Cold atomic spins are a great platform for developing and testing control and measurement techniques. This thesis presents experimental investigations into quantum control and measurement using laser cooled cesium atoms. On the control side, we present an experimental realization of a protocol to achieve full controllability of the entire hyperfine ground manifold of cesium. In particular, we demonstrate the ability to map between arbitrary states with fidelity greater than 0.99, using a combination of static, radio frequency, and microwave magnetic fields. On the measurement side, we present an experimental realization of quantum state tomography. The tomography protocol begins by measuring expectation values of an informationally complete set of observables using a weak optical probe in combination with dynamical control. The measurement record is processed using two different state estimation algorithms, allowing us to estimate a quantum state with fidelity greater than 0.9.

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Spine needle injections are widely applied to alleviate pain and to remove nerve sensation through anesthesia. Current treatment is performed either blindly having no image guidance or using fluoroscopy or computed tomography (CT). Both CT and fluoroscopy guidance expose patients to ionizing radiation. Alternatively, ultrasound (US) guidance for spine needle procedures is becoming more prevalent since US is a non-ionizing and more accessible image modality. An inherent challenge to US imaging of the spine is the acoustic shadows created by the bony structures of the vertebra limiting visibility. It is challenging to use US as the sole imaging modality for intraoperative guidance of spine needle injections. However, it is possible to enhance the anatomical information through a preoperative diagnostic CT. To achieve this, image registration between the CT and the US images is proposed in this thesis. Image registration integrates the anatomical information from the CT with the US images. The aligned CT augments anatomical visualization for the clinician during spinal interventions. To align the preoperative CT and intraoperative US, a novel registration pipeline is presented that involves automatic global and multi-vertebrae registration. The registration pipeline is composed of two distinct phases: preoperative and intraoperative. Preoperatively, artificial spring points are selected between adjacent vertebrae. Intraoperatively, the lumbar spine is first aligned between the CT and US followed by a multi-vertebrae registration. The artificial springs are used to constrain the movement of the individually transformed vertebrae to ensure the optimal alignment is a pose of the lumbar spine that is physically possible. Validation of the algorithm is performed on five clinical patient datasets. A protocol for US data collection was created to eliminate variability in the quality of acquired US images. The registration pipeline was able to register the datasets from initial misalignments of up to 25 mm with a mean TRE of 1.17 mm. From these results, it is evident that the proposed registration pipeline offers a robust registration between clinical CT and US data. / Thesis (Master, Computing) -- Queen's University, 2013-08-19 12:50:54.521

This thesis is part of a project focusedon investigating the possibility ofmeasuring void distributions usingtransmission tomography with fastneutrons. The measurements are plannedto be conducted at thermal hydraulictest loops. The project, called STUNT,is carried out at Uppsala University atthe division for applied nuclearphysics.The purpose of this work was to designand optimize a detection system for thedetection of fast neutrons in the abovementioned environment. For this purpose,detector elements consisting of theplastic scintillator material EJ208 wasmodeled using the particle transportcode MCNPX.Both plate shaped elements and fibers ofdifferent dimensions where tested forperformance.Through a comparison utilizing severalfigures of merit and MATLAB, the plateshape was selected with an element widthof 2.6 mm. During the optimizationprocess a possible detector design with73 detector plates was chosen. At anenergy threshold of 11 MeV the followingdesign parameters were found; adetection efficiency of 3.0 %, a signalto background ratio of 15, a totalmeasurement time of 3600 s and a pixelresolution of 1.4 mm.A point spread function was produced andtwo projection tests where conductedusing a water filled steel cylinder asobject. / STUNT

Permanent electrode arrays were set up at ten monitoring sites from Whitehorse, Yukon, to Fort St. John, British Columbia, in order to gain a clearer perspective of the effectiveness of electrical resistivity tomography (ERT) monitoring over an annual cycle of freezing and thawing. This research forms part of a longer-term project that is attempting to use ERT to examine changes in permafrost resulting from climate change. Inter-site and intra-site variability were examined by installing and maintaining data-loggers to monitor active layer and shallow permafrost temperatures, air temperatures, and snow depths at each site from August 2010 – August 2011. Additional site information was collected on each ERT survey date, including frost table depths, snow depths, and vegetation heights. Based on nearby community records, the climate in the region has been warming by a rate of 0.3 to 0.5 °C per decade since 1970. The permafrost at all ten sites was characteristic of sporadic discontinuous and isolated patches permafrost zones, and is classified as Ecosystem-protected. Nine of the ten permafrost sites had permafrost that was thinner than the 14 or 7 m penetration depth of the ERT survey (three-layer system consisting of an active layer, permafrost, and sub-permafrost perennially unfrozen zone). The most predictable results were achieved at the two-layer system site (active layer overlying permafrost to the base of the profile) in each of its virtual resistivity boreholes, relative resistivity change comparisons, and mean near-surface apparent resistivity progressions. ERT is an effective method of delineating permafrost boundaries in thin permafrost environments and does show strength when monitoring areas of seasonally frozen ground. Repeat surveys at a site indicate seasonal changes in three-layer conditions, but not as predictably as those in a two-layer system. In order to receive the most accurate information regarding permafrost extent and thickness, it appears ideal to conduct ERT surveys annually, within the same month as the previous year’s survey.

Space missions like Kepler have revolutionized asteroseismology, the science that infers the stellar interiors by studying oscillation frequency spectra of pulsating stars. Great advancements have been made in understanding solar-like oscillators. However, this is not the case for variable stars of intermediate masses, such asScutiand Doradus variables. By studying these stars in eclipsing binaries (EBs), model independent funda- mental parameters such as mass and radius can be inferred. On one hand, this synergy constrains the parameter space and facilitates the asteroseismic modeling, and this is shown for the Scuti type pulsating EB KIC 9851944. On the other hand, studies of binary stars must address the complexities such as mass transfer. KIC 8262223 is such an example, which consists of a mass-gaining Scuti primary and a pre-He white dwarf secondary. Some of the eccentric binary systems, the ‘heartbeat’ stars, show tidally excited oscillations. After briefly reviewing the linear theory of tidally forced stellar oscillations, we study the tidal pulsating binary KIC 3230227 and demonstrate that both amplitude and phase can be used to identify the tidally excited pulsation modes. We also discuss the variability of a Slowly Pulsating B-star KOI-81 and a Cataclysmic variable KIC 9406652. In the second part of this dissertation, we apply Bayesian statistics to some problems in binaries and asteroseismology with the help of packages BUGS and JAGS. Special attention is paid to the inverse problems (tomography) encountered in studying the double-line spectroscopic binaries.

Positron emission tomography (PET) employs short half-life positron emitting isotopes, typically ¹⁸F, for in vivo measurement of physiological processes. Easy access to structurally diverse radiolabelled probes would accelerate the rapid progress of PET imaging but, to date, radiochemistry is still limited by cost and efficiency. Nucleophilic fluorination with ¹⁸F-fluoride is the preferred “non-carrier-added” methodology in the synthesis of ¹⁸F-labelled pharmaceuticals because it leads to radiotracers with a high specific activity, a key feature allowing for investigations to be performed in sub-toxic doses. Chapter 1 serves as an introduction on radiochemistry, especially focussing on current radiosynthetic methods for the synthesis of ¹⁸F-labelled aromatics. Aromatic compounds without electron-withdrawing groups are notoriously difficult to label with ¹⁸F-fluoride. In this thesis, we present two novel methodologies to deliver ¹⁸F-labelled aromatic compounds from nucleophilic 18F-fluoride. Chapter 2 details the experimental efforts towards “Convergent Radiosynthesis” (Scheme 1). We proposed a convergent synthetic tactic that allows for simultaneous reaction between three or more substrates, including an ¹⁸F-labelled building block. This chemistry has been validated by the radiosynthesis of various structural scaffolds which are not responsive to direct nucleophilic fluorination. Chapter 3 presents our research into “Oxidative Nucleophilic ¹⁸F-Fluorination” (Scheme 2). We proposed that electron-rich aromatics, such as phenols, which are not responsive to nucleophilic fluorination may undergo umpolung reactivity under oxidative conditions. This “umpolung strategy” allows for the direct transformation from ¹⁸F-fluoride to 4-[¹⁸F]fluorophenol. Potentially, this established oxidative fluorination strategy could be adapted to the radiosynthesis of radiotracers containing a 4-fluorophenol sub-motif, such as 6-fluoro-meta-tyrosine. An appropriate precursor has been validated for the prospective radiosynthesis of 6-[18F]fluoro-meta-tyrosine.

In the first part of this work, we present two methods for improving the shape-threat detection performance of x-ray computed tomography. Our work uses a fixed-gantry system employing 25 x-ray sources. We first utilize Kullback-Leibler divergence and Mahalanobis distance to determine the optimal single-source single-exposure measurement. The second method employs gradient search on Bhattacharyya bound on error rate (P-e) to determine an optimal multiplexed measurement that simultaneously utilizes all available sources in a single exposure. With limited total resources of 10(6) photons, the multiplexed measurement provides a 41.8x reduction in P-e relative to the single-source measurement. In the second part, we consider multiple exposures and develop an adaptive measurement strategy for x-ray threat detection. Using the adaptive strategy, we design the next measurement based on information retrieved from previous measurements. We determine both optimal "next measurement" and stopping criterion to insure a target P-e using sequential hypothesis testing framework. With adaptive single-source measurements, we can reduce P-e by a factor of 40x relative to the measurements employing all sources in sequence. We also observe that there is a trade-off between measurement SNR and number of detectors when we study the performance of systems with reduced detector numbers. (C) 2016 Society of Photo-Optical Instrumentation Engineers (SPIE)

Emission Optical Projection Tomography (eO PT) is a relatively new imag- ing modality that bridges a gap between micro Magnetic Resonance Imag- ing and Confocal Laser Scanning Microscopy. eO PT can be used to image the anatomy and gene expression of intact biological specimens at high resolution and thus provides an alternative to time consuming methods such as serial sectioning. Tomographic image reconstruction for eOPT is currently performed using the Filtered Back Projection algorithm which, while being fast, does not account for the physics of image formation and thus can result in reconstructions of reduced resolution and questionable quantitative consistency. This thesis describes work that was done on eOPT in three areas, including image formation, tomographic reconstruction, and memory savings, the latter of which were required to bring implementation of 3D iterative reconstruction algorithms within reach for the relatively high-resolution eO PT imaging modality. In the area of image formation, measurements were taken to reveal the effects of optical blurring, diffraction and charge-coupled device (CCD) camera noise. Accurate models of each of these phenomena were developed and compared against the measurements. The subject of image reconstruction was first addressed with a modi- fication to the FBP algorithm designed to correct for the quantitative inaccuracies suspected of being introduced by the FBP algorithm when reconstructing specimens consisting of very fine detail. This was done by incorporating the quantitative aspects of the model of image formation into the FBP algorithm. The full model of image formation was incorpo- rated into the iterative Maximum Likelihood Expectation Maximisation (MLEM) algorithm. The third strand of this thesis focuses on various memory saving meth- ods developed to enable the implementation and testing of a variation of MLEM known as the Ordered Subsets Expectation Maximisation (OSEM). , Without such memory saving methods, the implementation of an iterative 3D reconstruction algorithm such as MLEM or OSEM using a full model of image formation would have remained beyond the capacity of modern computers for the foreseeable future, requiring several Terabytes of RAM. Comparisons were made between the quality of and the time required to produce FBP and OSEM reconstructions of the same data sets given the availability of limited computing resources. The feasibility of adopting OSEM reconstructions as an alternative to FBP reconstructions was dis- cussed, based on the use of currently available cutting edge computing hardware.