Optical Coherence Tomography (OCT) is a medical imaging technique which distinguishes itself by acquiring microscopic resolution images in-vivo at millimeter scale fields of view. The resulting in images are not only high-resolution, but often multi-dimensional to capture 3-D biological structures or temporal processes. The nature of multi-dimensional data presents a unique set of challenges to the OCT user that include acquiring, storing, and handling very large datasets, visualizing and understanding the data, and processing and analyzing the data. In this dissertation, three of these challenges are explored in depth: sub-resolution temporal analysis, 3-D modeling of fiber structures, and compressed sensing of large, multi-dimensional datasets. Exploration of these problems is followed by proposed solutions and demonstrations which rely on tools from multiple research areas including digital image filtering, image de-noising, and sparse representation theory. Combining approaches from these fields, advanced solutions were developed to produce new and groundbreaking results. High-resolution video data showing cilia motion in unprecedented detail and scale was produced. An image processing method was used to create the first 3-D fiber model of uterine tissue from OCT images. Finally, a compressed sensing approach was developed which we show to guarantee high accuracy image recovery of more complicated, clinically relevant, samples than had been previously demonstrated. The culmination of these methods represents a step forward in OCT image analysis, showing that these cutting edge tools can also be applied to OCT data and in the future be employed in a clinical setting.

Realistic modeling, rendering, and animation of physical and virtual shapes have matured significantly over the last few decades. Yet, the creation and subsequent modeling of three-dimensional shapes remains a tedious task which requires not only artistic and creative talent, but also significant technical skill. The perfection witnessed in computer-generated feature films requires extensive manual processing and touch-ups. Every researcher working in graphics and related fields has likely experienced the difficulty of creating even a moderate-quality 3D model, whether based on a mental concept, a hand sketch, or inspirations from one or more photographs or existing 3D designs. This situation, frequently referred to as the content creation bottleneck, is arguably the major obstacle to making computer graphics as ubiquitous as it could be. Classical modeling techniques have primarily dealt with local or low-level geometric entities (e.g., points or triangles) and criteria (e.g., smoothness or detail preservation), lacking the freedom necessary to produce novel and creative content. A major unresolved challenge towards a new unhindered design paradigm is how to support the design process to create visually pleasing and yet functional objects by users who lack specialized skills and training. Most of the existing geometric modeling tools are intended either for use by experts (e.g., computer-aided design [CAD] systems) or for modeling objects whose visual aspects are the only consideration (e.g., computer graphics modeling systems). Furthermore, rapid prototyping, brought on by technological advances 3D printing has drastically altered production and consumption practices. These technologies empower individuals to design and produce original objects, customized according to their own needs. Thus, a new generation of design tools is needed to support both the creation of designs within the domain's constraints, that not only allows capturing the novice user's design intent but also meets the fabrication constraints such that the designs can be realized with minimal tweaking by experts. To fill this void, the premise of this thesis relies on the following two tenets: 1. users benefit from an interactive design environment that allows novice users to continuously explore a design space and immediately see the tradeoffs of their design choices. 2. the machine's processing power is used to assist and guide the user to maintain constraints imposed by the problem domain (e.g., fabrication/material constraints) as well as help the user in exploring feasible solutions close to their design intent. Finding the appropriate balance between interactive design tools and the computation needed for productive workflows is the problem addressed by this thesis. This thesis makes the following contributions: 1. We take a close look at thin shells--materials that have a thickness significantly smaller than other dimensions. Towards the goal of achieving interactive and controllable simulations we realize a particular geometric insight to develop an efficient bending model for the simulation of thin shells. Under isometric deformations (deformations that undergo little to no stretching), we can reduce the nonlinear bending energy into a cubic polynomial that has a linear Hessian. This linear Hessian can be further approximated with a constant one, providing significant speedups during simulation. We also build upon this simple bending model and show how orthotropic materials can be modeled and simulated efficiently. 2. We study the theory of Chebyshev nets--a geometric model of woven materials using a two-dimensional net composed of inextensible yarns. The theory of Chebyshev nets sheds some light on their limitations in globally covering a target surface. As it turns out, Chebyshev nets are a good geometric model for wire meshes, free-form surfaces composed of woven wires arranged in a regular grid. In the context of designing sculptures with wire mesh, we rely on the mathematical theory laid out by Hazzidakis~\cite{Hazzidakis1879} to determine an artistically driven workflow for approximately covering a target surface with a wire mesh, while globally maintaining material and fabrication constraints. This alleviates the user from worrying about feasibility and allows focus on design. 3. Finally, we present a practical design tool for the design and exploration of reconfigurables, defined as an object or collection of objects whose transformation between various states defines its functionality or aesthetic appeal (e.g., a mechanical assembly composed of interlocking pieces, a transforming folding bicycle, or a space-saving arrangement of apartment furniture). A novel space-time collision detection and response technique is presented that can be used to create an interactive workflow for managing and designing objects with various states. This work also considers a graph-based timeline during the design process instead of the traditional linear timeline and shows its many benefits as well as challenges for the design of reconfigurables.

No description available.

Mars is one of the most intriguing planets in the solar system. It is the fourth terrestrial planet and is differentiated into a core, mantle and crust. The crust of Mars is divided into the Southern highlands and the Northern lowlands. The largest volcano in the solar system, Olympus Mons is found on the crustal dichotomy boundary. The presence of isolated volcanism on the surface suggests the importance of internal activity on the planet. In addition to volcanism in the past, there has been evidence of present day volcanic activity. Convective upwelling, including decompression melting, has remained an important contributing factor in melting history of the planet. In this thesis, I investigate the production of melt in the mantle for a Newtonian rheology, and compare it with the melt needed to create Tharsis. In addition to the melt production, I analyze the 3D structure of the mantle for a stagnant lithosphere. I vary different parameters in the Martian mantle to understand the production of low or high degree structures early on to explain the crustal dichotomy. This isothermal structure in the mantle contributes to the geoid and topography on the planet. I also analyze how much of the internal density contributes to the surface topography and areoid of Mars. In contrast to Mars, Ceres is a dwarf planet in the Asteroid belt. Ceres is an icy body and it is unclear if it is differentiated into a core, mantle and crust yet. However, studies show that it is most likely a differentiated body and the mantle consists of ice and silicate. The presence of brucite and serpentine on the surface suggests the presence of internal activity. Being a massive body and also believed to have existed since the beginning of the solar system, studying Ceres will shed light on the conditions of the early solar system. Ceres has been of great interest in the scientific community and its importance has motivated NASA to launch a mission, Dawn, to study the planet. Dawn will collect data from the dwarf planet when it arrives in 2015. In my modeling studies, I implement a similar technique on Ceres, as followed on Mars, and focus on the mantle convection process and the geoid and topography. The silicate-ice mixture in the mantle gives rise to a non-Newtonian rheology that depends on the grain size of the ice particle. The geoid and topography observed for different differentiated scenarios in my modeling can be compared with the data from the Dawn mission when it arrives at Ceres in 2015. / Ph. D.

The purpose of the study was to investigate the static and dynamic architecture of supraspinatus throughout its volume in the normal and pathological state. The architecture was first investigated in cadaveric specimens free of any tendon pathology. Using a serial dissection and digitization method tailored for supraspinatus, the musculotendinous architecture was modeled in situ. The 3D model reconstructed in Autodesk MayaTM allowed for visualization and quantification of the fiber bundle architecture i.e. fiber bundle length (FBL), pennation angle (PA), muscle volume (MV) and tendon dimensions. Based on attachment sites and architectural parameters, the supraspinatus was found to have two architecturally distinct regions, anterior and posterior, each with three subdivisions. The findings from the cadaveric investigation served as a map and platform for the development of an ultrasound (US) protocol that allowed for the dynamic fiber bundle architecture to be quantified in vivo in normal subjects and subjects with a full-thickness supraspinatus tendon tear. The architecture was studied in the relaxed state and in three contracted states (60º abduction with either neutral rotation, 80º external rotation, or 80º internal rotation). The dynamic changes in the architecture within the distinct regions of the muscle were not uniform and varied as a function of joint position. Mean FBL in the anterior region shortened significantly with contraction (p<0.05) but not in the posterior. In the anterior region, mean PA was significantly smaller in the middle part compared to the deep (p<0.05). Comparison of the normal and pathological muscle found large differences in the percentage change of FBL and PA with contraction. The architectural parameter that showed the largest changes with tendon pathology was PA. In sum, the results showed that the static and dynamic fiber bundle architecture of supraspinatus is heterogeneous throughout the muscle volume and may influence tendon stresses. The architectural data collected in this study and the 3D muscle model can be used to develop future contractile models. The US protocol may serve as an assessment tool to predict the functional outcome of rehabilitative exercises and surgery.

The study of rigid body rocking is applicable to a wide variety of structural and non-structural elements. The current applications range from bridge pier and shallow footing design to hospital and industrial equipment, even art preservation. Despite the increasing number of theoretical and simulation studies of rocking motion, few experimental studies exist. Of those that have been published, most are focused on a constrained version of the complete problem introducing modifications to the physical problem with the purpose of eliminating either sliding, uplift or the three dimensional response of the body. However, all of these phenomena may affect the response of an unrestrained rocking body. Furthermore, the majority of the experimental studies that have been published have used methods that are ill-suited to comprehensive three dimensional experimental analysis of the problem. The intent of this work is two-fold. First, to present a computer vision method that allows for the experimental measurement of the rigid body translation and rotation time histories in three dimensions. Experimental results obtained with this method will be presented to demonstrate that it obtains greater than 97% accuracy when compared against National Institute of Standards and Technology traceable displacement sensors. The experimental results highlight important phenomena predicted in some state-of-the-art models for 3D rocking behavior. Second, to present experimental evidence of the importance of characterizing the support medium as deformable instead of the commonly assumed rigid model. It will be shown in this work that this assumption of a rigid support may in some cases lead to non-conservative analysis that is unable to predict rocking motion and, in some cases, even failure.

In this study, Three-dimensional (3D) airflow and dispersion of pollutants were modeled under various excess wall temperature and traffic rate using the RNG k-£` turbulence model and Boussinesq approximation, which was solved numerically using the finite volume method. The street canyon is 60 m long (=L) and 20 m wide (=W). The height of five-story buildings on both sides of the street are about 16 m (=H). Hence, the street canyon has an aspect ratio (AR=H/W) of 0.8 and a length to width ratio of 3 (=L/W). Vehicle emissions were estimated from the measured traffic flow rates and modeled as banded line sources. 3D simulations reveal that the vortex line, joining the centers of cross-sectional vortices of the street canyon, meanders between street buildings. Notably, there is also a horizontal vortex within street canyon. Pollutant concentrations decline as the height increases, and are higher on the leeward side than on the windward side. The ratio of CO pollutants between leeward side and windward side is related to wind velocity. As wind smaller than 0.7 m/sec , the ratio is 1.23¡Fhowever, the ratio is 2.03 with more wind speed above 1.2 m/sec. The CO concentration reveals that the predicted values generally follow the hourly zigzag traffic rate, indicating that CO is closely related to the traffic emissions in a street canyon. The 3D airflow in the street canyon is dominated by both wind fields on buildings top and street exit. The 3D simulations reveal that air flux is 50% higher than 2D. Entrainment of outside air reduces pollutant concentrations, thus reducing concentrations of CO¡BNOx¡Band SO2 by about 51%¡B68% and 70% ,respectively. Thermal boundary layers are very thin. Entrainment of outside air increases and pollutant concentration decreases with increasing heating condition. For T = 5 K, the upward velocity on leeward side increases by about 10%, Also, the downward velocity on windward side decreases by about 28 %. Furthermore, simulation showed that the averaged inflow speed in the lateral direction increases by about 100% as compared with T = 0 K. Hence, the pollutant concentrations with T = 5 K is ony 50% of those without heating. Simulations are followed measurements in street canyon. The averaged simulated concentrations with no heating conditions are about 11~24% and 22~36% lower than measured for CO and NOx , respectively. For heating conditions and without outside traffic source, the averaged simulated concentrations with T = 2 K are 29~36% lower than the measurements. Even at T = 5 K , the concentrations are only about 54% of those without heating, due to the fact that pollutant dilution is enhanced by buoyancy force as to having more outside air entrained into the canyon. However, when traffic emissions outside two ends of canyon were considered, the simulated CO concentrations are 23% and 19% higher than those without outside traffic sources at T = 0 K and T = 2 K, respectively. Traffic-produced turbulence (TPT) enhances the turbulent kinetic energy and the mixing of temperature and admixtures in the canyon. Although the simulated means with the TPT effect are in better agreement with the measured means than those without the TPT effect, the average reduction of CO concentration by the TPT is only about 5% at a given height and heating conditions. Factors affecting the variations between this work and other studies are addressed and explained.

The purpose of the study was to investigate the static and dynamic architecture of supraspinatus throughout its volume in the normal and pathological state. The architecture was first investigated in cadaveric specimens free of any tendon pathology. Using a serial dissection and digitization method tailored for supraspinatus, the musculotendinous architecture was modeled in situ. The 3D model reconstructed in Autodesk MayaTM allowed for visualization and quantification of the fiber bundle architecture i.e. fiber bundle length (FBL), pennation angle (PA), muscle volume (MV) and tendon dimensions. Based on attachment sites and architectural parameters, the supraspinatus was found to have two architecturally distinct regions, anterior and posterior, each with three subdivisions. The findings from the cadaveric investigation served as a map and platform for the development of an ultrasound (US) protocol that allowed for the dynamic fiber bundle architecture to be quantified in vivo in normal subjects and subjects with a full-thickness supraspinatus tendon tear. The architecture was studied in the relaxed state and in three contracted states (60º abduction with either neutral rotation, 80º external rotation, or 80º internal rotation). The dynamic changes in the architecture within the distinct regions of the muscle were not uniform and varied as a function of joint position. Mean FBL in the anterior region shortened significantly with contraction (p<0.05) but not in the posterior. In the anterior region, mean PA was significantly smaller in the middle part compared to the deep (p<0.05). Comparison of the normal and pathological muscle found large differences in the percentage change of FBL and PA with contraction. The architectural parameter that showed the largest changes with tendon pathology was PA. In sum, the results showed that the static and dynamic fiber bundle architecture of supraspinatus is heterogeneous throughout the muscle volume and may influence tendon stresses. The architectural data collected in this study and the 3D muscle model can be used to develop future contractile models. The US protocol may serve as an assessment tool to predict the functional outcome of rehabilitative exercises and surgery.

Orientador: Ruis Camargo Tokimatsu / Resumo: A modelagem tridimensional muito já contribuiu com a indústria do entretenimento e agora tem sido amplamente utilizada na manufatura e criação de novos produtos. A possibilidade de se ter um modelo de um produto a um preço menor e com uma maior rapidez tem feito essa técnica ser cada vez mais aceita em todas as áreas da engenharia. Quando já se tem um modelo real e deseja-se realizar alguma modificação, simulação ou mesmo replicar o produto, a engenharia reversa muito pode contribuir, pois permite a obtenção do modelo tridimensional a partir do objeto real. Os equipamentos de digitalização tridimensional têm um alto custo de investimento, mesmo os de baixa precisão. A comunidade de entusiastas de software e hardware livre busca também distribuir e popularizar o conhecimento compartilhando suas descobertas e contribuindo abertamente com outras iniciativas. Buscamos nesse projeto construir um scanner 3D utilizando software e hardware livre utilizando componentes de baixo custo e fácil aquisição, estabelecendo seus limites técnicos, estimulando assim a adoção de técnicas de engenharia reversa. O processo de calibragem, captura e pós tratamento da nuvem de pontos obtidas foi detalhado na construção de modelos para comparação de dimensões e levantamento de características da superfície do material. / Mestre

Submitted by Sandro Moreira (moreira.sandro@gmail.com) on 2017-01-18T18:23:17Z No. of bitstreams: 1 SandroMoreira-DissertacaoMestradoFinal.pdf: 12934831 bytes, checksum: a63cb94b201b877dc272a7bccad284bc (MD5) / Approved for entry into archive by LUIZA DE MENEZES ROMANETTO (luizamenezes@reitoria.unesp.br) on 2017-01-23T19:48:34Z (GMT) No. of bitstreams: 1 moreira_ss_me_ilha.pdf: 12934831 bytes, checksum: a63cb94b201b877dc272a7bccad284bc (MD5) / Made available in DSpace on 2017-01-23T19:48:34Z (GMT). No. of bitstreams: 1 moreira_ss_me_ilha.pdf: 12934831 bytes, checksum: a63cb94b201b877dc272a7bccad284bc (MD5) Previous issue date: 2016-12-06 / A modelagem tridimensional muito já contribuiu com a indústria do entretenimento e agora tem sido amplamente utilizada na manufatura e criação de novos produtos. A possibilidade de se ter um modelo de um produto a um preço menor e com uma maior rapidez tem feito essa técnica ser cada vez mais aceita em todas as áreas da engenharia. Quando já se tem um modelo real e deseja-se realizar alguma modificação, simulação ou mesmo replicar o produto, a engenharia reversa muito pode contribuir, pois permite a obtenção do modelo tridimensional a partir do objeto real. Os equipamentos de digitalização tridimensional têm um alto custo de investimento, mesmo os de baixa precisão. A comunidade de entusiastas de software e hardware livre busca também distribuir e popularizar o conhecimento compartilhando suas descobertas e contribuindo abertamente com outras iniciativas. Buscamos nesse projeto construir um scanner 3D utilizando software e hardware livre utilizando componentes de baixo custo e fácil aquisição, estabelecendo seus limites técnicos, estimulando assim a adoção de técnicas de engenharia reversa. O processo de calibragem, captura e pós tratamento da nuvem de pontos obtidas foi detalhado na construção de modelos para comparação de dimensões e levantamento de características da superfície do material. / The three-dimensional modeling has contributed much to the entertainment industry and has now been widely used in manufacturing and creating new products. The possibility of having a model of a product at a lower price and a higher speed have made this technique is increasingly accepted in all fields of engineering. When there is already a real model and you want to make any changes, simulation or even replicate the product, reverse engineering can greatly contribute, as it allows to obtain three-dimensional model from the real object. The three-dimensional scanning equipment have a high investment cost, even low accuracy. The community of enthusiasts of open source and open hardware also distribute and popularize knowledge sharing his findings and openly contribute to other initiatives. We seek in this study, build a scanner 3D using free software and hardware components using low-cost and easy acquisition, establishing its technical limits, stimulating the adoption of reverse engineering techniques. The calibration, capture and post-treatment process of the cloud of points obtained was detailed in the construction of models for comparison of dimensions and survey of surface characteristics of the material.