur maximale de chaque événement de résorption ont été mesurés dans les images volumétriques de trois tranches d'os. Un convolution neural network (CNN) a ensuite été entraîné à identifier les événements de résorption sur les images μCT post-culture, puis le modèle a été appliqué à des tranches d'os d'archives (n=21), pour lesquelles l’aire de résorption en 2D, et la concentration du biomarqueur de résorption CTX-I étaient connues. Cela a permis d'obtenir des informations 3D sur la résorption des tranches d’os pour lesquels aucune imagerie n'avait été réalisée avant la mise en culture. La valeur modale du volume, la profondeur maximale et le ratio de forme des événements de résorption discrète étaient respectivement de 2,7*103µm3, 12 µm et 0,18. Le volume de résorption moyen par tranche d'os archivés était de 34155,34*103µm3. Le volume de résorption mesuré par le CNN était en forte corrélation avec les mesures de CTX-I (p <0,001) et d’aire (p <0,001). Cette technique de segmentation des images µCT des coupes osseuses assistée par apprentissage profond pour quantifier le volume de résorption osseuse des ostéoclastes équins permettra des recherches futures plus précises et plus approfondies sur l'activité des ostéoclastes. Par exemple, les effets antirésorptifs de médicaments tels que les corticostéroïdes et les bisphosphonates pourront être étudiés à l'avenir. / High cyclic loads induce the formation of microcracks in bone, initiating a process of targeted remodeling, led by osteoclasts, and followed by osteoblasts, aimed at repairing and preventing accumulation of damage. Racehorse bone is an ideal model for studying the effects of high-intensity loading, as it is subject to focal accumulation of microcracks and subsequent resorption within joints. Equine osteoclasts have rarely been investigated in vitro. The volume of osteoclast resorption is considered a direct parameter of osteoclast activity, but indirect 2D quantification methods are used more often. The objective of this study was to develop an accurate, high-throughput, deep learning-aided method to quantify equine osteoclast resorption volume in µCT 3D images. Equine osteoclasts were cultured on equine bone slices, imaged with μCT pre- and post-culture. Volume, aspect ratio (shape factor) and maximum depth of each resorption event were measured in volumetric images of three bone slices. A convolutional neural network (U-Net-like) was then trained to identify resorption events on post-culture μCT images and then the network was applied to archival bone slices (n=21), for which the area of resorption in 2D, and the concentration of a resorption biomarker CTX-I were known. This unlocked the 3D information on resorption for bone slices where no pre-culture imaging was done. The modal volume, maximum depth, and aspect ratio of discrete resorption events were 2.7*103µm3, 12 µm and 0.18 respectively. The mean resorption volume per bone slice on achieved bone samples was 34155.34*103µm3. The CNN-labeled resorption volume correlated strongly with both CTX-I (p <0.001) and area measurements (p <0.001). This technique of deep learning-aided feature segmentation of µCT images of bone slices for quantifying equine osteoclast bone resorption volume allows for more accurate and extensive future investigations on osteoclast activity. For example, the antiresorptive effects of medications like corticosteroids and bisphosphonates can be investigated in the future.

Osteoporose und gestörte Heilungsverläufe von Knochenbrüchen verursachen immer noch beachtliche klinische Komplikationen. Ein vielversprechender Ansatz für die nichtinvasive und nichtionisierende Abschätzung des Frakturrisikos und der Bildgebung von Frakturheilung ist quantitativer Ultraschall (QUS). Dennoch liegt die derzeitige Akzeptanz für die Knochenqualitätsabschätzung noch weit hinter herkömmlichen röntgenbasierten Anwendungen. Es wurden akustische Mikroskopie und Synchrotronstrahlen-Mikrotomographie für die Anatomie und altersabhängige Erfassung von strukturellen und elastischen Variationen auf der mikroskopischen Ebene von humanen Femora verwendet. Die gewonnenen Daten dienten als Grundlage für die Erstellung mikromechanischer Modelle von Knochen für numerische Simulationen der Schallausbreitung im humanen Femurhals. Dabei wurde der Aufbau eines US-basierten Femur-Scanners in transversaler Transmission (TT) nachempfunden. Im letzten Abschnitt der Arbeit wurde QUS in TT in in vitro Experimenten am Rattenfrakturmodell auf eine Anwendung für die Bildgebung der Frakturheilung getestet. Die Studien konnten zeigen, dass ein Großteil der adaptiven Fähigkeiten von Knochen auf mikroskopischer Ebene auf eine Kombination von extrazellulärer Matrixelastizität und Gewebeporosität zurückzuführen ist. Die Simulationen des zweiten Teils konnten die Existenz von geführten Wellen im humanen Femurhals bestätigen. Die sensitive Abhängigkeit von US-parametern von frakturrelevanten Knocheneigenschaften zeigt das hohe Potential von QUS für die Frakturrisikoabschätzung. Der zweite Teil der Arbeit konnte erfolgreich die Möglichkeit von QUS in TT zur Diskriminierung von zeitigen Heilungsstadien demonstrieren. Zusammenfassend bestätigt die Studie das hohe Potential von QUS für die Frakturrisikoabschätzung und die Bildgebung der Frakturheilung. / Osteoporosis and impaired bone healing are of high relevance. A promising non-invasive, non-ionizing candidate for fracture risk prediction and monitoring fracture healing is quantitative ultrasound (QUS). However, the acceptance of QUS for bone quality assessment is still not comparable to X-ray based methods. Scanning acoustic microscopy (SAM) and Synchrotron Radiation micro-computer tomography (SRµCT) has been used to investigate anatomical and age dependent variations of micro elastic, structural and mineralization parameters at the tissue level of human femoral bone. Femoral neck models were created based on these data for numerical sound propagation simulations emulating a transverse transmission (TT) setup of an in vivo QUS prototype. In the last part of the project the TT approach has been tested in ex vivo experiments in a rat healing model. The power of QUS, to discriminate two early healing stages has been compared to µCT measurements at the same specimens. It was found that the major contributor to bone adaptation is related to a combination of extracellular matrix elasticity and tissue porosity. It is hypothesized that these parameters are likely to have a considerable impact on the reliability of in silico models. The simulations of the second part confirmed the existence of guided wave propagation in the cortical shell and a high dependency of US parameters on fracture relevant bone properties. The results demonstrate the high potential for bone fracture risk prediction at the femoral neck using QUS. Finally, it was successfully demonstrated that early healing stage discrimination of QUS in TT was superior compared to µCT. In summary these investigations not only show the importance for a precise estimation of micro mechanical properties for numerical modelling but also demonstrate the feasibility and high potential of QUS for bone quality assessment and monitoring of fracture healing.

This thesis presents how a non-destructive method allows for analysis of archeological material, using three Neolithic anthropomorphic figurines attributed to the Pitted Ware Culture. Anthropomorphic figurines from this period are rare in Sweden and traditional destructive methods, such as thin section petrography is therefore not an option. Using µCT – Micro-Computed tomography as an archaeological method, information can be produced regarding the ceramic composition, forming technique and ornamentation of these figurines. Furthermore, this thesis shows how new advancements in computer imaging technology, such as 3D volume rendering of µCT-data, allows for the reconstruction of organic inclusions.

Im Rahmen der vorliegenden Dissertationsschrift „Semi-quantitative röntgentomographische Untersuchungen zur Biodistribution von magnetischen Nanopartikeln in biologischem Gewebe“ wurden tomographische Untersuchungen an biologischen Objekten durchgeführt. Bei diesen Objekten handelt es sich um Gewebeproben nach minimal-invasiven Krebstherapien wie zum Beispiel magnetischem Drug Targeting und magnetischer Wärmebehandlung. Der Erfolg dieser Therapien ist sowohl abhängig von der korrekten Verteilung der magnetischen Nanopartikel als auch von der Tatsache, dass diese in der Zielregion in einer ausreichenden Menge vorhanden sind. Das Vorliegen dieser beiden Voraussetzungen ist in der vorliegenden Arbeit untersucht worden. Dabei lag der Schwerpunkt der Arbeit auf der Quantifizierung von magnetischem Material in unterschiedlichen biologischen Gewebeproben mittels Röntgenmikrocomputertomographie (XµCT). Für diesen Zweck wurde ein Kalibrationssystem mit speziellen Phantomen entwickelt, mit dessen Hilfe eine Nanopartikelkonzentration einem Grauwert voxelweise zugewiesen werden kann. Mit Hilfe der Kalibration kann der Nanopartikelgehalt sowohl in monochromatischen als auch in polychromatischen tomographischen Daten im Vergleich zu magnetorelaxometrischen Ergebnissen mit wenigen Prozent Abweichung ermittelt werden. Trotz Polychromasie und damit einhergehenden Artefakten können 3-dimensionale röntgentomographische Datensätze mit einer geringfügigen Konzentrationsabweichung im Vergleich zur quantitativen Messmethode Magnetorelaxometrie semi-quantitativ ausgewertet werden. / The success of the minimal invasive cancer therapies, called magnetic drug targeting and magnetic heating treatment, depends strongly on the correct distribution of the magnetic nanoparticles on one side. On the other side it depends on the fact that a sufficient amount of magnetic nanoparticles carrying drugs is accumulated in the target region. To study whether these two requirements are fulfilled motivates this PhD thesis „Semi-quantitative X-ray-tomography examinations of biodistribution of magnetic nanoparticles in biological tissues“. The analysis of the distribution of the magnetic nanoparticles in tumours and other tissue examples is realized by means of X-ray-micro computer tomography (XμCT). The work focuses on the quantification of the magnetic nanoparticles in different biological tissue samples by means of XµCT. A calibration of the tomographic devices with adequate phantoms, developed in the frame of this work, opens now the possibility to analyze tomographic data in a semi-quantitative manner. Thus, the nanoparticle concentration can be allocated voxel-wise to the grey values of the three-dimensional tomographic data. With the help of calibration of the tomography equipments used, polychromatic as well as monochromatic three-dimensional representations of objects can be analyzed with regard to the biodistribution of magnetic nanoparticles as well as with regard to their quantity. The semi-quantitative results have been compared with results obtained with a quantitative measurement method magnetorelaxometry (MRX). Thereby a good agreement of the semi-quantitative and quantitative data has been figured out.