At the School of Technology and Health (STH) on KTH, a micro- CT is beeing build. The micro-CT-system need to be aligned in order to function correctly. The purpose of this bachelor thesis was to create an application that, from the micro-CT images, could calculate all the necessary parameters to make the alignment pos- sible. During the projekt, LabView-code for aligning a micro-CT system has been modified to being compatible with the micro-CT at the School of Technology and Health (STH) on KTH. The code has also partly been translated into the open-source and platform independent programming language Java. Due to delays in building the micro-CT at STH, neither the LabView- or Javacode could be validated with it. However, successful attempts have been made with images from another micro-CT and on simulated images of a phantom in a micro-CT.

Different tracing techniques of the subperiosteal and endosteal contours (manual, automatic, semi-automatic) or their combinations taken along femoral length in adult individuals can produce different values of cross-sectional geometric (CSG) parameters. Various tracing techniques are widely used in CSG studies of non-adult individuals as well, however, the accuracy of CSG parameters estimated along femoral diaphysis is not yet known for non-adult individuals. In this study, we investigate whether the manual tracing of the subperiosteal and endosteal contours taken at 80% of the femoral diaphyseal length in non-adult individuals can be replaced by another type of tracing in relation to CSG parameters estimation. We examine the effect of anatomical localization on accuracy of the CSG parameters estimated in non-adult individuals femora. We digitized the subperiosteal and endosteal contours in the micro-CT scans from femoral diaphyseal cross-sections in Early Medieval sample of non-adult individuals (N = 46). The digitization and computation of CSG parameters were made in Fiji software with EPJMacro implementation. The assessment of estimates' accuracy was expressed by percentage prediction error (%PE) and limits of agreement. Five percent of CSG parameter obtained from manually traced contours was...

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På CBH (Skolan för kemi, bioteknologi och hälsa) har en mikro-CT utvecklats, men med förbättringspotential gällande användbarheten. Målet med kandidatexamensarbetet var att förbättra mjukvaran genom att automatisera tre olika aspekter av manuell datahantering: Dels att placera filerna i en mapp med namn kopplat till valda bildtagningsinställningar. Dels att kopiera data via SCP mellan två datorer kopplade till mikro-CT:n. Samt att radera kopierade data från disken som preliminärt sparar filerna. För att möjliggöra en automatisk dataöverföring implementerades ett SSH-nyckelpar med publik nyckelautentisering mellan de två datorerna. Till den befintliga mjukvaran tillades ett skript samt en klass med handhavande över de tre automatiseringsaspekterna. Genom användargränssnittet hämtar klassen inledningsvis information om bildtagningsinställningarna till mappnamnet och när bildtagningen är klar anropar programkoden skriptfilen som utför SCP-kopieringen. Därefter kontrolleras att inga data gått förlorade under överföringen, varefter en radering av de kopierade filerna utförs på den ursprungliga disken. Den nya klassen förbättrar mikro-CT:ns användarvänlighet och underlättar hanteringen av data efter en bildtagning. / At CBH (The School of Engineering Sciences in Chemistry, Biotechnology and Health) a micro-CT has been developed, but the system has potential improvement regarding the usability. The purpose of this bachelor’s thesis was to improve the software by automatizing three aspects of manual data handling: Firstly to place the data in a folder with a name related to the obtained acquisition settings. Secondly to transfer files through SCP between the two computers connected to the micro-CT. Lastly to delete the copied data from the disk that initially saves the files. In order to automate the data transfer an SSH key pair with public key authentication was implemented between the two computers. To the existing software a script as well as a class controlling the three automation aspects were added. From the user interface, the class initially retrieves information about the acquisition settings to the folder name and when the acquisition is complete, the program code calls the script file that performs the SCP transfer. Afterwards a verification is made that no data was lost during the transfer, after which a deletion of the copied files is performed on the original disk. The new class improves the usability of the micro-CT and facilitates the handling of data after an acquisition.

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...

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.

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.

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.

Diplomová práce se zabývá detektory rentgenového záření pro mikro-CT systémy. Teoretická část zahrnuje standartní typy rentgenových detektorů a požadavky na kvalitu obrazu pro výslednou 3D rekonstrukci. V závěru jsou popsány fyzikální parametry reálných detektorů a metody jejich měření a vyhodnocení.

The preclinical imaging method micro-CT (microtomography) allows the visualization and quantification of the structure of samples at a resolution of micrometers. Its' importance is increasing globally. In addition to several advantages (non-destructive, the possibility of direct 3D analysis, time efficiency, etc.), micro-CT also has some significant limitations (problematic validation of results, image artifacts, significant influence of image modifications, etc.). This thesis focuses on the application of micro-CT in the field of research and development of metallic and non-metallic materials promoting bone healing with their possible clinical applications. The first part addresses the limitations of micro-CT through several studies. A comparison of pore sizes in biomaterials utilizing scanning electron microscopy (SEM) and micro-CT was performed, and the complications of pore size evaluation were presented. SEM image analysis leads to significantly higher values than micro-CT (approximately three times), which allows for comparison of the studies using only one of these methods. Validation of micro-CT 3D analysis results based on calibration phantoms with complex structure, to date, is not possible. We therefore developed software generating phantom datasets of 3D objects with well-defined...