This thesis will describe the latest work from the Feedback On Nanosecond Timescales project, commonly known as FONT. The goal of the FONT project is the development of a beamline feedback system to be installed at the interaction point (IP) of a future linear collider in order to maximize the luminosity that can be achieved. The prototype FONT feedback system is beam-based, meaning that the correction is determined from direct measurement of the position of the beam, and intra-train, meaning that the correction is applied within the duration of the current bunch train. The FONT system, consisting of three stripline beam position monitors, a digital processor unit built around a Field Programmable Gate Array (FPGA) and a pair of electromagnetic kickers, is described. Recent improvements to the position measurement process are detailed and the performance of the feedback system is presented. The modification of the firmware to operate on a machine with a large number of bunch trains, such as the International Linear Collider, is described and the design is verified through the use of a laboratory test bench developed to simulate such a machine. The FONT5 digital board is proved capable of operating on a train resembling the specification for the International Linear Collider: 2820 bunches separated in time by 308 ns.

The pyrolysis mechanics of Phenolic Impregnated Carbon Ablators (PICA) makes it a valued material for use in thermal protection systems for spacecraft atmospheric re-entry. The present study of the interaction of pyrolysis gases and char with plasma gases in the boundary layer over PICA and its substrate, FiberForm, extends previous work on this topic that has been done in the UVM 30 kW Inductively Coupled Plasma (ICP) Torch Facility. Exposure of these material samples separately to argon, nitrogen, oxygen, air, and carbon dioxide plasmas, and combinations of said test gases provides insight into the evolution of the pyrolysis gases as they react with the different environments. Measurements done to date include time-resolved absolute emission spectroscopy, location-based temperature response, flow characterization of temperature, enthalpy, and enthalpy flux, and more recently, spatially resolved and high-resolution emission spectroscopy, all of which provide measure of the characteristics of the pyrolysis chemistry and material response. Flow characterization tests construct an general knowledge of the test condition temperature, composition, and enthalpy. Tests with relatively inert argon plasmas established a baseline for the pyrolysis gases that leave the material. Key pyrolysis species such as CN Violet bands, NH, OH and Hydrogen Alpha (Hα) lines were seen with relative repeatability in temporal, spectral, and intensity values. Tests with incremental addition, and static mixtures, of reactive plasmas provided a preliminary image of how the gases interacted with atmospheric flows and other pyrolysis gases. Evidence of a temporal relationship between NH and Hα relating to nitrogen addition is seen, as well as a similar relationship between OH and Hα in oxygen based environments. Temperature analysis highlighted the reaction of the material to various flow conditions and displayed the in depth material response to argon and air/argon plasmas. The development of spatial emission analysis has been started with the hope of better resolving the previously seen pyrolysis behavior in time and space.

Interstitial and intracavitary brachytherapy plays an essential role in management of several malignancies. However, the achievable accuracy of brachytherapy treatment for prostate and cervical cancer is limited due to the lack of intraoperative planning and adaptive replanning. A major problem in implementing TRUS-based intraoperative planning is an inability of TRUS to accurately localize individual seed poses (positions and orientations) relative to the prostate volume during or after the implantation. For the locally advanced cervical cancer patient, manual drawing of the source positions on orthogonal films can not localize the full 3D intracavitary brachytherapy (ICB) applicator geometry. A new iterative forward projection matching (IFPM) algorithm can explicitly localize each individual seed/applicator by iteratively matching computed projections of the post-implant patient with the measured projections. This thesis describes adaptation and implementation of a novel IFPM algorithm that addresses hitherto unsolved problems in localization of brachytherapy seeds and applicators. The prototype implementation of 3-parameter point-seed IFPM algorithm was experimentally validated using a set of a few cone-beam CT (CBCT) projections of both the phantom and post-implant patient’s datasets. Geometric uncertainty due to gantry angle inaccuracy was incorporated. After this, IFPM algorithm was extended to 5-parameter elongated line-seed model which automatically reconstructs individual seed orientation as well as position. The accuracy of this algorithm was tested using both the synthetic-measured projections of clinically-realistic Model-6711 125I seed arrangements and measured projections of an in-house precision-machined prostate implant phantom that allows the orientations and locations of up to 100 seeds to be set to known values. The seed reconstruction error for simulation was less than 0.6 mm/3o. For the physical phantom experiments, IFPM absolute accuracy for position, polar angle, and azimuthal angel were (0.78 ± 0.57) mm, (5.8 ± 4.8)o, and (6.8 ± 4.0)o, respectively. It avoids the need to match corresponding seeds in each projection and accommodates incomplete data, overlapping seed clusters, and highly-migrated seeds. IFPM was further generalized from 5-parameter to 6-parameter model which was needed to reconstruct 3D pose of arbitrary-shape applicators. The voxelized 3D model of the applicator was obtained from external complex combinatorial geometric modeling. It is then integrated into the forward projection matching method for computing the 2D projections of the 3D ICB applicators, iteratively. The applicator reconstruction error for simulation was about 0.5 mm/2o. The residual 2D registration error (positional difference) between computed and actual measured applicator images was less than 1 mm for the intrauterine tandem and about 1.5 mm for the bilateral colpostats in each detector plane. By localizing the applicator’s internal structure and the sources, the effect of intra and inter-applicator attenuation can be included in the resultant dose distribution and CBCT metal streaking artifact mitigation. The localization accuracy of better than 1 mm and 6o has the potential to support more accurate Monte Carlo-based or 2D TG-43 dose calculations in clinical practice. It is hoped the clinical implementation of IFPM approach to localize elongated line-seed/applicator for intraoperative brachytherapy planning may have a positive impact on the treatment of prostate and cervical cancers.

BACKGROUND: The aim was to compare the thickness of the palatal masticatory mucosa as determined on a cone-beam computerized (CBCT) scan versus thickness determined via bone-sounding. METHODS: A total of twenty patients requiring palatal surgery participated. Thickness of the palatal tissue was measured at various points radiographically and clinically. The two techniques were compared to determine the agreement of the two measurement modalities. RESULTS: Analysis of variance determined that there was no significant difference between the two methods. A small bias of the radiographic measurement being larger was found to be statistically significant (0.09 ± 0.69mm; p <0.0001). Moreover, the tissue thickness was shown to increase as the distance from the gingival margin increased and the tissue over the molars was thinner than the tissue over the premolars. CONCLUSIONS: CBCT can be used to accurately determine the soft tissue thickness of the palatal masticatory mucosa with minimal bias.

Pre-surgical planning for endodontic microsurgery is facilitated by the use of cone beam computed tomography (CBCT). The purpose of this study was to determine whether limited field CBCT accurately predicts buccal cortical plate perforations due to endodontic lesions. Thirty-five roots that underwent microsurgical root end resection were included in this study. Prior to the surgery, 90 voxel CBCTs were taken with a Carestream 9300. The scans were analyzed by an endodontic resident and oral radiologist to determine the presence of a perforation in the buccal plate. These findings were compared to the clinical appearance of the bone. There was a significant relationship between a judgment of perforation made on the basis of CBCT and actual perforation as observed clinically. The CBCT prediction was accurate 83% of the time. A predicted perforation was validated in 88% of the instances and a predicted non-perforation was validated in 75% of the instances.

During the radio therapy treatment, it has been difficult to synchronize the radiation beam with the tumor position. Many compensation techniques have been used before. But all these techniques have some system latency, up to a few hundred milliseconds. Hence it is necessary to predict tumor position to compensate for the control system latency. In recent years, many attempts have been made to predict the position of a moving tumor during respiration. Analyzing external breathing signals presents a methodology in predicting the tumor position. Breathing patterns vary from very regular to irregular patterns. The irregular breathing patterns make prediction difficult. A solution is presented in this paper which utilizes neural networks as the predictive filter to determine the tumor position up to 500 milliseconds in the future. Two different neural network architectures, feedforward backpropagation network and recurrent network, are used for prediction. These networks are initialized in the same manner for the comparison of their prediction accuracies. The networks are able to predict well for all the 5 breathing cases used in the research and the results of both the networks are acceptable and comparable. Furthermore, the network parameters are optimized using a genetic algorithm to improve the performance. The optimization results obtained proved to improve the accuracy of the networks. The results of both the networks showed that the networks are good for prediction of different breathing behaviors.

Accounting for respiration motion during imaging helps improve targeting precision in radiation therapy. Respiratory motion can be a major source of error in determining the position of thoracic and upper abdominal tumor targets during radiotherapy. Thus, extracting respiratory motion is a key task in radiation therapy planning. Respiration-correlated or four-dimensional CT (4DCT) imaging techniques have been recently integrated into imaging systems for verifying tumor position during treatment and managing respiration-induced tissue motion. The quality of the 4D reconstructed volumes is highly affected by the respiratory signal extracted and the phase sorting method used. This thesis is divided into two parts. In the first part, two image-based respiratory signal extraction methods are proposed and evaluated. Those methods are able to extract the respiratory signals from CBCT images without using external sources, implanted markers or even dependence on any structure in the images such as the diaphragm. The first method, called Local Intensity Feature Tracking (LIFT), extracts the respiratory signal depending on feature points extracted and tracked through the sequence of projections. The second method, called Intensity Flow Dimensionality Reduction (IFDR), detects the respiration signal by computing the optical flow motion of every pixel in each pair of adjacent projections. Then, the motion variance in the optical flow dataset is extracted using linear and non-linear dimensionality reduction techniques to represent a respiratory signal. Experiments conducted on clinical datasets showed that the respiratory signal was successfully extracted using both proposed methods and it correlates well with standard respiratory signals such as diaphragm position and the internal markers’ signal. In the second part of this thesis, 4D-CBCT reconstruction based on different phase sorting techniques is studied. The quality of the 4D reconstructed images is evaluated and compared for different phase sorting methods such as internal markers, external markers and image-based methods (LIFT and IFDR). Also, a method for generating additional projections to be used in 4D-CBCT reconstruction is proposed to reduce the artifacts that result when reconstructing from an insufficient number of projections. Experimental results showed that the feasibility of the proposed method in recovering the edges and reducing the streak artifacts.

The top quark has been extensively studied since the Large Hadron Collider (LHC) began operating in 2010. The excellent performance of both the LHC and the Compact Muon Solenoid (CMS) detector has enabled complex analyses of many properties of the top quark. In this thesis inclusive and differential top pair (tt) production cross sections have been measured. Inclusive tt cross sections of 145.6 ± 8.2 (stat.) +38.1/28.3 (syst.) pb and 237.4 ± 1.9 (stat.) +20.4/-16.9 (syst.) pb were measured at 7 TeV and 8 TeV center-of-mass collision energies using luminosities of 1 fb⁻¹ and 19.7 fb⁻¹, respectively. These measurements were performed in the semi-leptonic channel by means of a maximum likelihood t of the lepton's pseudorapidity. The work in this thesis focuses specifically on the muon-plus-jets channel. The methods used for measuring the inclusive cross sections were built upon to measure differential cross sections with respect to event level observables. These observables include the missing transverse energy (Emiss T ) as well as some other kinematic distributions involving the jets, lepton and Emiss T in the decay. These results are unfolded to remove detector and selection effects and have uncertainties in the range of 3% to 15%. A low uncertainty is achieved by normalising the differential cross section using the total cross section. This leads to cancellations of some uncertainties. The results were compared with different Monte Carlo generators and with different input parameters. No significant deviations from predictions of the Standard Model were observed. This thesis also contains test beam results on CMS ECAL Endcap Lead Tungstate (PbWO4) crystals. These crystals had been damaged using various doses of proton irradiation. The damage for some crystals is expected to be roughly equivalent to 300 fb-1 of integrated luminosity at √s = 14 TeV. The energy resolution for these crystals was seen to reduce by close to a factor of 20.

Die vorliegende Arbeit beschreibt die Implementierung ionenstrahlanalytischer Methoden zur Charakterisierung der Probenzusammensetzung in einem Helium-Ionen-Mikroskop mit einem auf unter einen Nanometer fokussierten Ionenstrahl. Zur Bildgebung wird dieser im Mikroskop über Probenoberflächen gerastert und die lokale Ausbeute an Sekundärelektronen gemessen. Obwohl sich damit ein hoher topografischer Kontrast erzeugen lässt, lassen sich weder aus der Ausbeute noch aus der Energieverteilung der Sekundärelektronen verlässliche Aussagen zur chemischen Zusammensetzung der Probe treffen. Daher wurden in dieser Arbeit verschiedene ionenstrahlinduzierte Sekundärteilchen hinsichtlich ihrer Eignung für die Elementanalytik im Helium-Ionen-Mikroskop verglichen. Zur Evaluation standen der Informationsgehalt der Teilchen, deren Analysierbarkeit sowie deren verwertbare Ausbeute. Die Spektrometrie rückgestreuter Teilchen sowie die Sekundärionen-Massenspektrometrie wurden dabei als die geeignetsten Methoden identifiziert und im Detail untersucht. Gegenstand der Untersuchung waren physikalische Limitierungen und Nachweisgrenzen der Methoden sowie deren Eignung zum Einbau in ein Helium-Ionen-Mikroskop. Dazu wurden verschiedene Konzepte von Spektrometern evaluiert, erprobt und hinsichtlich ihrer Effizienz, Energieauflösung und Umsetzbarkeit im Mikroskop bewertet. Die Flugzeitspektrometrie durch Pulsen des primären Ionenstrahls konnte als die geeignetste Technik identifiziert werden und wurde erfolgreich in einem Helium-Ionen-Mikroskop implementiert. Der Messaufbau, die Signal- und Datenverarbeitung sowie vergleichende Simulationen werden detailliert beschrieben. Das Spektrometer wurde weiterhin ausführlich hinsichtlich Zeit-, Energie- und Massenauflösung charakterisiert. Es werden ortsaufgelöste Rückstreuspektren vorgestellt und damit erstmalig die Möglichkeit zur Ionenstrahlanalytik im Helium-Ionen-Mikroskop auf einer Größenskala von ≤ 60 nm aufgezeigt. Das Pulsen des primären Ionenstrahls erlaubt es zudem, die Technik der Sekundärionen-Massenspektrometrie anzuwenden. Diese Methode bietet Informationen zur molekularen Probenzusammensetzung und erreicht für einige Elemente niedrigere Nachweisgrenzen als die Rückstreuspektrometrie. Damit konnten erstmalig im Helium-Ionen-Mikroskop gemessene Sekundärionen-Massenspektren sowie die ortsaufgelöste Elementanalyse durch spektrometrierte Sekundärionen demonstriert werden. Die Ergebnisse dieser Arbeit sind in der Fachzeitschrift Ultramicroscopy Band 162 (2016) S. 91–97 veröffentlicht. Ab Oktober 2016 werden diese auch in Form eines Buchkapitels in dem Buch „Helium Ion Microscopy“, Springer Verlag Heidelberg zur Verfügung stehen. / The present work describes the implementation of ion beam analysis methods in a helium-ion-microscope for the determination of sample compositions with a focused ion beam of < 1 nm size. Imaging in the microscope is realized by scanning the focused ion beam over the sample surface while measuring the local secondary electron yield. Although this procedure leads to a high topographical contrast, neither the yield nor the energy distribution of the secondary electrons deliver reliable information on the chemical composition of the sample. For this purpose, in this work different ion beam induced secondary particles were compared with respect to their suitability for the analysis of the chemical composition in the helium-ion-microscope. In particular the information content of the particles, their analysability and their yield were evaluated. As a result, the spectrometry of backscattered particles and the mass spectrometry of sputtered secondary ions were identified as the most promising methods and regarded in detail. The investigation focused on physical limitations and detection limits of the methods as well as their implementability into a helium-ion-microscope. Therefor various concepts of spectrometers were evaluated, tested and validated in terms of their efficiency, energy resolution and practicability in the microscope. Time-of-flight spectrometry by pulsing the primary ion beam could be identified as the most suitable technique and has been successfully implemented in a helium-ion-microscope. The measurement setup, signal processing and data handling as well as comparative simulations are described in detail. Further the spectrometer was characterized explicitly in terms of time, energy and mass resolution. Spatially resolved backscattering spectra will be shown demonstrating the feasibility of performing ion beam analysis in a helium-ion-microscope for the first time on a size scale of ≤ 60 nm. By pulsing the primary ion beam the technique of secondary ion mass spectrometry becomes automatically accessible. This method provides information on the molecular composition of samples and can reach higher detection limits than those from backscattering spectrometry. For the first time, in a helium-ion-microscope measured secondary ion mass spectra and spatially resolved elemental analysis by spectrometry of secondary ions, could be demonstrated. The results of this work are published 2016 in the scientific journal Ultramicroscopy, volume 162 on pages 91 to 971. In October 2016 there will be another publication as a book chapter in „Helium Ion Microscopy“ (publisher: Springer Verlag Heidelberg).

The application of high temporal satellite image data for designation of the spectral characteristic of vegetation Abstract The objektive of this paper is to evaluate possibilities of high temporal satellite data assimilation for continuous monitoring of the spectral characteristic of vegetation. There is also given the suggestion of metodology for processing MERIS data and for continuous monitoring of spectral characteristic of landscape objects. Finally, vegetation cover database for the Czech Republic in the year 2009 is created from sectorial analysis. In the paper there is used the LSU classification and thresholding of vegetation indicies histograms. The universal decision algorithm for classification of vegetation landscape component are described and particular thresholding values for the year 2009 given. The finally product of this paper is Czech vegetation cover database for the year 2009 with overall accuracy of 63,35 %. Accuracy for forest is even over 80 %. Keywords: remote sensing, MERIS, vegetation, spectral reflectance, LSU, BEAM