Microwave tomography is a classical approach for non destructive evaluation. Microwave tomography has many biomedical applications such as brain imaging, temperature sensing in different biological tissues and breast cancer detection. In a microwave tomography system, numbers of radiators are used to transmit microwave signal into an object under test and the scattered fields are recorded. The collected data is used to quantitatively reconstruct the dielectric profiles of the object under test through inverse scattering mechanism. It has been shown that by using wide band data, highly stable and high resolution reconstructions can be obtained. Lower frequency components provide stability of the reconstructions, while higher frequency components contribute to the resolution.  Accordingly, ultra wideband antennas are required in UWB microwave tomography systems. In addition to ultra wide bandwidth, the antennas in a microwave tomography system should be easy to model with computational program. In this thesis Printed elliptical monopole antenna (PEMA) is investigated for microwave tomography. It is a multi resonant antenna with simple structure and yield ultra wide bandwidth. The performances of a single antenna and an antenna array are studied. The reflection coefficients of the antenna, mutual coupling between antennas and energy distribution in the near field are obtained by means of simulations in CST microwave studio.    The simulation result shows that reflection coefficients of the designed antenna are below         -10dB over the entire frequency band of interest (1-4.5GHz), mutual coupling between antennas at different locations are below -20dB over the entire frequency band of interest and the designed antenna also has good electric field distribution in an array configuration which makes the radiated power concentrating in the imaging region. These results indicate that PEMA is a potential antenna for microwave tomography applications.

The medical imaging system Sectra PACS from Sectra Imtec contains a 3D mode that can be used for visualising image stacks from e.g. computed tomography. Various structures of human anatomy can be visualised in the 3D mode, but visualisations of the bronchial tree of the lungs rarely become good enough to be useful. The goal of this work was to investigate ways of improving such visualisations. Various approaches were studied, evaluated and tested. The fact that most effort was needed for small structures with sizes similar to the resolution of the images made things slightly more complicated. A method classifying neighbourhoods based on local structure emerged as most promising, and was used as foundation for a proposed algorithm. It creates a mask representing the presence of bronchi, allowing the hiding of uninteresting structures in its proximity. The algorithm was then implemented so that it could be tested together with the existing system. The method was found to work well and was able to detect the smaller tubes of the bronchial tree and output the desired classification mask. Its usefulness was somewhat reduced by issues relating to speed, and the fact that many computed tomography image stacks lack the necessary resolution for visualising the finer details of the bronchial tree.

Abstract Both in the closed and open eye state the superior limbus is covered by the upper lid. This region is of physiological interest and clinical importance because in chronic hypoxia, neovascularization of the cornea commonly occurs here. The limbal region in general is additionally of importance as the stem cells which are the source of the new corneal cells are located in the epithelium of the limbus and these are vital for normal functioning and are affected under certain adverse conditions. Purpose: In this experiment I examined corneal morphology in the limbal area and in particular under the upper lid in order to primarily examine the variation in the corneal limbal epithelial and total thickness as well as epithelial and endothelial cell density. Methods: I measured 30 eyes OD/OS (chosen randomly) of thirty healthy subjects aged from 18 to 55 years in the first study and twelve participants in the second study, with refractive error ≤ ±4 D and astigmatism ≤ 2 D. The thickness and cell density of five positions: superior, inferior, temporal, nasal limbal and central cornea was determined with optical coherence tomography (OCT) and confocal microscopy. At least three scans of each position were taken in both studies with OCT. At least 40 of 100 adjacent sagittal scans of each image were measured using OCT software program. In the confocal study, image J software was used to determine cell densities. Results: The epithelial and corneal limbal thickness were significantly thicker than the epithelial and central corneal thickness (p<0.05). The limbal, inferior cornea is thinner than the three other positions and the temporal region of the cornea is the thickest both in epithelial and total cornea. Epithelial cell density was significantly lower in the superior cornea than the four other positions. There was no significant difference in the endothelial cell density. Conclusions: Using OCT with high resolution and cross-sectional imaging capability and confocal microscope with high magnification, I found that the limbal cornea is significantly thicker than the central cornea both in total and in epithelial thickness. In the limbus, one might expect the superior cornea (under the lid) to be thickest (because of the expected hypoxia) whereas I found the temporal cornea was thickest. The epithelial cell density was lower in the superior cornea but there was no significant difference in cell densities in the endothelium. Further morphological investigation is of interest.

Laser interference fringe tomography (LIFT) is within the class of optical imaging devices designed for volumetric microscope applications. LIFT is a very simple and cost-effective three-dimensional imaging device which is able to reliably produce low-quality imagery. It measures the reflectivity as a function of depth within a sample and is capable of producing three-dimensional images from optically scattering surfaces. The first generation of this instrument is designed and prototyped for optical microscopy. With an imaging spot size of 42 μm and a 180 μm axial resolution kernel, LIFT is capable of producing one- and two- dimensional images of various samples up to 1.5 mm thickness. The prototype was built using commercial-off-the-shelf components and cost ~ $1,000. It is possible that with effort, this device can become a reliable, stable, low-quality volumetric imaging microscope to be readily available to the consumer market at a very affordable price. This document will present the optical design of LIFT along with the complete mathematical description of the instrument. The design trade-offs and choices of the instrument are discussed in detail and justified. The theoretical imaging capabilities of the instrument are tested and experimentally verified. Finally, some imaging results are presented and discussed.

Larger and stronger muscles are positively associated with bone strength in the growing skeleton; however, less is known about the role of muscle properties on bone strength later in life. The primary objective of this study was to examine the relationship between muscle cross sectional area (MCSA), muscle force and rate of torque development (RTD) with bone strength indices (bone strength index (BSI) and strength strain index (SSI)) in the radius of healthy middle-aged adults. All bone and muscle measurements were determined in the non-dominant forearm in a sample of 40 healthy adults (23 men, 17 women: mean age 49.5, SD 2.3 yrs). Peripheral quantitative computer tomography (pQCT) was used to scan the distal and shaft sites of the radius bone in the forearm. MCSA was determined from the forearm shaft scan. Forearm muscle force was measured by hand grip dynamometry and RTD was obtained from isometric wrist flexion from an isokinetic dynamometry protocol. Hierarchical regression analyses were used to identify whether muscle properties (MCSA, grip force, and RTD) independently predicted radius bone strength indices (BSI and SSI), after adjusting for the confounders of sex, height and weight. Steps of the regression models that included sex, height, weight and a muscle property explained between 66% and 71% of variance in distal radius BSI and between 74% and 78% variance of estimated bone strength (SSI) at the shaft site (all steps p<0.001). MCSA explained a significant amount of variance in BSI (R2=0.08; p<0.01) and SSI (R2=0.04; p<0.05) at the radius. Grip force was also a significant predictor of SSI (R2=0.05; p<0.01) but not distal radius BSI (R2=0.03; p=0.07). Conversely, RTD explained a significant amount of variance in bone strength at the distal radius (R2=0.04; p<0.05), but not at the shaft (R2=0.01; p=0.17). These cross sectional findings support the theory that regional muscle size, force, and rate of torque development are related to estimated bone strength in the forearm at midlife. Further research should focus on targeted interventions to help determine which muscle property elicits a greater osteogenic response to optimize bone strength at distal and shaft sites of the radius.

Neutron stimulated emission computed tomography (NSECT) is being proposed as an experimental technique to diagnose iron overload in patients. Proof-of-concept experiments have suggested that NSECT may have potential to make a non-invasive diagnosis of iron overload in a clinical system. The technique's sensitivity to high concentrations of iron combined with tomographic acquisition ability gives it a unique advantage over other competing modalities. While early experiments have demonstrated the efficacy of detecting samples with high concentrations of iron, a tomography application for patient diagnosis has never been tested. As with any other tomography system, the performance of NSECT will depend greatly on the acquisition parameters that are used to scan the patient. In order to determine the best acquisition geometry for a clinical system, it is important to evaluate and understand the effects of varying each individual acquisition parameter on the accuracy of the reconstructed image. This research work proposes to use Monte-Carlo simulations to optimize a clinical NSECT system for iron overload diagnosis.Simulations of two NSECT systems have been designed in GEANT4, a spectroscopy system to detect uniform concentrations of iron in the liver, and a tomography system to detect non-uniform iron overload. Each system has been used to scan simulated samples of both disease models in humans to determine the best scanning strategy for each. The optimal scanning strategy is defined as the combination of parameters that provides maximum accuracy with minimum radiation dose. Evaluation of accuracy is performed through ROC analysis of the reconstructed spectrums and images. For the spectroscopy system, the optimal acquisition geometry is defined in terms of the number of neutrons required to detect a clinically relevant concentration of iron. For the tomography system, the optimal scanning strategy is defined in terms of the number of neutrons and the number of spatial and angular translation steps used during acquisition. Patient dose for each simulated system is calculated by measuring the energy deposited by the neutron beam in the liver and surrounding body tissue. Simulation results indicate that both scanning systems can detect wet iron concentrations of 5 mg/g or higher. Spectroscopic scanning with sufficient accuracy is possible with 1 million neutrons per scan, corresponding to a patient dose of 0.02 mSv. Tomographic scanning requires 8 angles that sample the image matrix at 1 cm projection intervals with 4 million neutrons per projection, which corresponds to a total body dose of 0.56 mSv. The research performed for this dissertation has two important outcomes. First, it demonstrates that NSECT has the clinical potential for iron overload diagnosis in patients. Second, it provides a validated simulation of the NSECT system which can be used to guide future development and experimental implementation of the technique. / Dissertation

<p>In this work, the simulation (forward problem) and reconstruction (inverse problem) in Thermoacoustic Tomography (TAT) are studied using a pseudospectral time-domain (PSTD) method with 4th-order time integration.</p><p>The objective of the TAT simulation is to solve for the thermoacoustic pressure field in an inhomogeneous medium. Using the PSTD method, the spatial derivatives of pressure field and particle velocity can be obtained using fast fourier transform (FFT). Since the Fourier transforms used to represent the spatial derivatives of smooth functions are exact, only 2 points per wavelength are needed in the spatial discretization. The time integration is achieved by a 4th-order method to effectively reduce the computational time. The results of the algorithm are validated by analytical solutions. Perfectly Matched Layers (PMLs) are applied to absorb the outgoing waves and avoid ``wraparound'' effect. The maximum attenuation coefficient of the PMLs has an optimum value to minimize the reflections due to discretization and wraparound effect for 2D and 3D problems. Different PML profiles are also compared, quadratic profile is chosen because it can minimize the overall reflection. Spatial smoothing is needed for PSTD to avoid Gibbs' phenomenon in the modeling of a point source, and the effect of the smoothing function is studied.</p><p>In the TAT reconstruction problem, the PSTD method is used to reconstruct the thermoacoustic sources by solving the thermoacoustic wave equations in a reversed temporal order within the framework of time reversal imaging. The back-propagated pressure waves then refocus at the spatial locations of the original sources. Most other TAT reconstruction algorithms are based on the assumption that the tissue medium is acoustically homogeneous. In practice, however, even the mild tissue inhomogeneity will cause large phase errors and cause spatial misplacement and distortion of the sources. The proposed PSTD method utilizes a two-step process to solve this problem. In the first step, a homogeneous time reversal reconstruction is performed. Since an inhomogeneity itself is usually a source because of spatially dependent electrical conductivity (thus microwave absorption), the spatial location and the shape of the inhomogeneity can be estimated. In the second step, the updated acoustic property map is loaded followed by an inhomogeneous reconstruction. Numerical results show that this method greatly improves the reconstruction results. Images with improved quality are reconstructed from experimental data.</p><p>A 3D PSTD algorithm is developed and validated. Numerical results show that the PSTD algorithm with the 4th-order time integration is capable of simulating large 3D acoustic problems accurately and efficiently. A 3D breast phantom model is used to study the inhomogeneous reconstruction in 3D. Improved results over the homogeneous method are observed.</p><p>A preliminary study of the Thermoacoustic Tomography (TAT) using continuous-wave (CW) modulated microwaves is summarized. The theoretical background, system configuration, experiment setup, and measurement results are presented.</p> / Dissertation

The growth plate is a cartilaginous tissue responsible for the longitudinal growth of long bones. It is a complex tissue composed of chondrocytes whose maturation and proliferation is tightly regulated by a biochemical feedback loop. Injury to this tissue can result in a limb length discrepancy or angular deformity that may lead to life long disability. Given the recent rise in the number of growth plate injuries and the variability in success of current therapies, there is a significant need for a greater understanding of growth plate injury pathology and the development of improved treatment strategies. Cartilage tissue engineering strategies offer an attractive alternative to regenerating growth plate tissue and restoring growth function. Bone marrow-derived stem cells (BMSCs) have been shown to be able to undergo chondrogenic differentiation and in vitro and in vivo and therefore offers an appealing and abundant cell resource for developing tissue engineering strategies for the treatment of growth plate defects. However, the dependence of chondrogenic differentiation and matrix accumulation on monolayer expansion protocols and three-dimensional (3D) culture environment has received little attention. Prior to developing treatment strategies for growth plate injury repair, it is essential to first understand the interconnection between alterations in growth plate morphology and subsequent limb deformities. To that end, we have established a surgical defect model of growth plate injury in Sprague Dawley rats and developed a novel technique to quantitatively monitor growth plate morphology in health and disease using microcomputed tomography (micro-CT) imaging. In an effort to develop a tissue engineering treatment strategy for growth plate injury, the role of monolayer expansion, 3D scaffold, and growth factor regimen in the chondrogenic differentiation of rat BMSCs was also examined. This research study has demonstrated the utility of micro-CT as a non-invasive imaging modality for assessing growth plate injury and repair. This work has also provided an improved understanding of the interrelationship of monolayer expansion, 3D culture environment, and growth factor regimen in BMSC chondrogenic differentiation. Finally, this work suggests that an injectable in situ gelling hydrogel is a feasible method for decreasing limb length discrepancies, however, neither implantation of agarose alone into the defect nor the inclusion of BMSCs fully corrects growth disruption.

Recently, with the escalating demands for optical communications, the need for bandwidth in optical communication network has increased. The technology breakthrough indry fiber fabrication opens the possibility for fiber bandwidth form 1.3 to 1.6 £gm. Cr4+:YAG double-clad crystal fiber (DCF) grown by the co-drawing laser-heated pedestal growth method has a strong spontaneous emission spectum form 1.3 to 1.6 £gm. Such fiber is therefore, eminently suitable for optical coherence tomography (OCT), broadband optical amplifier, amplifier spontaneous emission (ASE) light source, and tunable solid-state laser applications. In this thesis, multilayer dielectric thin films were directly deposited by E-gun coating onto the end faces of the Cr4+:YAG DCF. To improve the thin-film quality, to increase transmittance of laser output, and to design for the high power laser. For broadband optical amplifier in dual-pump and double-pass scheme, a 3.0-dB gross gain, a 3.0-dB insertion loss, and a 0-dB net gain at 1.4-£gm signal wavelength have been successfully developed with HR coating onto one of the Cr4+:YAG DCF end faces. In addition, we have successfully developed the Cr4+:YAG DCF laser by direct HR coatings onto fiber end faces and increase transmittance of laser output. A record-low threshold of 31.2 mW with a slope efficiency of 7.5% was achieved at room temperature.

Molecular imaging using fluorescence spectroscopy-based techniques is generally inefficient due to the low quantum yield of most naturally occurring biomolecules. Current fluorescence imaging techniques tag these biomolecules chemically or through genetic manipulation, increasing the complexity of the system. A technique capable of imaging these biomolecules without modifying the chromophore and/or its environment could provide vital biometric parameters and unique insights into various biological processes at a molecular level. Pump probe spectroscopy has been used extensively to study the molecular properties of poorly fluorescing biomolecules, because it utilizes the known absorption spectrum of these chromophores. Optical Coherence Tomography (OCT) is an optical imaging modality that harnesses the power of low coherence interferometry to measure the 3-D spatially resolved reflectivity of a tissue sample. We plan to develop a new molecular imaging modality that combines these techniques to provide 3-D, highresolution molecular images of various important biomolecules. The system uses a Fourier domain OCT setup with a modified sample arm that combines the "pump" and "probe" beams. The pump beam drives the molecules from the ground state to excited state and the probe interrogates the population change due to the pump and is detected interferometrically. The pump and the probe beam wavelengths are optimized to maximize absorption at the pump wavelength and maximize the penetration depth at the probe wavelength. The pump-probe delay can be varied to measure the rate at which the excited state repopulates the ground state, i.e., the ground state recovery time. The ground state recovery time varies for different chromophores and can potentially be used to identify different biomolecules. The system was designed and optimized to increase the SNR of the PPOCT signals. It was tested by imaging hemoglobin and melanin samples and yielded encouraging results. Potential applications of imaging hemoglobin using this technique include the mapping of tissue microvasculature and measuring blood-oxygen saturation levels. These applications could be used to identify hypoxic areas in tissue. Melanin imaging can provide means of demarcation of melanoma in various organs such as skin, eye and intestines.