Η παρούσα διδακτορική διατριβή αποτελεί μια μελέτη σύγκρισης και βελτιστοποίησης διάφορων αλγορίθμων ανακατασκευής δεδομένων, τα οποία προέρχονται από ένα πρότυπο σύστημα ΡΕΤ ικανό για απεικονίσεις μικρών ζώων. Η σύγκριση αφορά υπάρχοντες αλγορίθμους ανακατασκευής ενώ παρουσιάζεται και ένας νέος επαναληπτικός αλγόριθμος o ISWLS. Το δεύτερο μέρος της παρούσας διδακτορικής διατριβής ασχολείται με ένα άλλο σημαντικό στάδιο της επεξεργασίας ιατρικών δεδομένων την τμηματοποίηση της ιατρικής εικόνας. Παρουσιάζονται διάφορες τεχνικές παραμετρικών ελαστικών μοντέλων. Συγκεκριμένα παρουσιάζονται το κλασσικό μοντέλο φιδιού (snake), το μοντέλο gradient vector flow (gvf-snake) και τα t-snakes (topology-adaptive snakes). Επίσης παρουσιάζεται η μέθοδος self-affine mapping σαν μια εναλλακτική των παραπάνω παραμετρικών ελαστικών μοντέλων και εισάγεται ένα νέο κριτήριο σύγκλισής της. Όλες οι τεχνικές εφαρμόζονται σε οφθαλμικές εικόνες με σκοπό την τμηματοποίηση του οπτικού δίσκου / Small animal imaging is the conjunctive ring between experimental research and clinical implementation. Positron Emission Tomography (PET) has proven a valuable tool for in vivo small animal functional imaging. Image reconstruction in PET uses the collected projection data of the object/patient under examination. The purpose of this study is to assess the performance of iterative reconstruction methods, using phantom data from a prototype small-animal PET system. The algorithms being compared are the simultaneous versions of ART (SART), EM-ML, ISRA and WLS and a new iterative algorithm being introduced under the short name ISWLS. In the second part of this thesis elastic or deformable models are studied. Various methods of parametric elastic models are presented, namely the classical snake, the gradient vector field snake (gvf-snake) and the topogy-adaptive snake (t-snake). Also presented the method of self-affine mapping system as an alternative of elastic models. Further a new comparison criterion for the self affine mapping system method is introduced. All methods are applied to retinal images with the purpose of segmenting the optical disk. Moreover the aforementioned methods are compared in terms of segmentation accuracy.

<p>Quality assurance (QA) is a critical component of radiation oncology medical physics for both effective treatment and patient safety, particularly as innovations in technology allow movement toward advanced treatment techniques that require increasingly higher accuracy in delivery. Comprehensive 3D dosimetry with PRESAGE® 3D dosimeters read out via optical CT has the potential to detect errors that would be missed by current systems of measurement, and thereby improve the rigor of current QA techniques through providing high-resolution, full 3D verification for a wide range of clinical applications. The broad objective of this dissertation research is to advance and strengthen the standards of QA for radiation therapy, both by driving the development and optimization of PRESAGE® 3D dosimeters for specific clinical and research applications and by applying the technique of high resolution 3D dosimetry toward addressing clinical needs in the current practice of radiation therapy. The specific applications that this dissertation focuses on address several topical concerns: (1) increasing the quality, consistency, and rigor of radiation therapy delivery through comprehensive 3D verification in remote credentialing evaluations, (2) investigating a reusable 3D dosimeter that could potentially facilitate wider implementation of 3D dosimetry through improving cost-effectiveness, and (3) validating deformable image registration (DIR) algorithms prior to clinical implementation in dose deformation and accumulation calculations.</p><p>3D Remote Dosimetry: The feasibility of remote high-resolution 3D dosimetry with the PRESAGE®/Optical-CT system was investigated using two nominally identical optical-CT scanners for 3D dosimetry were constructed and placed at the base (Duke University) and remote (IROC Houston) institutions. Two formulations of PRESAGE® (SS1, SS2) were investigated with four unirradiated PRESAGE® dosimeters imaged at the base institution, then shipped to the remote institution for planning and irradiation. After each dosimeter was irradiated with the same treatment plan and subsequently read out by optical CT at the remote institution, the dosimeters were shipped back to the base institution for remote dosimetry readout 3 days post-irradiation. Measured on-site and remote relative 3D dose distributions were registered to the Pinnacle dose calculation, which served as the reference distribution for 3D gamma calculations with passing criteria of 5%/2mm, 3%/3mm, and 3%/2mm with a 10% dose threshold. Gamma passing rates, dose profiles, and dose maps were used to assess and compare the performance of both PRESAGE® formulations for remote dosimetry. Both PRESAGE® formulations under study maintained high linearity of dose response (R2>0.996) over 14 days with response slope consistency within 4.9% (SS1) and 6.6% (SS2). Better agreements between the Pinnacle plan and dosimeter readout were observed in PRESAGE® formulation SS2, which had higher passing rates and consistency between immediate and remote results at all metrics. This formulation also demonstrated a relative dose distribution that remained stable over time. These results provide a foundation for future investigations using remote dosimetry to study the accuracy of advanced radiation treatments.</p><p>A Reusable 3D Dosimeter: New Presage-RU formulations made using a lower durometer polyurethane matrix (Shore hardness 30-50A) exhibit a response that optically clears following irradiation and opens up the potential for reirradiation and dosimeter reusability. This would have the practical benefit of improving cost-effectiveness and thereby facilitating the wider implementation of comprehensive, high resolution 3D dosimetry. Three formulations (RU-3050-1.7, RU-3050-1.5, and RU-50-1.5) were assessed with multiple irradiations of both small volume samples and larger volume dosimeters, then characterized and evaluated for dose response sensitivity, optical clearing, dose-rate independence, dosimetric accuracy, and the effects of reirradiation on dose measurement. The primary shortcoming of these dosimeters was the discovery of age-dependent gradients in dose response sensitivity, which varied dose response by as much as 30% and prevented accurate measurement. This is unprecedented in the standard formulations and presumably caused by diffusion of a desensitizing agent into the lower durometer polyurethane. The effect of prior irradiation on the dosimeters would also be a concern as it was seen that the relative amount of dose delivered to any given region of the dosimeter will affect subsequent sensitivity in that area, which would in effect create spatially-dependent variable dose sensitivities throughout the dosimeter based on the distributions of prior irradiations. While a successful reusable dosimeter may not have been realized from this work, these studies nonetheless contributed useful information that will affect future development, including in the area of deformable dosimetry, and provide a framework for future reusable dosimeter testing.</p><p>Validating Deformable Image Registration Algorithms: Deformable image registration (DIR) algorithms are used for multi-fraction dose accumulation and treatment response assessment for adaptive radiation therapy, but the accuracy of these methods must be investigated prior to clinical implementation. 12 novel deformable PRESAGE® 3D dosimeter formulations were introduced and characterized for potential use in validating DIR algorithms by providing accurate, ground-truth deformed dose measurement for comparison to DIR-predicted deformed dose distributions. Two commercial clinical DIR software algorithms were evaluated for dose deformation accuracy by comparison against a measured deformed dosimeter dose distribution. This measured distribution was obtained by irradiating a dosimeter under lateral compression, then releasing it from compression so that it could return to its original geometry. The dose distribution within the dosimeter deformed along with the dosimeter volume as it regained to its original shape, thus providing a measurable ground truth deformed dose distribution. Results showed that intensity-based DIR algorithms produce high levels of error and physically unrealistic deformations when deforming a homogeneous structure; this is expected as lack of internal structure is challenging for intensity-based DIR algorithms to deform accurately as they rely on matching fairly closely spaced heterogeneous intensity features. A biomechanical, intensity-independent DIR algorithm demonstrated substantially closer agreement to the measured deformed dose distribution with 3D gamma passing rates (3%/3mm) in the range of 90-91%. These results underscore the necessity and importance of validating DIR algorithms for specific clinical scenarios prior to clinical implementation.</p> / Dissertation

No description available.

Current problems on the interaction of complex liquids (i.e. droplets or foams) with complex surfaces (i.e. soft deformable or porous surfaces) are addressed in the following areas: (1) wetting of deformable substrates and surface forces, (2) kinetics of wetting and spreading of non-Newtonian liquids over porous substrates, (3) kinetics of spreading of non-Newtonian solutions over hair, (4) free drainage of foams produced from non-Newtonian solutions, and (5) foam drainage placed on porous substrates. Equilibrium of liquid droplets on deformable substrates was investigated and the effect of disjoining pressure action in the vicinity of the apparent three phase contact line was taken into account. It was proven that the deformation of soft solids is determined by the action of surface forces inside the transition zone. Spreading/imbibition of blood, which is a power law shear thinning non-Newtonian liquid, over a dry porous layer was investigated from both theoretical and experimental points of view. It was found that blood droplet spreading/imbibition over porous substrates shows two different behaviours: (i) partial wetting case with three subsequent stages: initial fast spreading, constant maximum droplet base and the shrinkage of the droplet base; (ii) complete wetting case with only two stages: initial fast spreading and the shrinkage of the droplet base. The wetting of hair tresses by aqueous solutions of two commercially available polymers, AculynTM 22 (A22) and AculynTM 33 (A33) was investigated experimentally. Both A22 and A33 solutions demonstrate well pronounced shear thinning behaviour. Initial contact angle of the A22 and A33 solutions on hair tresses was about 100o. The A22 droplets remained on the hair tress after spreading for at least half an hour. However, a fast penetration of the A33 droplets inside the hair tresses was observed when advancing contact angle in the course of spreading reached a critical value of about 60o. This could be explained by Cassie-Wenzel wetting transition which is caused by filling the pores inside the porous media by liquid. The influence of non-Newtonian rheology of A22 and A33 solutions on foam drainage was also investigated experimentally and a new theory of foam drainage was presented for the case of free drainage. For lowly viscous polymeric solutions and under the assumption of rigid surface of the Plateau border, the predicted values of the time evolution of the foam height and liquid content were in good agreement with the experimental data. However, in the case of highly viscous solutions an interfacial mobility at the surface of the Plateau border has to be taken into account. A completely new theory of foam drainage placed on porous substrate was developed. It was found that there are three different regimes of the process: (i) a rapid imbibition, the imbibition into the porous substrate dominates as compared with the foam drainage; (ii) an intermediate imbibition, that is, the imbibition into the porous substrate and the rate of drainage are comparable; (iii) a slow imbibition, the rate of drainage inside the foam is higher than the imbibition into the porous substrate for a period of time and a free liquid layer is formed over the porous substrate.

O crescente número de sistemas de animação que utilizam a cinemática para gerar movimento de objetos vem levando os pesquisadores a buscar outras alternativas para produzir resultados mais realistas. Com base nesta premissa, vários autores começaram a estudar a geração de movimento de objetos sintéticos através da aplicação da dinâmica. Assim surgiram os modelos baseados em leis físicas. Num primeiro momento foram abordados apenas objetos rígidos, passando-se mais tarde a considerar objetos articulados e, por fim, aqueles com características elásticas, também denominados de objetos flexíveis ou deformáveis. O objetivo principal do trabalho é a definição de um modelo para simulação de objetos deformáveis no espaço euclidiano. São abordados tanto o modelo geométrico utilizado como o modelo físico, sendo ressaltadas as forças aplicadas sobre o objeto e as restrições que podem ser impostas pelo mundo virtual no qual o mesmo está inserido. Dentre as forças descritas, pode-se destacar: força gravitacional, elasticidade, força de curvatura e torção, colisão e atrito. A fundamentação do trabalho desenvolvido é apresentada na forma de uma introdução aos sistemas de animação, enfatizando os sistemas baseados em leis físicas e de uma revisão bibliográfica dos métodos de deformação existentes. No que diz respeito à colisão de objetos elásticos, são descritos tanto os métodos estudados para a solução das mesmas, como as técnicas para detecção do choque. A simulação do movimento é descrita sob dois aspectos: o algoritmo utilizado para a geração do movimento e a integração numérica das equações diferenciais no tempo. É abordado ainda, em detalhe, o protótipo desenvolvido com o propósito de validar o modelo proposto, sendo descrita a linguagem criada a fim de permitir a especificação da animação e parâmetros diversos do modelo. Por fim, são apresentados e avaliados os resultados obtidos através do desenvolvimento do modelo proposto por intermédio do protótipo FLEX3D. É dedicada ainda especial atenção às perspectivas futuras deste trabalho. / The growing number of animation systems that use kinematics to generate the motion of objects have led to other alternatives to produce more realistic results. Some authors began to study the animation of synthetic objects through the application of the dynamic concepts, creating the modern physically based models. At first, only rigid objects were treated; later on articulated objects were considered. At last, those with elastic characteristics (called flexible or deformable objects) were taken into consideration. The main goal of this work is to define a simulation model for deformable objects in the euclidean space. Both the geometric and the physical models are presented, considering the forces applied to the object and the constraints defined by the virtual world. Described forces include gravity, elasticity, dumping force, collision and attrition. This work presents an introduction to animation systems focusing the physically based systems. After this, a bibliographic review of the existent deformation methods is made. Methods for detecting and solving the collision between two elastic objects are described. Two aspects of the motion simulation are described: the algorithm used to generate the motion and the numeric integration of the differential equations in time. A prototype named FLEX3D is presented to validate the proposed model. The language used for specifying the animation is described and results obtained through the use of FLEX3D are also presented. Special attention is given to the possible future works.

Simulação computacional de ambientes cirúrgicos têm sido amplamente utilizados, normalmente para treinamentos, ajudando no desenvolvimento de habilidades essenciais e minimizando erros em procedimentos cirúrgicos. Para estes ambientes, é essencial a obtenção de um comportamento mais realista, sendo importante o uso de técnicas com alta precisão, além de uma simulação em tempo real. A fim de melhor controlar este trade-off entre eficiência e eficácia, apresentamos um ambiente híbrido e adaptativo que combina um conjunto de métodos para alcançar uma boa precisão e desempenho na simulação. Nosso sistema mescla métodos físicos de deformação (Método de Elementos Finitos e Mass-Mola) com um método não-físico que aproxima o comportamento dos primeiros (Green Coordinates), sendo capaz de utilizar o método apropriado dependendo da situação. Para melhor simular um ambiente cirúrgico completo, foram implementadas ferramentas adicionais para interação, permitindo pegar e manipular, queimar, e sentir os objetos do cenário. Nosso sistema proporciona grande imersão ao usuário, consumindo menos recursos computacionais e aumentando as taxas de atualização da simulação. / Computational simulation of surgical environments have been widely used usually for trainings, improving essential skills and minimizing errors in surgical procedures. As these environments are always looking for a more realistic behavior, it is important to use high-precision techniques while ensuring a real-time simulation. In order to better manage this trade-off between efficiency and effectiveness, we present a hybrid and adaptive environment that combines a set of methods to achieve good accuracy and performance for a simulation. Our system merges physically deformation methods (Finite Elements Method and Mass Spring Damper) with a non-physical method that approximates the formers behavior (Green Coordinates), being able to use the appropriate method depending on the situation. To simulate an approximation of a complete surgical environment, we also implement interaction tools, such as picking, burning, and haptic feedback. Our system provides great immersion for the user, consuming less computational resources and increasing update rates.

Anatomic changes occur throughout head and neck radiotherapy, and a new treatment plan is often required to mitigate the resulting changes in delivered dose to key structures. This process is known as adaptive radiotherapy (ART), and can be labour-intensive. The aim of this thesis is to optimise ART, addressing some of the technical and clinical challenges facing its routine clinical implementation. Optimising the frequency and timing of adaptive replanning is important, and it has been shown here that intensity modulated radiotherapy (IMRT) and volumetric modulated arc therapy (VMAT) are equally robust to weight loss during head and neck radiotherapy. Plan adaptation strategies that have previously been developed for IMRT are therefore applicable to VMAT.Contour propagation is an important component of ART, and it is essential to ensure that propagated contours are accurate. A method for assessing the suitability of a metric for measuring automatic segmentation accuracy has been developed and applied to the head and neck. For the parotids and larynx, metrics based on surface agreement were better than the commonly used Dice similarity coefficient. By establishing a consensus on which metrics should be used to assess segmentation accuracy, comparison of different algorithms is more objective and should lead to more accurate automatic segmentation. A novel method of assessing contour propagation accuracy on a patient-specific basis has also been developed. This was demonstrated on a cohort of head and neck patients and shows potential as a tool for identifying propagated contours that are subject to a high degree of uncertainty. This is a novel tool that will increase the efficiency of automatic segmentation and, therefore, ART.Optimum ART requires consideration of different radiotherapy-related toxicities, and image-based data mining is a powerful technique for spatially localising dose-response relationships. Correction for multiple comparisons through permutation testing is essential, but has so far only been applied to categorical data. A novel method has been developed for performing permutation testing and image-based data mining with a continuously variable clinical endpoint. Application to trismus for head and neck radiotherapy identified a region with a dose-response relationship in the ipsilateral masseter. Sparing this structure during radiotherapy should reduce the severity of radiation-induced trismus. ART mitigates the dosimetric effects of anatomic changes, and this thesis has addressed technical and clinical challenges that have so far limited its clinical implementation. Detailed knowledge of dose-response relationships will enable selection of patients for ART based on potential clinical benefit, and accurate contour propagation will make ART more efficient, facilitating its routine implementation.

Radiation therapy, one of the most common forms of cancer treatment, is continually evolving with the introduction of new technology, more complex treatments and more advanced radiation dose calculations. To ensure the effectiveness and safety of modern radiation therapy, dose measurement tools must improve to accommodate these advances. X-ray computed tomography (CT) polymer gel dosimetry is a unique type of dosimeter that has many advantages and the potential to address some of the challenges in the verification of dose delivery and calculation in radiation therapy. This dissertation investigates the advancement of an x-ray CT polymer gel dosimetry system for use in clinical applications and in particular for deformable dose verification. The first part of this work consists of a reproducibility study of an established x-ray CT polymer gel dosimetry system in an effort to determine the accuracy and precision of dose measurements made with this system and the feasibility of interbatch and generic calibration. Gel measurements were found to have excellent agreement with Monte Carlo dose calculation when using a generic calibration curve. The excellent dosimetric and spatial accuracy established in this study suggest that this dosimetry system is ideally suited for the measurement of high-dose fractionation treatments such as stereotactic radiosurgery (SRS) or stereotactic body radiation therapy (SBRT). The second stage was the development and characterization of the first deformable x-ray CT polymer gel dosimetry system. This study established the setup reproducibility, deformation characteristics and dose response of the new deformable system. The dose response was found to be similar to that of the non-deformable system with similar dosimetric and spatial accuracy when compared to Monte Carlo dose calculation. The system was also found to have sub-millimetre setup reproducibility and the deformable dosimeter was found to reproducibly deform and relax for external compression of up to 30 mm and over 100 consecutive compressions. This work established several important characteristics of the new deformable dosimetry system and it shows excellent potential for use in the evaluation of deformable dose accumulation algorithms. The final component of this dissertation was the use of the newly developed deformable dosimetry system in the evaluation of a novel deformable dose accumulation algorithm, defDOSXYZ. Gel measurements and defDOSXYZ showed excellent agreement in the case of a static control case and this set a benchmark for deformable dose measurements. Measurements of deformed dose by the gel dosimeter showed significant disagreement with dose deformed by defDOSXYZ and the dosimetric differences were well outside the uncertainties established in the first two studies of this dissertation. The results from this study provided some insight into potential avenues of improvement for both the deformable dose calculation and deformable dose measurements. These results were also the first example of deforming dose measured by an x-ray CT read out gel dosimetry system. Overall, the results in this dissertation represent a significant advancement in x-ray CT polymer gel dosimetry and establish its suitability for several clinical applications. / Graduate / 2019-12-06

abstract: This dissertation presents my work on development of deformable electronics using microelectromechanical systems (MEMS) based fabrication technologies. In recent years, deformable electronics are coming to revolutionize the functionality of microelectronics seamlessly with their application environment, ranging from various consumer electronics to bio-medical applications. Many researchers have studied this area, and a wide variety of devices have been fabricated. One traditional way is to directly fabricate electronic devices on flexible substrate through low-temperature processes. These devices suffered from constrained functionality due to the temperature limit. Another transfer printing approach has been developed recently. The general idea is to fabricate functional devices on hard and planar substrates using standard processes then transferred by elastomeric stamps and printed on desired flexible and stretchable substrates. The main disadvantages are that the transfer printing step may limit the yield. The third method is "flexible skins" which silicon substrates are thinned down and structured into islands and sandwiched by two layers of polymer. The main advantage of this method is post CMOS compatible. Based on this technology, we successfully fabricated a 3-D flexible thermal sensor for intravascular flow monitoring. The final product of the 3-D sensor has three independent sensing elements equally distributed around the wall of catheter (1.2 mm in diameter) with 120° spacing. This structure introduces three independent information channels, and cross-comparisons among all readings were utilized to eliminate experimental error and provide better measurement results. The novel fabrication and assembly technology can also be applied to other catheter based biomedical devices. A step forward inspired by the ancient art of folding, origami, which creating three-dimensional (3-D) structures from two-dimensional (2-D) sheets through a high degree of folding along the creases. Based on this idea, we developed a novel method to enable better deformability. One example is origami-enabled silicon solar cells. The solar panel can reach up to 644% areal compactness while maintain reasonable good performance (less than 30% output power density drop) upon 40 times cyclic folding/unfolding. This approach can be readily applied to other functional devices, ranging from sensors, displays, antenna, to energy storage devices. / Dissertation/Thesis / Doctoral Dissertation Electrical Engineering 2014

Simulação computacional de ambientes cirúrgicos têm sido amplamente utilizados, normalmente para treinamentos, ajudando no desenvolvimento de habilidades essenciais e minimizando erros em procedimentos cirúrgicos. Para estes ambientes, é essencial a obtenção de um comportamento mais realista, sendo importante o uso de técnicas com alta precisão, além de uma simulação em tempo real. A fim de melhor controlar este trade-off entre eficiência e eficácia, apresentamos um ambiente híbrido e adaptativo que combina um conjunto de métodos para alcançar uma boa precisão e desempenho na simulação. Nosso sistema mescla métodos físicos de deformação (Método de Elementos Finitos e Mass-Mola) com um método não-físico que aproxima o comportamento dos primeiros (Green Coordinates), sendo capaz de utilizar o método apropriado dependendo da situação. Para melhor simular um ambiente cirúrgico completo, foram implementadas ferramentas adicionais para interação, permitindo pegar e manipular, queimar, e sentir os objetos do cenário. Nosso sistema proporciona grande imersão ao usuário, consumindo menos recursos computacionais e aumentando as taxas de atualização da simulação. / Computational simulation of surgical environments have been widely used usually for trainings, improving essential skills and minimizing errors in surgical procedures. As these environments are always looking for a more realistic behavior, it is important to use high-precision techniques while ensuring a real-time simulation. In order to better manage this trade-off between efficiency and effectiveness, we present a hybrid and adaptive environment that combines a set of methods to achieve good accuracy and performance for a simulation. Our system merges physically deformation methods (Finite Elements Method and Mass Spring Damper) with a non-physical method that approximates the formers behavior (Green Coordinates), being able to use the appropriate method depending on the situation. To simulate an approximation of a complete surgical environment, we also implement interaction tools, such as picking, burning, and haptic feedback. Our system provides great immersion for the user, consuming less computational resources and increasing update rates.