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X-ray computed tomography of mouse embryo
Šejnohová, Marie ; Walek, Petr (referee) ; Kolář, Radim (advisor)
The aim of this semestral thesis is to compare the possibilities of available micro-CT systems. Theoretic part of this thesis there deals with possibilities of staining soft tissues and embryos because of enhancement the contrast of micro-CT images. Here follows a description of sources X-ray and detectors of available micro-CT systems. In practice there was realized the staining of embryo in cooperation with Department of histology and embryology in Brno. Then followed a measuring on FSI in Brno, ČVUT in Prague and synchrotron Elettra in Italy. In semestral thesis are described of the thesis there are compared the micro-CT systems and results of measuring embryos by means of presented systems and results are compared.The best results were obtained on micro-CT in Brno, where X-ray tube and flat panel detector were used. This images were used for a segmentation of cartilage olfactory system by means of 3D region growing. From results they were created 3D models for comparison with a manually segmented model. A less accurate results were obtain with the semi-automatic segmentation but this method isn’t too time-consuming.
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Computational simulation of the compression test of the open cell metal foam
Homola, Václav ; Skalka, Petr (referee) ; Ševeček, Oldřich (advisor)
The thesis presents computational simulation of compression test of a nickel foam and the 3D reconstruction of micro-CT images was utilized to generate the foam’s model of geometry. Explicit FEM is used to simulate compression test using software tool LS-DYNA and the stress–deformation curve is obtained together with deformed model’s mesh used for subsequent analysis. Sensitivity analyses were performed to configure the model and ensure best fit with values obtained during real-life experiment. The ANSYS Classic environment was then used to simulate tensile test of the foam compressed to various thicknesses. The tensile moduli in three mutually perpendicular directions of nickel foam were computed and the results were compared to experimental values as well. The results of tensile test simulation revealed considerable anisotropy of the foam’s elastic behavior. It can be said that the measured experimental data correspond very well with the elastic properties obtained from simulation up to certain level of compression. Analysis of the relationship between the element size and tensile moduli showed a significant difference between fine and coarse mesh. The optimal level of discretization and the overall model configuration ensuring high level of accuracy is proposed in this thesis.
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Segmentation and morphological analysis of mouse embryo choroid plexus
Parobková, Viktória ; Jakubíček, Roman (referee) ; Chmelík, Jiří (advisor)
Choroidálny plexus je regulovanou bránou medzi krvou a mozgovomiechovým mokom a má niekoľko funkcií spojených s nervovým systémom. Mnohé funkcie sú však stále neznáme, čo je spôsobené krehkosťou, umiestnením a tvarom plexu. Preto sa na prístup k tejto kľúčovej súčasti mozgu, ktorá sa nachádza v komorách, používajú neinvazívne techniky. Okrem toho existuje súvislosť medzi jeho tvarom a patologickými stavmi mozgu. Cieľom tohto projektu bolo extrahovať ChP 4. komory implementáciou segmentačných metód a následnou morfologickou analýzou s cieľom odhaliť zákonitosti medzi tvarom a ochorením.
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Blood vessel tree segmentation of the mouse liver in CT data
Smékalová, Veronika ; Odstrčilík, Jan (referee) ; Kolář, Radim (advisor)
The methodology of visualization of soft tissue is in biology and medicine a topic for many years. During this period there were approving many techniques how to achieve accurate and authentic image of the researched object or structure. X-ray computed tomography is very helpful to get this goal but is necessary to improve contrasting techniques as well as the techniques of image post-processing. This thesis deals with imaging soft tissue. Specifically, it focuses on mouse liver contrasting with the artificial resin Microfil. Thesis also describes image processing technique (thresholding and region growing) for the data of the measurement with the goal of the visualization of the sample in 3D.
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Estimation of mechanical properties of the cancellous bone tissue of the proximal tibia
Leinweber, Vít ; Valášek, Jiří (referee) ; Marcián, Petr (advisor)
This bachelor thesis is focused on the determination of mechanical properties of cancellous bone tissue of proximal tibia. In the beginning of the work there is theoretical part which consists of a description of the tibia anatomy from macroscopic and microscopic view, treatise on the bone tissue growth, influences affecting the bone tissue growth and description of mechanical properties of the bone tissue. In the end of the theoretical part there is a detailed review of related literature to this work. In the practical part morphometric parameters are measured using software ImageJ and plugin BoneJ. The process of creating a computational model is described and results of mechanical properties are presented. Regression models of mechanical properties and histomorphometric parameters are created from these results.
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The effect of the growth and development of the endosteal surface on the estimation of cross-sectional properties
Königová, Viktória ; Sládek, Vladimír (advisor) ; Friedl, Lukáš (referee)
Past studies concerning deriving periosteal and endosteal contours from micro-CT scans of non-adult long bones found the greatest error to stem from the automatic processing of the endosteal contours. Furthermore, with increasing age, a decrease in the estimation error of the cross-sectional properties was observed. This study aims to identify the specific source of the estimation error and to optimize the use of the automatic method of deriving endosteal contours. Four parameters (circularity, solidity, roundness, and aspect ratio) were used to quantify the shape properties of the endosteal contour. These parameters were tested on 91 individuals from birth to early adulthood. As for the ontogenic changes in the endosteal contour, a continuous decrease in the jaggedness of the endosteal contour had been observed, mainly based on the changes in the circularity. Circularity was chosen as the parameter upon which the criteria of use of the automatic method of deriving the endosteal contour was based. The criterium is based on the prediction of whether the customary threshold of 5 % percent prediction error would be surpassed while using the automatic method at a certain level of circularity. Applying the criteria of the minimum threshold of circularity (0,83 for MA, 0,71 for CA, and 0,7 for ZP) will...
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Segmentation and morphological analysis of mouse embryo choroid plexus
Parobková, Viktória ; Jakubíček, Roman (referee) ; Chmelík, Jiří (advisor)
Choroidálny plexus je regulovanou bránou medzi krvou a mozgovomiechovým mokom a má niekoľko funkcií spojených s nervovým systémom. Mnohé funkcie sú však stále neznáme, čo je spôsobené krehkosťou, umiestnením a tvarom plexu. Preto sa na prístup k tejto kľúčovej súčasti mozgu, ktorá sa nachádza v komorách, používajú neinvazívne techniky. Okrem toho existuje súvislosť medzi jeho tvarom a patologickými stavmi mozgu. Cieľom tohto projektu bolo extrahovať ChP 4. komory implementáciou segmentačných metód a následnou morfologickou analýzou s cieľom odhaliť zákonitosti medzi tvarom a ochorením.
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Morphology of the Abdominal Aortic Aneurysm
Eberlová, Lada ; Valenta, Jiří (advisor) ; Stingl, Josef (referee) ; Šebesta, Pavel (referee)
Dissertation Abstract Abdominalaortic aneurysm (AAA) is a serious disease. Its prevalence is in the developed countries about 3%. As an aneurysm is considered a dilatation of all layers of a vessel wall over 3 cm. Majority of AAA are small and asymptomatic, and although the risk of rupture increases with the size of aneurysm sack, even the small aneurysms rupture. The rupture mortaliry ranges about 70 %. Surgical treatment is indicated in the asymptomatic patients in diameter of AAA over 5 cm. The average speed of growth of AAA is 0.3 cm per year, e.g. in the early diagnosed patients there is a several years interval for a pharmacolocical influencing of the progression of this disease. Knowledge of pathogenesis is essential for any targeted pharmacological treatment. Our prospective, non-randomised studies are based on the application of the stereological methods for the histopathological assessment of the AAA samples. The acquired data enable the statistical analysis, including the null hypothesis testing. In our study analyzing the histopathology of AAA aortae of 65 patients (65 walls and 55 thrombi) and 6 normal abdominal aortae from the organ donors we assessed the following parameters: the area fractions of collagen and elastin, and the length density of elastin in intima and media, the area...
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Estimation of mechanical properties of the cancellous bone tissue of the proximal tibia
Leinweber, Vít ; Valášek, Jiří (referee) ; Marcián, Petr (advisor)
This bachelor thesis is focused on the determination of mechanical properties of cancellous bone tissue of proximal tibia. In the beginning of the work there is theoretical part which consists of a description of the tibia anatomy from macroscopic and microscopic view, treatise on the bone tissue growth, influences affecting the bone tissue growth and description of mechanical properties of the bone tissue. In the end of the theoretical part there is a detailed review of related literature to this work. In the practical part morphometric parameters are measured using software ImageJ and plugin BoneJ. The process of creating a computational model is described and results of mechanical properties are presented. Regression models of mechanical properties and histomorphometric parameters are created from these results.
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