Stabilization and Imaging of Cohesionless Soil Specimens

abstract: This dissertation describes development of a procedure for obtaining high quality, optical grade sand coupons from frozen sand specimens of Ottawa 20/30 sand for image processing and analysis to quantify soil structure along with a methodology for quantifying the microstructure from the images. A technique for thawing and stabilizing frozen core samples was developed using optical grade Buehler® Epo-Tek® epoxy resin, a modified triaxial cell, a vacuum/reservoir chamber, a desiccator, and a moisture gauge. The uniform epoxy resin impregnation required proper drying of the soil specimen, application of appropriate confining pressure and vacuum levels, and epoxy mixing, de-airing and curing. The resulting stabilized sand specimen was sectioned into 10 mm thick coupons that were planed, ground, and polished with progressively finer diamond abrasive grit levels using the modified Allied HTP Inc. polishing method so that the soil structure could be accurately quantified using images obtained with the use of an optical microscopy technique. Illumination via Bright Field Microscopy was used to capture the images for subsequent image processing and sand microstructure analysis. The quality of resulting images and the validity of the subsequent image morphology analysis hinged largely on employment of a polishing and grinding technique that resulted in a flat, scratch free, reflective coupon surface characterized by minimal microstructure relief and good contrast between the sand particles and the surrounding epoxy resin. Subsequent image processing involved conversion of the color images first to gray scale images and then to binary images with the use of contrast and image adjustments, removal of noise and image artifacts, image filtering, and image segmentation. Mathematical morphology algorithms were used on the resulting binary images to further enhance image quality. The binary images were then used to calculate soil structure parameters that included particle roundness and sphericity, particle orientation variability represented by rose diagrams, statistics on the local void ratio variability as a function of the sample size, and the local void ratio distribution histograms using Oda's method and Voronoi tessellation method, including the skewness, kurtosis, and entropy of a gamma cumulative probability distribution fit to the local void ratio distribution.Dissertation/ThesisM.S. Civil Engineering 201

Improved terrain type classification using UAV downwash dynamic texture effect

The ability to autonomously navigate in an unknown, dynamic environment, while at the same time classifying various terrain types, are significant challenges still faced by the computer vision research community. Addressing these problems is of great interest for the development of collaborative autonomous navigation robots. For example, an Unmanned Aerial Vehicle (UAV) can be used to determine a path, while an Unmanned Surface Vehicle (USV) follows that path to reach the target destination. For the UAV to be able to determine if a path is valid or not, it must be able to identify the type of terrain it is flying over. With the help of its rotor air flow (known as downwash e↵ect), it becomes possible to extract advanced texture features, used for terrain type classification. This dissertation presents a complete analysis on the extraction of static and dynamic texture features, proposing various algorithms and analyzing their pros and cons. A UAV equipped with a single RGB camera was used to capture images and a Multilayer Neural Network was used for the automatic classification of water and non-water-type terrains by means of the downwash e↵ect created by the UAV rotors. The terrain type classification results are then merged into a georeferenced dynamic map, where it is possible to distinguish between water and non-water areas in real time. To improve the algorithms’ processing time, several sequential processes were con verted into parallel processes and executed in the UAV onboard GPU with the CUDA framework achieving speedups up to 10x. A comparison between the processing time of these two processing modes, sequential in the CPU and parallel in the GPU, is also presented in this dissertation. All the algorithms were developed using open-source libraries, and were analyzed and validated both via simulation and real environments. To evaluate the robustness of the proposed algorithms, the studied terrains were tested with and without the presence of the downwash e↵ect. It was concluded that the classifier could be improved by per forming combinations between static and dynamic features, achieving an accuracy higher than 99% in the classification of water and non-water terrain.Dotar equipamentos moveis da funcionalidade de navegação autónoma em ambientes desconhecidos e dinâmicos, ao mesmo tempo que, classificam terrenos do tipo água e não água, são desafios que se colocam atualmente a investigadores na área da visão computacional. As soluções para estes problemas são de grande interesse para a navegação autónoma e a colaboração entre robôs. Por exemplo, um veículo aéreo não tripulado (UAV) pode ser usado para determinar o caminho que um veículo terrestre não tripulado (USV) deve percorrer para alcançar o destino pretendido. Para o UAV conseguir determinar se o caminho é válido ou não, tem de ser capaz de identificar qual o tipo de terreno que está a sobrevoar. Com a ajuda do fluxo de ar gerado pelos motores (conhecido como efeito downwash), é possível extrair características de textura avançadas, que serão usadas para a classificação do tipo de terreno. Esta dissertação apresenta uma análise completa sobre extração de texturas estáticas e dinâmicas, propondo diversos algoritmos e analisando os seus prós e contras. Um UAV equipado com uma única câmera RGB foi usado para capturar as imagens. Para classi ficar automaticamente terrenos do tipo água e não água foi usada uma rede neuronal multicamada e recorreu-se ao efeito de downwash criado pelos motores do UAV. Os re sultados da classificação do tipo de terreno são depois colocados num mapa dinâmico georreferenciado, onde é possível distinguir, em tempo real, terrenos do tipo água e não água. De forma a melhorar o tempo de processamento dos algoritmos desenvolvidos, vários processos sequenciais foram convertidos em processos paralelos e executados na GPU a bordo do UAV, com a ajuda da framework CUDA, tornando o algoritmo até 10x mais rápido. Também são apresentadas nesta dissertação comparações entre o tempo de processamento destes dois modos de processamento, sequencial na CPU e paralelo na GPU. Todos os algoritmos foram desenvolvidos através de bibliotecas open-source, e foram analisados e validados, tanto através de ambientes de simulação como em ambientes reais. Para avaliar a robustez dos algoritmos propostos, os terrenos estudados foram testados com e sem a presença do efeito downwash. Concluiu-se que o classificador pode ser melhorado realizando combinações entre as características de textura estáticas e dinâmicas, alcançando uma precisão superior a 99% na classificação de terrenos do tipo água e não água

A Virtual Grain Structure Representation System for Micromechanics Simulations

Representing a grain structure within a combined finite element computer aided engineering environment is essential for micromechanics simulations. Methods are required to effectively generate high-fidelity virtual grain structures for accurate studies. A high-fidelity virtual grain structure means a statistically equivalent structure in conjunction with desired grain size distribution features, and must be represented with realistic grain morphology. A family of controlled Poisson Voronoi tessellation (CPVT) models have been developed in this work for systematically generating virtual grain structures with the aforementioned properties. Three tasks have been accomplished in the development of the CPVT models: (i) defining the grain structure’s regularity that specifies the uniformity of a tessellation as well as deriving a control parameter based on the regularity; (ii) modelling the mapping from a grain structure’s regularity to its grain size distribution; and (iii) establishing the relation between a set of physical parameters and a distribution function. A one-gamma distribution function is used to describe a grain size distribution characteristic and a group of four physical parameters are employed to represent the metallographic measurements of a grain size distribution property. Mathematical proofs of the uniqueness of the determination of the distribution parameter from the proposed set of physical parameters have been studied, and an efficient numerical procedure is provided for computing the distribution parameter. Based on the general scheme, two- and three-dimensional CPVT models have been formulated, which respectively define the quantities of regularity and control parameters, and model the mapping between regularity and grain size distribution. For the 2D-CPVT model, statistical tests have been carried out to validate the accuracy and robustness of regularity and grain size distribution control. In addition, micrographs with different grain size distribution features are employed to examine the capability of the 2D-CPVT model to generate virtual grain structures that meet physical measurements. A crystal plasticity finite element (CPFE) simulation of plane strain uniaxial tension has been performed to show the effect of grain size distribution on local strain distribution. For the 3D-CPVT model, a set of CPFE analyses of micro-pillar compression have been run and the effects of both regularity and grain size on deformation responses investigated. Further to this, a multi-zone scheme is proposed for the CPVT models to generate virtual gradient grain structures. In conjunction with the CPVT model that controls the seed generating process within individual zones, the multi-zone CPVT model has been developed by incorporating a novel mechanism of controlling the seed generation for grains spanning different zones. This model has the flexibility of generating various gradient grain structures and the natural morphology for interfacial grains between adjacent zones. Both of the 2D- and 3D-CPVT models are capable of generating a virtual grain structure with a mean grain size gradient for the grain structure domain and grain size distribution control for individual zones. A true gradient grain structure, two simulated gradient grain structure, and a true gradient grain structure with an elongated zone have been used to examine the capability of the multi-zone CPVT model. To facilitate the CPFE analyses of inter-granular crack initiation and evolution using the cohesive zone models, a Voronoi tessellation model with non-zero thickness cohesive zone representation was developed. A grain boundary offsetting algorithm is proposed to efficiently produce the cohesive boundaries for a Voronoi tessellation. The most challenging issue of automatically meshing multiple junctions with quadrilateral elements has been resolved and a rule-based method is presented to perform the automatically partitioning of cohesive zone junctions, including data representation, edge event processing and cut-trim operations. In order to demonstrate the novelty of the proposed cohesive zone modelling and junction partitioning schemes, the CPFE simulations of plane strain uniaxial tension and three point bending have been studied. A software system, VGRAIN, was developed to implement the proposed virtual grain structure modelling methods. Via user-friendly interfaces and the well-organised functional modules a virtual grain structure can be automatically generated to a very large-scale with the desired grain morphology and grain size properties. As a pre-processing grain structure representation system, VGRAIN is also capable of defining crystallographic orientations and mechanical constants for a generated grain structure. A set of additional functions has also been developed for users to study a generated grain structure and verify the feasibility of the generated case for their simulation requirements. A well-built grain structure model in VGRAIN can be easily exported into the commercial FE/CAE platform, e.g. ABAQUS and DEFORM, via script input, whereby the VGRAIN system is seamlessly integrated into CPFE modelling and simulation processing

Example-based image color and tone style enhancement

Color and tone adjustments are among the most frequent image enhancement operations. We define a color and tone style as a set of explicit or implicit rules governing color and tone adjustments. Our goal in this paper is to learn implicit color and tone adjustment rules from examples. That is, given a set of examples, each of which is a pair of corresponding images before and after adjustments, we would like to discover the underlying mathematical relationships optimally connecting the color and tone of corresponding pixels in all image pairs. We formally define tone and color adjustment rules as mappings, and propose to approximate complicated spatially varying nonlinear mappings in a piecewise manner. The reason behind this is that a very complicated mapping can still be locally approximated with a low-order polynomial model. Parameters within such low-order models are trained using data extracted from example image pairs. We successfully apply our framework in two scenarios, low-quality photo enhancement by transferring the style of a high-end camera, and photo enhancement using styles learned from photographers and designers. © 2011 ACM.postprin

標的アイソトープ治療に向けたアスタチン211イメージングのためのコンプトンカメラの開発

Tohoku University渡部浩司課

Appearance Modelling and Reconstruction for Navigation in Minimally Invasive Surgery

Minimally invasive surgery is playing an increasingly important role for patient care. Whilst its direct patient benefit in terms of reduced trauma, improved recovery and shortened hospitalisation has been well established, there is a sustained need for improved training of the existing procedures and the development of new smart instruments to tackle the issue of visualisation, ergonomic control, haptic and tactile feedback. For endoscopic intervention, the small field of view in the presence of a complex anatomy can easily introduce disorientation to the operator as the tortuous access pathway is not always easy to predict and control with standard endoscopes. Effective training through simulation devices, based on either virtual reality or mixed-reality simulators, can help to improve the spatial awareness, consistency and safety of these procedures. This thesis examines the use of endoscopic videos for both simulation and navigation purposes. More specifically, it addresses the challenging problem of how to build high-fidelity subject-specific simulation environments for improved training and skills assessment. Issues related to mesh parameterisation and texture blending are investigated. With the maturity of computer vision in terms of both 3D shape reconstruction and localisation and mapping, vision-based techniques have enjoyed significant interest in recent years for surgical navigation. The thesis also tackles the problem of how to use vision-based techniques for providing a detailed 3D map and dynamically expanded field of view to improve spatial awareness and avoid operator disorientation. The key advantage of this approach is that it does not require additional hardware, and thus introduces minimal interference to the existing surgical workflow. The derived 3D map can be effectively integrated with pre-operative data, allowing both global and local 3D navigation by taking into account tissue structural and appearance changes. Both simulation and laboratory-based experiments are conducted throughout this research to assess the practical value of the method proposed

Design and implementation of PET detectors based on monolithic crystals and SiPMs

Esta tesis doctoral se centra tanto en el diseño como en la validación experimental de detectores de rayos gamma para escáneres de tomografía por emisión de positrones (PET, del inglés Positron Emission Tomography). El objetivo principal de esta tesis es el diseño de innovadores bloques detectores PET de alto rendimiento. La técnica PET constituye una de las principales herramientas diagnósticas en medicina nuclear, que es una especialidad médica que utiliza sustancias radiactivas con fines diagnósticos y terapéuticos. Esta técnica de imagen médica permite visualizar procesos fisiológicos y bioquímicos del cuerpo humano in vivo, mediante la administración del elemento radiotrazador. Los radiotrazadores son compuestos químicos, similares a las sustancias naturales del cuerpo, en las que uno o más átomos son sustituidos por radionúclidos emisores de fotones, para su uso en gamma cámaras y SPECT, o de positrones (la antipartícula del electrón) para PET. En el primer capítulo de la tesis se introducen las principales técnicas de imagen médicas utilizadas en la actualidad, incluyendo las técnicas de imagen funcional, de imagen anatómica y su fusión para dar lugar a imágenes multimodales. En el segundo capítulo, dado que la técnica PET es el foco de estudio central de la tesis, se describe en detalle su historia mostrando los avances de los últimos 60 años, hasta establecerse en la actualidad como una herramienta diagnóstica imprescindible en medicina. En este capítulo se describen también los principios físicos de la técnica, los algoritmos de reconstrucción y las correcciones de imagen que se emplean. Así mismo el capítulo describe el papel fundamental del tiempo de vuelo de los fotones producidos en la aniquilación del positrón y el electrón, y de la coordenada de profundidad de interacción (DOI, del inglés Depth of Interaction). A continuación, en el tercer capítulo, se describen con detalle los materiales y métodos empleados en PET, haciendo especial énfasis en aquellos utilizados para el desarrollo de esta tesis. En la actualidad, la mayoría de sistemas PET comerciales están constituidos por bloques detectores basados en cristales centelleadores pixelados (matrices de pequeños cristales). Dichos cristales permiten estimar las coordenadas (x, y) del impacto del fotón de manera sencilla, sin embargo, la obtención de la coordenada de profundidad de interacción (z), imprescindible para obtener una buena resolución espacial sobretodo en los bordes del campo de visión del escáner, resulta una tarea difícil que requiere el uso de materiales adicionales y por tanto incrementan el precio del escáner. Una alternativa a la configuración anterior, es el uso de cristales monolíticos o continuos los cuales están constituidos por una única pieza de material centelleador que permite “observar” la distribución de fotones ópticos generada. Esta información es utilizada para obtener con precisión las coordenadas 3D de impacto del fotón (x, y, z) en el cristal sin necesidad de otros materiales. Por este motivo, en esta tesis doctoral se ha llevado a cabo el diseño de detectores basados en estos cristales monolíticos acoplados a fotosensores de estado sólido compatibles con equipos de resonancia magnética. En este capítulo se muestran los resultados obtenidos en la caracterización de diferentes tipos de cristales, geometrías y tratamientos aplicados a la superficie de los bloques detectores. Finalmente se presenta una breve descripción de los equipos que han motivado los estudios realizados en la tesis. Dado que el formato de esta tesis esta basado en un compendio de los artículos más relevantes publicados durante el transcurso de los estudios de doctorado, el cuarto capítulo incluye una copia de los artículos publicados más relevantes tal y como se muestran en las revistas científicas. Se presentan un total de 6 artículos que recogen los principales resultados obtenidos durante los estudios de doctorado. Dada la calidad de los resultados globales obtenidos, dos de los bloques detectores diseñados constituyen la base de dos sistemas PET dedicados al estudio del cerebro humano, el inserto MINDView (proyecto europeo FP7) y el escáner CareMiBrain (proyecto europeo Horizont 2020). El equipo MINDView, que es un inserto compatible con todas las resonancias magnéticas del mundo, ha sido instalado en el hospital de la Universidad Técnica de Múnich y actualmente está en la fase previa a comenzar un estudio con pacientes. En la tesis se recogen las pruebas de validación realizadas tanto a nivel del bloque detector como del equipo final. Respecto al equipo CareMiBrain, que es un escáner PET dedicado al estudio del Alzheimer y de otras enfermedades de deterioro cognitivo, ha sido instalado en Madrid y los primeros pacientes ya han sido escaneados satisfactoriamente. En la tesis se recoge el diseño y los resultados de caracterización del bloque detector. Además del diseño y caracterización de dichos bloques detectores, se muestran también los resultados y conclusiones obtenidas en otros estudios de investigación, tales como la caracterización de una gran variedad de geometrías de detectores, la optimización de la extracción de la luz en cristales BGO (fueron pioneros en los equipos PET pero se sustituyeron por los nuevos cristales que son más rápidos), tanto en forma pixelada como en bloques monolíticos, y un enfoque de detector híbrido que utiliza capas monolíticas y pixeladas en un mismo bloque detector. Se ha prestado especial atención a la caracterización y determinación de la DOI dentro de los bloques monolíticos, reduciendo el error de paralaje en la imagen final reconstruida. El quinto capítulo contiene un resumen y conclusiones de los resultados de esta tesis. El sexto y séptimo capítulo, contienen un resumen en castellano y valenciano respectivamente, de los objetivos, motivación, materiales, métodos, resultados y conclusiones de la tesis doctoral. Finalmente, el Apéndice A muestra una lista completa de los artículos científicos publicados durante la tesis (incluyendo los seleccionados para el compendio).This doctoral thesis focuses on both the design and experimental validation of gamma-ray detectors suitable for Positron Emission Tomography (PET) scanners. The main objective is the design of high efficiency PET detector blocks. The PET technique constitutes one of the main diagnostic tools in Nuclear Medicine, which is a medical specialty that uses radioactive substances for diagnostic and therapeutic purposes. This Medical Imaging technique allows one to visualize physiological and biochemical processes of the human body in vivo, by means of the administration of a radiotracer element. Radiotracers are chemical compounds, similar to the body's natural substances, in which one or more atoms are replaced by radionuclides that emit photons, for use in gamma and SPECT cameras, or positrons (the antiparticle of the electron) for PET. The first chapter of the thesis introduces the main Medical Imaging techniques that are currently used, including functional and anatomical imaging as well as their possible merging generating multimodal images. In the second chapter, since PET imaging is the focus of this thesis, an extensive description of this technique is outlined. The chapter begins with a brief history of PET, showing the advances over the last 60 years until being established as an essential diagnostic tool in medicine. This chapter also describes the physical principles of PET, the reconstruction algorithms and the applied image corrections techniques. In addition to the basic concepts, the role of Time of Flight (TOF) and DOI in PET are described in this chapter. The third chapter describes in detail the materials and methods used in PET, making special emphasis on those used for the development of this work. Currently, most commercial PET systems consist of detector blocks based on pixelated scintillation crystals (matrices of small crystals). These crystals allow one for an easy estimation of the planar impact coordinates of the gamma-ray within the crystal (x, y). However, estimating the depth of interaction coordinate (z), which is essential to obtain a good spatial resolution especially at the edges of the field of view of the scanner, is a difficult task that requires the use of extra materials and therefore increases the price of the scanner. An alternative to that configuration is the use of monolithic crystals, which are constituted by a single piece of scintillating material that permits to characterize the complete, flashing light distribution. This information is used to obtain the 3D impact coordinates of the photon (x, y, z) within the crystal with high resolution and without the need for extra materials. For this reason, this doctoral thesis focusses on the design of PET detector blocks based on monolithic crystals coupled to solid state photosensors. These components are compatible with magnetic fields and therefore, suitable for their simultaneous use with Magnetic Resonance Imaging (MRI) systems. This chapter summarizes the results obtained in the characterization of different types of crystals, geometries and treatments applied to the crystal surface of the detector blocks. Finally, a brief description of the PET systems that have motivated the studies carried out in the thesis is presented. Since this thesis is based on a compendium of the most relevant articles published during the course of the PhD studies, Chapter 4 presents a copy of those research articles, as exactly shown in the different per-reviewed journals, including a brief introduction highlighting their main results. A total of 6 articles are presented, which contain the main results obtained during the doctoral studies. Given the quality of the overall obtained results, two of the designed detector blocks have been selected as the basis of two PET systems dedicated to the study of the human brain namely, i) the MINDView insert (European Union FP7 project) and, ii) the CareMiBrain stand-alone scanner (European Union project Horizon 2020). The MINDView system, which is a PET insert compatible with MRI scanners, has been installed at Technical University of Munich and is currently starting scanning patients with depression and schizophrenia. The thesis includes the validation tests carried out at the level of the detector block and of the final equipment. The CareMiBrain system, which is a PET scanner dedicated to the study of the Alzheimer disease and other causes of cognitive decline, has been installed in a hospital in Madrid and the first patients have already been successfully scanned. The thesis contains the design and results of characterization of the CareMiBrain detector block. In addition to the design and characterization of those detector blocks, other research studies have been carried out during the course of this thesis, such as the characterization of a large variety of photosensor geometries, the optimization of light extraction in BGO crystals, both in pixelated and monolithic geometries, and a hybrid detector approach that uses monolithic and pixellated layers in the same detector block. Special emphasis has been given to the characterization and estimation of the DOI coordinate within monolithic blocks, reducing the parallax error in the reconstructed final image. Chapter 5 contains a summary of the results and conclusions of this thesis. Chapters 6 and 7 summarize, in Spanish and Valencian, respectively, the objectives, motivation, materials, methods, results and conclusions of this doctoral thesis. A complete list of all the per-reviewed articles (including those selected for this compendium) and the conference proceedings published during the development of this thesis can be found in Appendix A

The nature of growth in the biofuel feedstock and bloom-forming green macroalga Ulva

Ulva is a genus of multicellular green algae that is phylogenetically similar to uni- cellular green algae such as Chlamydomonas and Ostreococcus. Ulva is present in much of the coastal benthic zones worldwide, and is of great interest for three main reasons. Firstly, Ulva is an important feedstock for biofuels. Secondly, many Ulva species are massively proliferating organisms that cause Harmful Algal Blooms, which are ecologically devastating. Finally, Ulva is an important model organism that could elucidate the evolution of multicellularity. This thesis investigates the physiology of growth in Ulva in four sequential results chapters. The first establishes a statistical proof for the goodness of fit of gene family occupancy data to a discrete power law model. This was an assumption used in the only Ulva genome study, which found no genomic signature for multicellularity. This establishes the baseline for the in- vestigation of bottom-up morphogenesis in Ulva. The second is the investigation of differential growth, by identifying cell tessellation patterns in different morphologies of Ulva thalli, namely the “ribbon” and “leaf” morphotypes, with mathematical mod- els using Voronoi tessellations. The third expands investigates differential growth in the ribbon and leaf morphotypes with a focus on identifying potential mechanisms with further mathematical models using Centroidal Voronoi Tessellations. The fourth aims to develop experimental techniques to confirm the hypotheses arising from the mathematical modelling in the second and third chapters. The first part involves the use of EdU cellular proliferation assays. The remainder of the chapter will investigate the development of a live-imaging biomass monitoring system that aims to improve the accuracy, reliability and temporal resolution of aquatic biomass measurements. It can be concluded that Ulva does not show a genomic signature for multicellularity, and bottom-up mechanisms likely explain its morphogenesis and morphologies

Development and Performance Evaluation of High Resolution TOF-PET Detectors Suitable for Novel PET Scanners

Tesis por compendio[ES] La Tomografía por Emisión de Positrones (PET) es una de las técnicas más importantes en la medicina de diagnóstico actual y la más representativa en el campo de la Imagen Molecular. Esta modalidad de imagen es capaz de producir información funcional única, que permite la visualización en detalle, cuantificación y conocimiento de una variedad de enfermedades y patologías. Áreas como la oncología, neurología o la cardiología, entre otras, se han beneficiado en gran medida de esta técnica. A pesar de que un elevado número de avances han ocurrido durante el desarrollo del PET, existen otros que son de gran interés para futuras investigaciones. Uno de los principales pilares actualmente en PET, tanto en investigación como en desarrollo, es la obtención de la información del tiempo de vuelo (TOF) de los rayos gamma detectados. Cuando esto ocurre, aumenta la sensibilidad efectiva del PET, mejorando la calidad señal-ruido de las imágenes. Sin embargo, la obtención precisa de la marca temporal de los rayos gamma es un reto que requiere, además de técnicas y métodos específicos, compromisos entre coste y rendimiento. Una de las características que siempre se ve afectada es la resolución espacial. Como discutiremos, la resolución espacial está directamente relacionada con el tipo de centellador y, por lo tanto, con el coste del sistema y su complejidad. En esta tesis, motivada por los conocidos beneficios en imagen clínica de una medida precisa del tiempo y de la posición de los rayos gamma, proponemos configuraciones de detectores TOF- PET novedosos capaces de proveer de ambas características. Sugerimos el uso de lo que se conoce como métodos de "light-sharing", tanto basado en cristales monolíticos como pixelados de tamaño diferente al del fotosensor. Estas propuestas hacen que la resolución espacial sea muy alta. Sin embargo, sus capacidades temporales han sido muy poco abordadas hasta ahora. En esta tesis, a través de varios artículos revisados, pretendemos mostrar los retos encontrados en esta dirección, proponer determinadas configuraciones y, además, indagar en los límites temporales de éstas. Hemos puesto un gran énfasis en estudiar y analizar las distribuciones de la luz centellante, así como su impacto en la determinación temporal. Hasta nuestro conocimiento, este es el primer trabajo en el que se estudia la relación de la determinación temporal y la distribución de luz de centelleo, en particular usando SiPM analógicos y ASICs. Esperamos que esta tesis motive y permita otros muchos trabajos orientados en nuevos diseños, útiles para instrumentación PET, así como referencia para otros trabajos. Esta tesis esta organizada como se describe a continuación. Hay una introducción compuesta por tres capítulos donde se resumen los conocimientos sobre imagen PET, y especialmente aquellos relacionados con la técnica TOF-PET. Algunos trabajos recientes, pero aún no publicados se muestran también, con el objetivo de corroborar ciertas ideas. En la segunda parte se incluyen las cuatro contribuciones que el candidato sugiere para el compendio de artículos.[CA] La Tomografia per Emissió de Positrons (PET) és una de les tècniques més importants en la medicina de diagnòstic actual i la més representativa en el camp de la Imatge Molecular. Esta modalitat d'imatge és capaç de produir informació funcional única, que permet la visualització en detall, quantificació i coneixement d'una varietat de malalties i patologies. Àrees com l'oncologia, neurologia o la cardiologia, entre altres, s'han beneficiat en gran manera d'aquesta tècnica. Tot i que un elevat nombre d'avanços han ocorregut durant el desenvolupament del PET, hi ha altres que són de gran interés per a futures investigacions. Un dels principals pilars actuals en PET, tant en investigació com en desenvolupament, és l'obtenció de la informació del temps de vol (TOF en anglès) dels raigs gamma detectats. Quan açò ocorre, augmenta la sensibilitat efectiva del PET, millorant la qualitat senyal-soroll de les imatges. No obstant això, l'obtenció precisa de la marca temporal dels raigs gamma és un repte que requerix, a més de tècniques i mètodes específics, compromisos entre cost i rendiment. Una de les característiques que sempre es veu afectada és la resolució espacial. Com discutirem, la resolució espacial està directament relacionada amb el tipus de centellador, i per tant, amb el cost del sistema i la seua complexitat. En aquesta tesi, motivada pels coneguts beneficis en imatge clínica d'una mesura precisa del temps i de la posició dels raigs gamma, proposem nouves configuracions de detectors TOF-PET capaços de proveir d'ambduess característiques. Suggerim l'ús del que es coneix com a mètodes de "light-sharing", tant basat en cristalls monolítics com pixelats de diferent tamany del fotosensor. Aquestes propostes fan que la resolució espacial siga molt alta. No obstant això, les seues capacitats temporals han sigut molt poc abordades fins ara. En aquesta tesi, a través de diversos articles revisats, pretenem mostrar els reptes trobats en aquesta direcció, proposar determinades configuracions i, a més, indagar en els límits temporals d'aquestes. Hem posat un gran èmfasi a estudiar i analitzar les distribucions de la llum centellejant, així com el seu impacte en la determinació temporal. Fins al nostre coneixement, aquest és el primer treball en què s'estudia la relació de la determinació temporal i la distribució de llum de centelleig, en particular utilitzant SiPM analògics i ASICs. Esperem que aquesta tesi motive i permeta molts altres treballs orientats en nous dissenys, útils per a instrumentació PET, així com referència per a altres treballs. Aquesta tesi esta organitzada com es descriu a continuació. Hi ha una introducció composta per tres capítols on es resumeixen els coneixements sobre imatge PET i, especialmente, aquells relacionats amb la tècnica TOF-PET. Alguns treballs recents, però encara no publicats es mostren també, amb l'objectiu de corroborar certes idees. La segona part de la tesi conté els quatre articles revisats que el candidat suggereix.[EN] Positron Emission Tomography (PET) is one of the greatest tools of modern diagnostic medicine and the most representative in the field of molecular imaging. This imaging modality, is capable of providing a unique type of functional information which permits a deep visualization, quantification and understanding of a variety of diseases and pathologies. Areas like oncology, neurology, or cardiology, among others, have been well benefited by this technique. Although numerous important advances have already been achieved in PET, some other individual aspects still seem to have a great potential for further investigation. One of the main trends in modern PET research and development, is based in the extrapolation of the Time- Of-Flight (TOF) information from the gamma-ray detectors. In such case, an increase in the effective sensitivity of PET is accomplished, resulting in an improved image signal-to-noise ratio. However, the direction towards a precise decoding of the photons time arrival is a challenging task that requires, besides specific approaches and techniques, tradeoffs between cost and performance. A performance characteristic very habitually compromised in TOF-PET detector configurations is the spatial resolution. As it will be discussed, this feature is directly related to the scintillation materials and types, and consequently, with system cost and complexity. In this thesis, motivated by the well-known benefits in clinical imaging of a precise time and spatial resolution, we propose novel TOF-PET detector configurations capable of inferring both characteristics. Our suggestions are based in light sharing approaches, either using monolithic detectors or crystal arrays with different pixel-to-photosensor sizes. These approaches, make it possible to reach a precise impact position determination. However, their TOF capabilities have not yet been explored in depth. In the present thesis, through a series of peer-reviewed publications we attempt to demonstrate the challenges encountered in these kinds of configurations, propose specific approaches improving their performance and eventually reveal their limits in terms of timing. High emphasis is given in analyzing and studying the scintillation light distributions and their impact to the timing determination. To the best of our knowledge, this is one of the first works in which such detailed study of the relation between light distribution and timing capabilities is carried out, especially when using analog SiPMs and ASICs. Hopefully, this thesis will motivate and enable many other novel design concepts, useful in PET instrumentation as well as it will serve as a helpful reference for similar attempts. The present PhD thesis is organized as follows. There is an introduction part composed by three detailed sections. We attempt to summarize here some of the knowledge related to PET imaging and especially with the technique of TOF-PET. Some very recent but still unpublished results are also presented and included in this part, aiming to support statements and theories. The second part of this thesis lists the four peer-reviewed papers that the candidate is including.This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No 695536). It has also been supported by the Spanish Ministerio de Economía, Industria y Competitividad under Grants No. FIS2014-62341-EXP and TEC2016-79884-C2-1-R. Efthymios Lamprou has also been supported by Generalitat Valenciana under grant agreement GRISOLIAP-2018-026.Lamprou, E. (2021). Development and Performance Evaluation of High Resolution TOF-PET Detectors Suitable for Novel PET Scanners [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/162991TESISCompendi

Correcting misclassification errors in crowdsourced ecological data: A Bayesian perspective

Many research domains use data elicited from "citizen scientists" when a direct measure of a process is expensive or infeasible. However, participants may report incorrect estimates or classifications due to their lack of skill. We demonstrate how Bayesian hierarchical models can be used to learn about latent variables of interest, while accounting for the participants' abilities. The model is described in the context of an ecological application that involves crowdsourced classifications of georeferenced coral-reef images from the Great Barrier Reef, Australia. The latent variable of interest is the proportion of coral cover, which is a common indicator of coral reef health. The participants' abilities are expressed in terms of sensitivity and specificity of a correctly classified set of points on the images. The model also incorporates a spatial component, which allows prediction of the latent variable in locations that have not been surveyed. We show that the model outperforms traditional weighted-regression approaches used to account for uncertainty in citizen science data. Our approach produces more accurate regression coefficients and provides a better characterization of the latent process of interest. This new method is implemented in the probabilistic programming language Stan and can be applied to a wide number of problems that rely on uncertain citizen science data.Comment: 18 figures, 5 table