Current oil production technologies recover only about one‐third to one‐half of the oil originally present in an oil reservoir. Given current oil prices, even a modest increase in oil recovery efficiency is fiscally attractive. One novel approach to increase oil recovery efficiency is a process called microbial enhanced oil recovery (MEOR), where microorganisms are either used as a clogging agent to redirect flow or to produce biosurfactant that reduces interfacial tension. This dissertation aims to understand the MEOR pore‐scale mechanisms relevant to oil recovery by taking a two‐fold approach where transparent 2‐dimensional micromodel experiments imaged with stereo microscopy and 3‐dimensional column experiments imaged with x‐ray computed microtomography (CMT) are utilized. Micromodel experiments allow for direct visualization of the biological phase (i.e. biofilm), however, only 2‐dimensional information is provided. Conversely, CMT experiments provide 3‐dimensional pore‐scale information, but lack the ability to image the biological phase. With this two‐fold approach, it is possible to distinguish multiple fluid interfaces, quantify fluid phase saturations, measure oil blob size distributions, and visualize the biological phase. Furthermore, a method to measure interfacial curvature from 3‐dimensional images is developed, providing researchers a new perspective from which to study multiphase flow experiments. Overall, the presented research utilizes pore‐scale imaging techniques to study the interfacial interactions occurring during MEOR in an effort to better explain the physics, and thus, increase the efficacy of MEOR. / Graduation date: 2012

Rentgenová počítačová mikrotomografie (CT) je metoda pro trojrozměrné (3D) zobrazování vnitřní struktury objektů. Laboratoř rentgenové počítačové mikro a nanotomografie na CEITEC VUT (Středoevropský technologický institut, Vysoké učení technické v Brně) se zaměřuje zejména na nedestruktivní analýzu v průmyslovém odvětví. Ukázalo se ale, že tato metoda nachází široké uplatnění i v dalších vědeckých oblastech včetně vývojové biologie. Tato práce poskytuje propojení mezi materiálovými a živými vědami. Kompletní proces vedoucí k vytvoření 3D modelu různých anatomických struktur je detailně popsán. Tento postup zahrnuje kontrastování vzorků, samotné CT měření a analýzu dat. Právě zpracování dat je mnohdy považováno za nejdůležitější část v rentgenové počítačové tomografii a proto je této oblasti věnována v práci největší část. Úpravou měřicích parametrů byl dále optimalizován CT přístroj GE v|tome|x L 240 za účelem umožnění automatické segmentace. Navíc je diskutována možnost měření na synchrotronu za účelem zvýšení prostorového rozlišení a diferenciálního kontrastu. Předpokládá se, že v blízké budoucnosti získají průmyslové CT přístroje podobné zobrazovací vlastnosti, a to jak díky nedávnému vývoji v oblasti hardwaru, tak v oblasti zpracování dat.

The study of internal structure of materials has always been an essential issue in a variety of application fields, from the medical radiology to the materials science. X-ray computed microtomography (with both conventional and synchrotron radiation sources) has a great potential for these purposes because its three-dimensional and non destructive nature as well as the fact that it does not require any sample preparation and it allows to study samples under stress or after consecutive treatments. The recent developments of new X-ray sources with innovative imaging techniques, as well as novel high resolution detectors, allow moving forward the maximum achievable resolution of this technique to a few micrometers or even less. This contributed to increase its application in biomedical purposes, but also to raise the need for quantitative analysis of the reconstructed data. Indeed in most of the cases a quantitative characterization of the samples microstructures is needed to better understand their physical and chemical behavior, the effects of manufacturing process or the response to stress. Dedicated software packages have been developed to perform a geometrical and morphological characterization of the samples texture and to evaluate some typical parameters commonly used to classify porous media such as porosity, cell size distribution, connectivity and anisotropy. In this work two case studies have been considered for the application of a quantitative analysis approach to microtomography datasets: the first concerns the characterization of bone ingrowth within tissue engineering scaffolds, while the second is related to the extraction of morphological descriptors for the architecture of human skull bones. It will be shown how suitable image processing and analysis techniques are able to effectively quantify significant parameters such as the trabecular thickness of the skull bones as well as the porosity and the degree of connectivity of bone tissue engineering scaffolds. Similar quantitative analysis methods applied to microtomography images have to be considered as an effective methodology for a comprehensive characterization of other biomedical samples.

This work deals with processing and analysis of micro-CT images of dental-canals filled by~two materials (AH-plus and NaMPC). For that reason, six dog-teeth were scanned in the X-Ray Micro CT Research Lab. The main aim was to produce an algorithm (in Matlab) that evaluates the quality of filling of dental canals (quality of filling materials). The algorithm performs the segmentation of dental canals and calculates their borders. Also, the algorithm measures the percentage contacts of filling materials with dental walls. Moreover, the algorithm provides masks of dental canals according to requirements of the commercial program VG Studio, that evaluates the porosity of filling materials. The results of percentage contacts and porosities show on not-remarkable differences of tested filling materials.

A microtomografia computadorizada (computed microtomography - μCT) permite uma análise não destrutiva de amostras, além de possibilitar sua reutilização. A μCT permite também a reconstrução de objetos tridimensionais a partir de suas seções transversais que são obtidas interceptando a amostra através de planos paralelos. Equipamentos de μCT oferecem ao usuário diversas opções de configurações que alteram a qualidade das imagens obtidas afetando, dessa forma, o resultado esperado. Nesta tese foi realizada a caracterização e análise de imagens de μCT geradas pelo microtomógrafo SkyScan1174 Compact Micro-CT. A base desta caracterização é o processamento de imagens. Foram aplicadas técnicas de realce (brilho, saturação, equalização do histograma e filtro de mediana) nas imagens originais gerando novas imagens e em seguida a quantificação de ambos os conjuntos, utilizando descritores de textura (probabilidade máxima, momento de diferença, momento inverso de diferença, entropia e uniformidade). Os resultados mostram que, comparadas às originais, as imagens que passaram por técnicas de realce apresentaram melhoras quando gerados seus modelos tridimensionais. / X-ray Computed Microtomography (μCT) allows a non destructive analysis of samples besides making it possible to reuse them. μCT also allows the reconstruction of tridimensional objects from its transverse sections obtained intersecting the sample through parallel planes. μCT devices offer the user several configuration options which alter the quality of the images obtained affecting, this way, the results expected. In this study, the characterization and analysis of μCT images generated by the X-ray tomograph scannerSkyScan1174 Compact Micro-CT was performed. The basis of this characterization is the processing of images. Enhancement techniques were applied (brightness, saturation, histogram equalization and median filter) in the original images creating new images. Next, the quantification of both sets was performed, using texture descriptors (maximum likelihood, moment of difference, inverse difference moment , entropy and uniformity). The results show that, compared to the originals, the images which went through enhancement techniques had improved when their three-dimensional models were generated.

A microtomografia computadorizada (computed microtomography - μCT) permite uma análise não destrutiva de amostras, além de possibilitar sua reutilização. A μCT permite também a reconstrução de objetos tridimensionais a partir de suas seções transversais que são obtidas interceptando a amostra através de planos paralelos. Equipamentos de μCT oferecem ao usuário diversas opções de configurações que alteram a qualidade das imagens obtidas afetando, dessa forma, o resultado esperado. Nesta tese foi realizada a caracterização e análise de imagens de μCT geradas pelo microtomógrafo SkyScan1174 Compact Micro-CT. A base desta caracterização é o processamento de imagens. Foram aplicadas técnicas de realce (brilho, saturação, equalização do histograma e filtro de mediana) nas imagens originais gerando novas imagens e em seguida a quantificação de ambos os conjuntos, utilizando descritores de textura (probabilidade máxima, momento de diferença, momento inverso de diferença, entropia e uniformidade). Os resultados mostram que, comparadas às originais, as imagens que passaram por técnicas de realce apresentaram melhoras quando gerados seus modelos tridimensionais. / X-ray Computed Microtomography (μCT) allows a non destructive analysis of samples besides making it possible to reuse them. μCT also allows the reconstruction of tridimensional objects from its transverse sections obtained intersecting the sample through parallel planes. μCT devices offer the user several configuration options which alter the quality of the images obtained affecting, this way, the results expected. In this study, the characterization and analysis of μCT images generated by the X-ray tomograph scannerSkyScan1174 Compact Micro-CT was performed. The basis of this characterization is the processing of images. Enhancement techniques were applied (brightness, saturation, histogram equalization and median filter) in the original images creating new images. Next, the quantification of both sets was performed, using texture descriptors (maximum likelihood, moment of difference, inverse difference moment , entropy and uniformity). The results show that, compared to the originals, the images which went through enhancement techniques had improved when their three-dimensional models were generated.

Submitted by Eunice Novais (enovais@uepg.br) on 2018-06-28T19:18:21Z No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Talita Rosas Ferreira.pdf: 3918159 bytes, checksum: 3af8401f079b1540a49f10a3f6fd3b2d (MD5) / Made available in DSpace on 2018-06-28T19:18:21Z (GMT). No. of bitstreams: 2 license_rdf: 811 bytes, checksum: e39d27027a6cc9cb039ad269a5db8e34 (MD5) Talita Rosas Ferreira.pdf: 3918159 bytes, checksum: 3af8401f079b1540a49f10a3f6fd3b2d (MD5) Previous issue date: 2018-04-23 / No presente estudo, foram investigados os efeitos da calagem superficial sobre: os atributos químicos, as propriedades de interação com a radiação e a estrutura (sistema poroso) de um Cambissolo Háplico alumínico. A estrutura do solo foi analisada em escala micrométrica, considerando monólitos (8×8×8 cm) e pequenos agregados do solo (2-4 e 1-2 mm de diâmetro). O experimento consistia de cinco faixas, uma delas em área de pasto, considerada como referência (REF) e representando as condições do solo antes da implementação do sistema de plantio direto (SPD), e as demais, sob SPD, receberam as seguintes doses de calcário: 0 (C0), 10 (C10), 15 (C15) e 20 (C20) t ha-1 aplicadas na superfície do solo. A coleta das amostras se deu aos trinta meses após o procedimento de calagem, nas camadas 0-10 cm (A) e 10-20 cm (B). Os atributos químicos do solo foram caracterizados de acordo com procedimentos experimentais padrões e a composição de óxidos do solo, obtida por meio de análise de espectroscopia de fluorescência de raios X (FRX), foi usada para o cálculo do coeficiente de atenuação de massa do solo (μm), por meio do código computacional XCOM, para as energias de ≈ 60 keV (241Am) e ≈ 662 keV (137Cs). Os valores de μm foram utilizados para calcular as demais propriedades de interação da radiação com o solo e para simular as variações causadas na densidade (D) e porosidade total (Pt) do solo. Para a análise da estrutura do solo, foram utilizadas imagens 3D de microtomografia computadorizada de raios X (μTC), com resolução espacial de 60 μm (monólitos), e de μTC utilizando radiação síncrotron (μTC-RS), com resolução espacial de 1,64 μm (agregados). A visualização, processamento e análise das imagens foram realizadas com o software Avizo Fire. Foram determinadas as seguintes propriedades micromorfológicas e geométricas: porosidade baseada na imagem (P’), número de poros (NP), distribuições de P’ e NP em função de intervalos de volume, comprimento, alongamento, formato, conectividade e tortuosidade dos poros (monólitos); e: P’, distribuições de P’ e NP em função de intervalos de volume, conectividade, tortuosidade e dimensão fractal (agregados). Complementarmente, a composição elementar dos agregados do solo foi avaliada por meio de medidas de FRX. Na maioria dos casos, os efeitos da calagem concentraram-se na camada A, onde houve melhora nos atributos químicos e, portanto, no grau de acidez do solo, bem como houve aumento nas propriedades de interação da radiação em função das doses de calcário. O aumento nas propriedades de interação da radiação foi mais acentuado para a energia de ≈ 60 keV em relação a ≈ 662 keV e, no primeiro caso, as mudanças causadas em μm promoveram variação considerável na D e Pt do solo, demonstrando a relevância do estudo. A exemplo dos efeitos da calagem sobre o sistema poroso de monólitos do solo, na camada A, ressalta-se o aumento de P’ e do número de poros em que o poro principal foi separado, os quais foram identificados como sendo mais alongados e mais conectados devido à calagem. A calagem promoveu ainda alterações no arranjo dos poros separados, em ambas as camadas, com a formação de poros cilíndricos na direção horizontal, o que pode ser atribuído ao estímulo da atividade da fauna do solo. Para os agregados de solo, na camada A, a porcentagem de cálcio foi elevada a um valor mais alto em agregados de 1-2 mm em comparação com aqueles de 2-4 mm, em função das doses de calcário. A calagem afetou negativamente a estrutura de pequenos agregados do solo, diminuindo a P’ e aumentando a tortuosidade de poros para agregados de 1-2 mm. Além disso, a calagem reduziu a dimensão fractal em agregados de ambas as classes de tamanhos, em acordo com o fato de que, com a calagem, poros maiores foram substituídos por poros menores em agregados de 1-2 mm, conforme análises de natureza quantitativa e qualitativa. / In the present study, effects of surface liming on: chemical attributes, soil-radiation interaction properties and the structure (porous system) of a Dystrudept soil were investigated. The soil structure was analyzed in micrometric scale, considering monoliths (8×8×8 cm) and tiny aggregates (2-4 and 1-2 mm in diameter). The trial consisted of five stripes, one of them under pasture, considered here as reference (REF), representing the soil conditions before the no-till system (NTS) implementation, and the remaining, under NTS, received the following lime rates: 0 (C0), 10 (C10), 15 (C15) and 20 (C20) t ha-1 on the soil surface. Samples were collected thirty months after the liming procedure, at the 0-10 cm (A) and 10-20 cm (B) soil layers. The soil chemical attributes were characterized according to standard experimental procedures and the soil oxide composition, obtained by X-ray fluorescence spectroscopy (XRF), was used for the calculation of the soil mass attenuation coefficient (μm), by means of the computer code XCOM, for the energies of ≈ 60 keV (241Am) amd ≈ 662 keV (137Cs). The μm values were used to calculate the remaining soil-radiation interaction properties and to simulate variations caused on soil density (D) and total porosity (Pt). For the soil structure analysis, 3D images of X-ray computed microtomography (μCT), with spatial resolution of 60 μm (monoliths), and 3D images of synchrotron radiation based X-ray computed microtomography (SR-μCT), with spatial resolution of 1,64 μm (aggregates) were used. The image visualization, processing and analysis were performed in the Avizo Fire software. The following micromorphological and geometrical properties were determined: image-based porosity (P’), number of pores (NP), distributions of P’ and NP as function of volume intervals, length, elongation, shape, connectivity, and tortuosity of pores (monoliths); and: P’, distributions of P’ and NP as function of volume intervals, connectivity, tortuosity, and fractal dimension (aggregates). Additionally, the elemental composition of the soil aggregates was evaluated by XRF. In the majority of cases, liming effects were concentrated at layer A, where there was an improvement of soil chemical attributes and, therefore, of soil acidity level, as well as there was an increase in the soil-radiation interaction properties as function of lime rates. The increase in soil-radiation interaction properties was more accentuated for the energy of ≈ 60 keV in relation to ≈ 662 keV and, in the former case, the μm variation promoted considerable variation in D and Pt, demonstrating the relevance of the study. Highlighted instances of liming effects on the porous system of the soil monoliths, at layer A, were an increase in P’ and in the number of pores into which the main soil pore was separated, which were identified as being longer and more connected due to liming. Moreover, liming promoted changes in the arrangement of the separated pores, at both soil layers, with the formation of cylindrical pores in the horizontal orientation, which can be attributed to stimulation of the soil fauna activity. Regarding the soil aggregates, at layer A, calcium was raised to a higher percentage in aggregates of 1-2 mm when compared to those of 2-4 mm, as function of the lime rates. Liming affected negatively the structure of the soil tiny aggregates, decreasing P’ and increasing the tortuosity of pores for 1-2 mm aggregates. Besides, liming decreased the fractal dimension in aggregates from both size classes, in accord to the fact that, with liming, larger pores were replaced by smaller ones in 1-2 mm aggregates, as both quantitatively and qualitatively analyzed.