<p> Image segmentation entails the partitioning of an image domain, usually two or three dimensions, so that each partition or segment has some meaning that is relevant to the application at hand. Accurate image segmentation is a crucial challenge in many disciplines, including medicine, computer vision, and geology. In some applications, heterogeneous pixel intensities; noisy, ill-defined, or diffusive boundaries; and irregular shapes with high variability can make it challenging to meet accuracy requirements. Various segmentation approaches tackle such challenges by casting the segmentation problem as an energy-minimization problem, and solving it using efficient optimization algorithms. These approaches are broadly classified as either region-based or edge (surface)-based depending on the features on which they operate. </p><p> The focus of this dissertation is on the development of a surface-based energy model, the design of efficient formulations of optimization frameworks to incorporate such energy, and the solution of the energy-minimization problem using graph cuts. This dissertation utilizes a set of four papers whose motivation is the efficient extraction of the left atrium wall from the late gadolinium enhancement magnetic resonance imaging (LGE-MRI) image volume. This dissertation utilizes these energy formulations for other applications, including contact lens segmentation in the optical coherence tomography (OCT) data and the extraction of geologic features in seismic data. </p><p> Chapters 2 through 5 (papers 1 through 4) explore building a surface-based image segmentation model by progressively adding components to improve its accuracy and robustness. The first paper defines a parametric search space and its discrete formulation in the form of a multilayer three-dimensional mesh model within which the segmentation takes place. It includes a generative intensity model, and we optimize using a graph formulation of the <i> surface net</i> problem. The second paper proposes a Bayesian framework with a Markov random field (MRF) prior that gives rise to another class of surface nets, which provides better segmentation with smooth boundaries. The third paper presents a maximum a posteriori (MAP)-based surface estimation framework that relies on a generative image model by incorporating global shape priors, in addition to the MRF, within the Bayesian formulation. Thus, the resulting surface not only depends on the learned model of shapes,but also accommodates the test data irregularities through smooth deviations from these priors. Further, the paper proposes a new shape parameter estimation scheme, in closed form, for segmentation as a part of the optimization process. Finally, the fourth paper (under review at the time of this document) presents an extensive analysis of the MAP framework and presents improved mesh generation and generative intensity models. It also performs a thorough analysis of the segmentation results that demonstrates the effectiveness of the proposed method qualitatively, quantitatively, and clinically. </p><p> Chapter 6, consisting of unpublished work, demonstrates the application of an MRF-based Bayesian framework to segment coupled surfaces of contact lenses in optical coherence tomography images. This chapter also shows an application related to the extraction of geological structures in seismic volumes. Due to the large sizes of seismic volume datasets, we also present fast, approximate surface-based energy minimization strategies that achieve better speed-ups and memory consumption.</p>

The purpose of this thesis research was to explore the feasibility of spectral imaging using a microbolometer infrared camera and a step-scan Fourier transform infrared spectrometer (FTIR). Spectral imaging is usually carried out using cryogenically cooled semiconductor based focal plane arrays (FPAs) which provide higher sensitivity compared to microbolometer FPAs based on thermal sensors. The key advantage of spectral imaging is the ability to extract spatial variations of spectral information. During the measurement, images were collected as the moving mirror of the FTIR stepped across the zero crossings of the on-axis portion of the interferogram. The preliminary data indicate that interferograms can be successfully recorded using the microbolometer camera, and that data from individual pixels of the camera showed the expected intensity profile. The interferograms from the individual pixels were inverse Fourier transformed to recover the intensity of the broadband infrared source of the FTIR at different pixels. The initial data showed relatively low signal to noise ratio indicating that signal averaging is necessary at each mirror step by collecting several images as well as optimizing the image collecting optics.

Dissertation submitted in full compliance with the requirements for the Master's degree in Technology: Radiography, Durban Institute of Technology, Durban, 2004. / The object of this study was to use Transvaginal ultrasound to evaluate the thickness of the endometrium to exclude endometrial abnormality in Black South African women with postmenopausal uterine bleeding. Transvaginal ultrasound is an excellent diagnostic method for assessing endometrial pathology. The study was carried out at the Gynaecological Ultrasound Department, King Edward VIII Hospital. The study included 76 Black women with postmenopausal uterine bleeding. The thickness of the endometrium was measured by Transvaginal ultrasound. The measurement included both endometrial layers (double-layer technique). The Transvaginal ultrasound measurement was compared with the histopathological diagnosis of the biopsy specimens. At the end of the investigation, findings obtained were 3.9% non-representative, 44.8% endometrial adenocarcinomas, 14.5% benign polyp, 3.9% chronic Endometritis, 17.1% benign endometrium, 5.3% endometrial hyperplasia, 9.2% atrophic endometrium, 3.9% myometrial invasion and 1.3% Malignant Mixed Mullerian Tumour. In this study, the thickness of the endometrial echo varied from 5mm to 35mm, with a mean of 18,2mm. When the thickness of the endometrial echo was compared with the histopathological results, the mean value for non-representative was 7.83mm, much lower than the thickness of an active endometrium (13.25mm). In cases with atrophic endometrium, the thickness ranged from 6mm to 30mm with a mean of 15.86mm. The mean value obtained for cases with endometrial adenocarcinoma was 20.32mm (range 11 to 35mm). The sensitivity, specificity and accuracy of Transvaginal ultrasound for detecting endometrial malignancy were 100% if the cutoff limit of 4mm was used In conclusion, this study using Transvaginal ultrasound demonstrated that a thickness limit greater than 8mm was considered in detecting malignancy. No malignant endometrium was thinner than 5mm. Therefore in women with postmenopausal uterine bleeding and an endometrium less than 4mm, it may be justified not to perform further investigations. Transvaginal ultrasound is a simple, well-tolerated safe and reliable method for identifying endometrial thickness in postmenopausal Black South African women. / M

<p> While MR-only treatment planning has shown promise, there are still several well-known challenges that are currently limiting widespread clinical implementation. Firstly, MR images are affected by both patient-induced and system-level geometric distortions that can significantly degrade treatment planning accuracy. In addition, the availability of comprehensive distortion analysis software is currently limited. Also while many groups have been working toward a synthetic CT solution, further study is needed on the implementation of synCTs as the reference datasets for linac-based image-guided radiation therapy (IGRT) to help determine their robustness in an MR-only workflow. </p><p> To determine candidate materials for phantom and software development, 1.0 T MR and CT images were acquired of twelve urethane foam samples of various densities and strengths. Samples were precision machined to accommodate 6 mm diameter paintballs used as landmarks. Final material candidates were selected by balancing strength, machinability, weight, and cost. Bore sizes and minimum aperture width resulting from couch position were tabulated from the literature. Bore geometry and couch position were simulated using MATLAB to generate machine-specific models to optimize the phantom build. Previously developed software for distortion characterization was modified for several magnet geometries, compared against previously published 1.0 T results, and integrated into the 3DSlicer application platform. </p><p> To evaluate the performance of synthetic CTs in an image guided workflow, magnetic resonance simulation and CT simulation images were acquired of an anthropomorphic skull phantom and 12 patient brain cancer cases. SynCTs were generated using fluid attenuation inversion recovery, ultrashort echo time, and Dixon data sets through a voxel-based weighted summation of 5 tissue classifications. The DRRs were generated from the phantom synCT, and geometric fidelity was assessed relative to CT-generated DRRs through bounding box and landmark analysis. An offline retrospective analysis was conducted to register cone beam CTs to synCTs and CTs using automated rigid registration in the treatment planning system. Planar MV and KV images were rigidly registered to synCT and CT DRRs using an in-house script. Planar and volumetric registration reproducibility was assessed and margin differences were characterized by the van Herk formalism. </p><p> Over the sampled FOV, non-negligible residual gradient distortions existed as close as 9.5 cm from isocenter, with a maximum distortion of 7.4mm as close as 23 cm from isocenter. Over 6 months, average gradient distortions were -0.07&plusmn;1.10 mm and 0.10&plusmn;1.10 mm in the x and y-directions for the transverse plane, 0.03&plusmn;0.64 and -0.09&plusmn;0.70 mm in the sagittal plane, and 0.4&plusmn;1.16 and 0.04&plusmn;0.40 mm in the coronal plane. After implementing 3D correction maps, distortions were reduced to &lt; 1 pixel width (1mm) for all voxels up to 25 cm from magnet isocenter. </p><p> Bounding box and landmark analysis of phantom synCT DRRs were within 1 mm of CT DRRs. Absolute planar registration shift differences ranged from 0.0 to 0.7 mm for phantom DRRs on all treatment platforms and from 0.0 to 0.4 mm for volumetric registrations. For patient planar registrations, the mean shift differences were 0.4&plusmn;0.5 mm, 0.0&plusmn;0.5 mm, and 0.1&plusmn;0.3 mm for the superior-inferior (S-I), left-right (L-R), and anterior-posterior (A-P) axes, respectively. The mean shift differences in volumetric registrations were 0.6&plusmn;0.4 mm (range, 0.2 to 1.6 mm), 0.2&plusmn;0.4 mm, and 0.2&plusmn;0.3 mm for the S-I, L-R, and A-P axes, respectively. The CT-SIM and synCT derived margins were &lt;0.3mm different. </p><p> This work has characterized the inaccuracies related to GNL distortion for a previously uncharacterized MR-SIM system at large FOVs, and established that while distortions are still non-negligible after current vendor corrections are applied, simple post-processing methods can be used to further reduce these distortions to less than 1mm for the entire field of view. Additionally, it was important to not only establish effective corrections, but to establish the previously uncharacterized temporal stability of these corrections. This work also developed methods to improve the accessibility of these distortion characterizations and corrections. We first tested the application of a more readily available 2D phantom as a surrogate for 3D distortion characterization by stepping the table with an integrated batch script file. Later we developed and constructed a large modular distortion phantom using easily obtainable materials, and showed and constructed a large modular distortion phantom using easily obtainable materials, and used it to characterize the distortion on several widely available MR systems. To accompany this phantom, open source software was also developed for easy characterization of system-dependent distortions. Finally, while the dosimetric equivalence of synCT with CT has been well established, it was necessary to characterize any differences that may exist between synCT and CT in an IGRT setting. This work has helped to establish the geometric equivalence of these two modalities, with some caveats that have been discussed at length. (Abstract shortened by ProQuest.) </p>

Novel characteristics of spin-based phenomena are intensively researched in the hope of discovering effects that could be used to develop new types of high-performance spintronic devices. Recent dynamics studies have revealed new principles for spintronic devices to sense microwaves. The capabilities for detecting both microwave electric field and magnetic field could make the spintronic microwave sensor as ubiquitous as semiconductor devices in microwave applications in the future. In this thesis, the feasibility of spintronic sensors in microwave applications has been researched and developed. Thanks to the high conversion efficiency of microwave rectification in the magnetic tunnel junction (MTJ) based spintronic sensor, it can directly measure the coherent spatially scattered microwave field distribution and detect a hidden object by analyzing the reflected microwave amplitude pattern. To enable the “real-time” vector measurement of the microwave field, a sensor based rapid phase detection technique is also developed. Combining the rapid phase detection technique and the microwave holography principle, a two-dimensional microwave holographic imaging system using a spintronic sensor was built. The high sensitivity of the microwave phase measurement allows the coherent imaging of the target to be reconstructed in noisy environments. By adapting the broadband measurement, not only the shape but also the distance of the target can be determined, which implies that three-dimensional imaging is achievable using a spintronic device. Combining the broadband microwave measurement and a wavefront reconstruction algorithm with a spintronic microwave sensor in circular trajectory, the reconstructed images of targets are obtained. The reconstructed images clearly indicate the targets' positions even when the targets were immersed in a liquid to simulate an inhomogeneous tissue environment. Our spintronic techniques provide a promising approach for microwave imaging, with the potential to be used in various areas, such as biomedical applications, security services, and material characterization. / October 2016

<p> Amyloid-&beta; (A&beta;) peptide is generated after sequential cleavage of the constitutively expressed amyloid precursor protein (APP) by &gamma; and &beta; secretases, and is recognized as the primary causative agent underlying the neuropathogenesis of Alzheimer&rsquo;sDisease (AD). Once generated, monomeric A&beta; demonstrates a high propensity to aggregate into toxic A&beta; oligomers (A&beta;O) of various sizes, which eventually accumulate in the brain in the form of amyloid plaques. Mutations in either the gene for APP or one or both of its processing genes, presenilin-1 (PS1) and presenilin-2 (PS2) of the secretases complex leading to accumulation of A&beta; and early-onset familial AD. Late onset AD is modulated by mutations in the gene for apolipoprotein E (apo-E), with the isoform apo-E4 leading to an approximate eight-fold increase in risk for AD, and by environmental and life style factors. The Alzheimer&rsquo;s disease process develops over decades, with substantial neurological loss occurring before a clinical diagnosis of dementia can be rendered. A major roadblock to the management of AD is the inability to definitively diagnose AD until post-mortem examination. It is therefore imperative to develop methods that permit safe, early detection and monitoring of disease progression. Magnetic resonance imaging (MRI) is a non-invasive way to detect and monitor AD progression and therapy, but so far MRI contrast has been obtained only using Gd(III) based contrast agents. Fluorene compounds have garnered attention as amyloid imaging agents. Our lab has developed a spin labeled fluorene (SLF) compound that contains a fluorene moiety with known affinity for A&beta; and a pyrroline nitroxyl spin-label moiety. We hypothesized that the SLF compound will specifically coat assemblies of amyloid beta in the brain and, by establishing a boundary of magnetic field inhomogeneity, produce MRI contrast in tissues with elevated levels of the A&beta; peptide. I found that labeling of brain specimens with the SLF compound produces negative contrast in samples from AD model mice whereas no negative contrast is seen in specimens harvested from wild-type mice. Injection of SLF into live mice resulted in good brain penetration, with the compound able to generate contrast 24-hr post injection. (Abstract shortened by ProQuest.)</p>

Positron Emission Tomography (PET) images reconstructed without adequate scatter corrections introduce noise and degrade image contrast. In commercial imaging systems, misalignment between computed tomography (CT) and PET images can introduce biases in the activity distribution. Recently, several reconstruction algorithms have been proposed, which made direct use of single scattered photons in the activity reconstruction. However, the realistic dataset contains single and higher order scattered photons, and current scatter reconstruction methods do not distinguish them. In this study, a novel reconstruction algorithm that is capable of processing higher order scattered photons was developed. A restricted attenuation correction method was created to avoid overcorrecting for scattered photons. The simulation outcomes have shown that the proposed methods can, under ideal energy resolution, reconstruct images that are qualitatively and quantitatively better than those obtained using existing algorithms, and that the methods show promise for use under more realistic clinical conditions. / October 2016

<p> The proposed project presents a methodology to detect how susceptible or resistant certain bacteria are to an applied antibiotic. This detection is achieved by calculating the area of Zone of Inhibition (ZOI) regions present in the petri dish and comparing the results to the prescribed standards. The ZOI regions are empty areas formed around an antibiotic disc when placed on a petri dish containing a sample of the bacterial culture. Digital image processing techniques are employed to automate the process of ZOI detection. Experimental results show that the proposed project is successful in detecting ZOI regions of various shapes, such as perfectly circular, irregular, and overlapping. The experimental results also show that the accuracy of detection is typically over 95%, and it remains above 90%, even when the image is degraded by additive Gaussian noise.</p><p>

The initial aim of this project was to improve the performance of a chromatographic bioreactor-separator (CBRS). In such a system, a dilute enzyme solution is pumped continuously through a preparative chromatographic column, while pulses of substrate are periodically injected on to the column. Enzymic reaction and separation are therefore performed in a single unit operation. The chromatographic columns used were jacketed glass columns ranging from 1 to 2 metres long with an internal diameter of 1.5 cm. Linking these columns allowed 1, 2, 3 and 4 metre long CBRS systems to be constructed. The hydrolysis of lactose in the presence of β~galactosidase was the reaction of study. From previous work at Aston University, there appeared to be no difficulties in achieving complete lactose hydrolysis in a CBRS. There did, however, appear to be scope for improving the separative performance, so this was adopted as an initial goal. Reducing the particle size of the stationary phase was identified as a way of achieving this improvement. A cation exchange resin was selected which had an average particle size of around half that previously used when studying this reaction. A CBRS system was developed which overcame the operational problems (such as high pressure drop development) associated with use of such a particle size. A significant improvement in separative power was achieved. This was shown by an increase in the number of theoretical plates (N) from about 500 to about 3000 for a 2 metre long CBRS, coupled with higher resolution. A simple experiment with the 1 metre column showed that combined bioreaction and separation was achievable in this system. Having improved the separative performance of the system, the factors affecting enzymic reaction in a CBRS were investigated; including pulse volume and the degree of mixing between enzyme and substrate. The progress of reaction in a CBRS was then studied. This information was related to the interaction of reaction and separation over the reaction zone. The effect of injecting a pulse over a length of time as in CBRS operation was simulated by fed batch experiments. These experiments were performed in parallel with normal batch experiments where the substrate is mixed almost instantly with the enzyme. The batch experiments enabled samples to be taken every minute and revealed that reaction is very rapid. The hydrodynamic characteristics of the two injector configurations used in CBRS construction were studied using Magnetic Resonance Imaging, combined with hydrodynamic calculations. During the optimisation studies, galactooligosaccharides (GOS) were detected as intermediates in the hydrolysis process. GOS are valuable products with potential and existing applications in food manufacture (as nutraceuticals), medicine and drug targeting. The focus of the research was therefore turned to GOS production. A means of controlling reaction to arrest break down of GOS was required. Raising temperature was identified as a possible means of achieving this within a CBRS. Studies were undertaken to optimise the yield of oligosaccharides, culminating in the design, construction and evaluation of a Dithermal Chromatographic Bioreactor-separator.

Fast field-cycling MRI (FFC-MRI) is a novel technique that promises to expand upon the diagnostic capabilities of conventional MRI by allowing the main magnetic field, B0, to be varied during the imaging pulse sequence. By doing this it is possible to gain access to information that is hidden to conventional scanners - namely the variation of the spin-lattice relaxation time, T1, with field strength, known as T1 dispersion. However, adding B0 as a new dimension to the imaging process necessitates a longer scan time which can limit the techniques application to clinical research. In this thesis, several methods are explored for reducing FFC-MRI scan times. A rapid imaging pulse sequence based on the well-known Fast Spin-Echo imaging sequence is presented, as well as an adaptation of the “keyhole” acquisition strategy. A method of determining T1 which requires significantly less data - and hence scan time - is also presented. When combined, these techniques are demonstrated to reduce total scan time from several hours to minutes without compromising access to T1 dispersion information. The techniques are demonstrated in phantom studies and in vivo results from volunteers are presented as proof of concept. The reduction in scan time demonstrated by these methods will significantly improve the applicability of FFC-MRI for clinical trials which are currently being worked towards.