The root system is a vital and dynamic part of a plant throughout its lifetime. Its spatial distribution is the consequence of multiple interactions with the surrounding soil medium. In particular, the presence of pathogens in soil may influence the development of the plant, especially the below-ground part, in both its physiology and its structure. Studies of diseased plant roots may take different approaches and investigate disease effects at different levels. In this study, two groups of four potato (Solanum tuberosum L.) plants were grown in middle-sized plastic pots in a greenhouse, and their root systems, together with the soil medium (i.e., sieved and autoclaved homogeneous sand), were submitted to computed tomography (CT) scanning every two weeks until 10 weeks after planting. For the "diseased" group, sand was inoculated with Streptomyces scabies EF-35, the causal agent of potato common scab, at the time of planting. Disease effects on tissue density of roots and below-ground organs, space occupancy and complexity were assessed by analyzing the CT scanning data in the spatio-temporal approach. Fluctuations of tissue density over time were different, on average, between the two groups. They were characterized by an increase of density in Week 2 for the diseased group, reflecting a hardening of tissue, and a delayed decrease relative to the "healthy" group, suggesting a slower transfer of energy from the seed potato to growing roots. Space occupancy, which was studied via volumetric growth rates evaluated from CT scan data, and complexity, which was quantified by the fractal dimension estimated from skeletonized 3-D images constructed from CT scan data, also showed differences in the first part of the experiment. Original analytical procedures based on data transformation and curve fitting in histogram analysis of CT numbers were developed to obtain those results. In conclusion, the new approach presented here, which is based on the advanced processing of CT scanning data collected over time on developing plant root systems and below-ground organs, can be recommended for future phytopathological applications.

Circular source and detector trajectories in cone-beam computed tomography (CT) are known to collect insufficient data for accurate object reconstruction. One model predicts that the lacking information corresponds to a shift-variant cone of missing spatial frequency components in the local Fourier domain. These predictions were experimentally verified by imaging small, localized objects and observing their Fourier transforms. Measurements indicated that the internal angle of the ‘missing cone’ varies as the angle of locally intersecting x rays with respect to the horizontal plane, as expected. Object recovery was also found to depend greatly on the distribution of the object’s frequency spectrum relative to the missing cone, as predicted. Findings agreed with more anatomically relevant phantoms, which showed preferential intensity discrepancies at gradients oriented within or near the missing cone. Methods for artefact correction are in general limited to approximation unless a priori information is incorporated.

Diabetes mellitus is a systemic condition that remains undiagnosed in a large portion of the population, which presents potential challenges for implant-based rehabilitation. Currently, the effects of diabetes on bone healing are not fully understood. Thus prior to employing a model of diabetes in studies of peri-implant healing, it was important to investigate the temporal effects of hyperglycemia on bone healing. Bone healing of femoral drill-defects was compared between streptozotocin-induced hyperglycemic (DB) and normoglycemic (NDC) rats at 5, 10, 15, and 30 days P.O. Quantitative assessment of bone samples using μCT demonstrated a delay in bone formation occurring up to 10 days in DB animals. Histological assessment confirmed these quantitative findings. Additionally, fluorescently stained bone samples indicated possible defects in mineralization of bone in DB group. In summary hyperglycemia affects bone healing at the early stages of bone formation, concurrent with the osteoconduction phase of bone healing.

Circular source and detector trajectories in cone-beam computed tomography (CT) are known to collect insufficient data for accurate object reconstruction. One model predicts that the lacking information corresponds to a shift-variant cone of missing spatial frequency components in the local Fourier domain. These predictions were experimentally verified by imaging small, localized objects and observing their Fourier transforms. Measurements indicated that the internal angle of the ‘missing cone’ varies as the angle of locally intersecting x rays with respect to the horizontal plane, as expected. Object recovery was also found to depend greatly on the distribution of the object’s frequency spectrum relative to the missing cone, as predicted. Findings agreed with more anatomically relevant phantoms, which showed preferential intensity discrepancies at gradients oriented within or near the missing cone. Methods for artefact correction are in general limited to approximation unless a priori information is incorporated.

Diabetes mellitus is a systemic condition that remains undiagnosed in a large portion of the population, which presents potential challenges for implant-based rehabilitation. Currently, the effects of diabetes on bone healing are not fully understood. Thus prior to employing a model of diabetes in studies of peri-implant healing, it was important to investigate the temporal effects of hyperglycemia on bone healing. Bone healing of femoral drill-defects was compared between streptozotocin-induced hyperglycemic (DB) and normoglycemic (NDC) rats at 5, 10, 15, and 30 days P.O. Quantitative assessment of bone samples using μCT demonstrated a delay in bone formation occurring up to 10 days in DB animals. Histological assessment confirmed these quantitative findings. Additionally, fluorescently stained bone samples indicated possible defects in mineralization of bone in DB group. In summary hyperglycemia affects bone healing at the early stages of bone formation, concurrent with the osteoconduction phase of bone healing.

In the area of translational research, stent developers consult pathologists to obtain the best and most complete amount of data from implanted test devices in the most efficient manner. Through the use of micron-scale computed tomography along with post-fixation staining techniques in this study, full volumes of previously implanted stents have been analyzed in-situ in a non-destructive manner. The increased soft tissue contrast imparted by metal-containing stains allowed for a qualitative analysis of the vessel’s response to the implant with greater sensitivity and specificity while reducing beam-hardening artifact from stent struts. The developed staining techniques included iodine-potassium iodide, phosphomolybdic acid, and phosphotungstic acid, all of which bind to soft tissue and improve image quality through their ability to attenuate high energy X-rays. With these stains, the overall soft tissue contrast increased by up to 85 percent and contrast between medial and neointimal layers of the vessel increased by up to 22 percent. Beam hardening artifact was also reduced by up to 38 percent after staining. Acquiring data from the entirety of the stent and the surrounding tissue increased the quality of stent analysis in multiple ways. The three dimensional data enabled a comprehensive analysis of stent performance, lending information such as neointimal hyperplasia, percent stenosis, delineation of vessel wall layers, stent apposition, and stent fractures. By providing morphological data about stent deployment and host response, this method circumvents the need to make the more traditional histology slides for a morphometric analysis. These same data may also be applied to target regions of interest to ensure histology slides are cut from the optimal locations for a more in-depth analysis. The agents involved in such techniques are readily available in most pathology laboratories, are safe to work with, and allow for rapid processing of tissue. The ability to forego histology altogether or to highly focus what histology is performed on a vessel has the potential to hasten the development process of any coronary stent.

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.

This project initiated with the aim for improving the ultrahigh resolution optical coherence tomography (UHR-OCT) system performance by considering the limitations to the axial OCT resolution for in vivo imaging of human and animal retina. To this end, a computational model was developed to simulate the effect of wavelength-dependant water absorption on the detected spectral shape of the broad-bandwidth light source used in UHR-OCT at 1060nm wavelength region, which effectively determines the axial OCT resolution in the retina. For experimental verification of the computational model, a custom built light source with a re-shaped spectrum (Superlum Inc.) was interfaced to the state-of-the-art UHR-OCT system. About 30% improvement of the axial OCT resolution in the rat retina and ~12% improvement of the axial OCT resolution in the human retina was achieved compared to the case of the almost Gaussian shaped spectrum of the standard, commercially available SLD. Although water absorption in the 1060nm spectral region strongly affects the sample beam, selecting a suitable light source with specific spectral shape can compensate for the undesired water absorption effect and thus result in significantly improved axial resolution in in vivo OCT retinal images. To demonstrate the advantages of the state-of-the-art OCT technology for non invasive retinal imaging, an established animal model of outer retina degeneration (sodium iodate (NaIO3)-induced retina degeneration) was employed for longitudinal monitoring of the degeneration and investigation of possible early and dynamic signs of damage undetected by other imaging modalities. The long-term (up to 3 months) and short-term (up to 12 hours) effect of sodium iodate toxicity on the layered structure of retina was monitored longitudinally and in vivo for the first time using OCT. An initial acute swelling of the retina, followed by progressive disruption and degeneration of outer retina was observed as a result of sodium iodate-induced damage. Changes in the thickness and optical reflectivity of individual retinal layers were extracted from the OCT images to quantify the changes occurring at different stages of the disease model. Results from this project present the theoretical and practical limits to the highest axial OCT resolution achievable for retina imaging in the 1060nm spectral range both in small animals and humans, and provided a framework for future development of novel light sources. Furthermore, UHR-OCT imaging was shown to be an effective and valuable modality for in vivo, non invasive investigation of retina degenerative disease.

Corrosion is the most important mechanical integrity issues the petrochemical industry has to deal with. While significant research has been dedicated to studying corrosion, it is still the leading cause of pipeline failure in the oil and gas industry. Not only is it the main contributor to maintenance costs, but also it accounts for about 15-20% of releases from the petrochemical industry and 80% of pipeline leaks. Enormous costs are directed towards fixing corrosion in facilities across the globe every year. Corrosion has caused some of the worst incidents in the history of the industry and is still causing more incidents every year. This shows that the problem is still not clearly understood, and that the methods that are being used to control it are not sufficient. A number of methods to detect corrosion exist; however, each one of them has shortcomings that make them inapplicable in some conditions, or generally, not accurate enough. This work focuses on studying a new method to detect corrosion under insulation. This method needs to overcome at least some of the shortcomings shown by the commercial methods currently used. The main method considered in this project is X-ray computed tomography. The results from this work show that X-ray computed tomography is a promising technique for corrosion under insulation detection. Not only does it detect corrosion with high resolution, but it also does not require the insulation to be removed. It also detects both internal and external corrosion simultaneously. The second part of this research is focused on studying the behavior of erosion/corrosion through CFD. This would allow for determining the erosion/corrosion rate and when it would take place before it starts happening. Here, the operating conditions that led to erosion/corrosion (from the literature) are used on FLUENT to predict the flow hydrodynamic factors. The relationship between these factors and the rate of erosion/corrosion is studied. The results from this work show that along with the turbulence and wall shear stress, the dynamic pressure imposed by the flow on the walls also has a great effect on the erosion/corrosion rate.

The prospects for enhanced Positron Emission Tomography imaging using liquid xenon (LXe) gamma ray detectors had been examined. Monte-Carlo simulations using GEANT4 were performed and the results were used to study the expected performance of a small animal PET scanner in comparison with a simulated conventional small animal scanner (LSO Focus 120). A NEMA-like cylinder phantom and an image contrast phantom were simulated with both scanners to compare performance characteristics. A Compton reconstruction algorithm was developed for the LXe scanner, and its performance and limitations studied.