CAPES : CNPq / Pessoas com paralisia cerebral apresentam grande diversidade de alterações posturais, sendo mais características as consequentes da espasticidade. Objetivando a otimização do desempenho funcional, juntamente com outros objetivos terapêuticos pode ser prescrito o uso órteses. Neste contexto a manufatura aditiva pode se apresentar como uma alternativa à fabricação de produtos personalizados de Tecnologia Assistiva, tais como as órteses. Para este fim a digitalização 3D é uma etapa importante, considerando que a geometria da anatomia do usuário será a referência para o desenvolvimento do produto em ambiente CAD 3D para posterior fabricação. No entanto os equipamentos de digitalização 3D possuem custos elevados, sendo um dos fatores que dificultam a popularização desta solução. Deste modo este trabalho visa avaliar a utilização de sistemas de baixo custo para realizar a digitalização 3D, no contexto do desenvolvimento de órteses personalizadas para punho, mão e dedos a serem fabricadas por manufatura aditiva. Foi proposto um método estruturado em três fases sendo: definição das ferramentas e sistemas a serem avaliados, definição dos parâmetros para avaliação e dos protocolos de utilização dos sistemas digitalização 3D; avaliação dos sistemas de digitalização 3D de baixo custo a partir da digitalização de uma peça padrão; e avaliação dos sistemas de digitalização 3D de baixo custo aplicados ao contexto de órteses para punho, mão e dedos. Os sistemas selecionados para a avaliação foram o Kinect 360 utilizando o programa Skanect, o sistema Kinect One com o programa 3DScan e o sistema ReMake com uma câmera Canon T3i. Os protocolos para a utilização dos sistemas de digitalização 3D de baixo custo foram: protocolo 1, com marcações visuais apenas no ambiente de digitalização; protocolo 2, com aplicação de adesivos coloridos sobre o objeto; e o protocolo 3, com a aplicação de linhas desenhadas à mão formando um xadrez sobre o objeto. Foi desenvolvida e fabricada uma peça padrão, composta por três elementos (um cone, um cilindro e um cubo seccionado). Para a avaliação dimensional foram considerados os parâmetros altura do cone, diâmetro do cilindro e medidas paralelas aos eixos X, Y e Z aferidas pela distância entre as faces opostas do cubo. Também foi realizada a análise dos desvios utilizando o programa Geomagic e uma avaliação da qualidade onde se verificou visualmente a formação dos vértices e das arestas. Para a avaliação aplicada ao contexto do desenvolvimento de órteses, foi aplicado mesmo procedimento sobre um molde da geometria do punho, mão e dedos confeccionado em atadura gessada. As digitalizações geraram 27 malhas 3D da peça padrão e 9 malhas 3D do molde. As avaliações indicaram que os sistemas Kinect 360 e Kinect One não apresentaram variação significativa entre os diferentes protocolos. Já o sistema ReMake foi o mais sensível, sendo o protocolo 3 o que gerou malhas 3D com os melhores resultados dimensionais e de qualidade em relação a todos os sistemas, com valores variando entre 0,07 mm e 0,27 mm nas análises dos desvios realizadas sobre a peça padrão. / People with cerebral palsy could have wide range of postural changes, the most characteristic are resulting from spasticity. Custom orthosis use can be prescribed in this context aiming increase functional performance and other therapeutic goals. The additive manufacturing is an alternative to the custom assistive products fabrication, such as orthoses. In this context 3D scanning is an important step, considering that the user anatomy is a geometric reference to product development in 3D CAD for further fabrication. However, the 3D scanners have high costs, one of the factors that hinder the popularization of this solution. Thus, this study aims to evaluate the use of low cost systems to perform 3D scanning in the context of custom orthoses development for wrist, hand and fingers to be fabricated by additive manufacturing. A three-phases method was proposed as follows: definition of tools and systems to be evaluated, definition of parameters for assessment, and definition of protocols for using 3D scanning systems; evaluation of low-cost 3D scanning systems using a standard piece; and evaluation of low-cost 3D scanning systems applied to context of orthosis for wrist, hand and fingers. The selected systems for the evaluation were 360 Kinect using Skanect software, Kinect One system with 3DScan software and the ReMake system with a Canon T3i camera. The low-cost 3D scanning systems used protocols were: Protocol 1, with visual markings only on the scanning environment; Protocol 2, with colored stickers application on the object; and protocol 3, with the use of hand drawn lines forming a chess pattern on the object. A standard piece was developed and manufactured, composed of three elements (a cone, a cylinder and a sectioned cube). The cone height, cylinder diameter and parallel measures to axes X, Y and Z were considered as the dimensional evaluation parameters. Also, a Deviations Analysis was performed using Geomagic software and a visual-quality evaluation that observed the formation of vertices and edges. For the evaluation on orthoses development context, the same procedure was applied on a cast of the wrist, hand and fingers. This cast was made of plaster bandages. The procedure generated 27 standard piece 3D mesh and 9 cast 3D meshes. The evaluations indicated that Kinect 360 and Kinect One systems have no significant variation between the different protocols. The ReMake system was the most sensitive, and the protocol 3 generated 3D meshes with the best dimensional and quality results among all systems. The deviations analysis performed on the standard piece indicated errors ranging between 0.07 mm and 0.27 mm for the ReMake’s 3D meshes.

The development of techniques targeting the manipulation of particles of different<p>sizes - mostly in the nano to millimeter scale - when dispersed in a carrier medium, is an increasingly important topic in many fields such as biotechnology,nanotechnology, medicine, biophysics and environmental monitoring and remediation. The underlying rationale for using such techniques stands in the sometimes compelling requirements of avoiding clogging as in micro/nano channel flows, of limiting sedimentation and wall interactions in particle/cell counting, of enhancing particle-surface interaction as in bio-sensing or of facilitating characterization and sorting as in bio-physical applications. Being developed in the frame of a Belgian national project devoted to the characterization and counting of pollutant in water media by digital holographic microscopy, this thesis tackles a peculiar class of particle manipulation techniques, commonly known as Focusing. The main goal of focusing is to avoid at best wall particle interactions and sedimentation, prevalent issues for dispersions owing in micro/mini-channels especially for applications such as optical characterization and counting.<p><p>The main attention was given to two flow focusing techniques - Hydrodynamic and Acoustic Focusing - for their wide range applicability and cost effectiveness. Hydrodynamic Focusing consists in controlling the position and spreading of the sample under investigation by means of a so-called sheath flow. A low-cost, nevertheless effective, prototype has been conceived, designed, manufactured and tested. It allowed for controlling the spreading of the sample stream and achieving a focusing ratio accounting for only 4% of the original stream width.<p><p>Acoustic Focusing takes advantage of the time-averaged pressure fields induced by the creation of standing waves in channels to manipulate and focus the dispersed particles. In the frame of this thesis, several devices have been developed using square cross section glass mini-channels. Aside from the cost-effectiveness, particles where focused in a somehow unexpected but high reproducible 3D matrix-like structure. A novel numerical model has also been implemented in order to study the conditions leading to the 3D structure formation. A good agreement between experimental and numerical results was found./Ce projet de thèse portant sur la manipulation de micro-particules dans des minicanaux s'inscrit dans le développement de cellules de flux pour des applications biologiques, qui est l'une des problématiques du projet HOLOFLOW, soutenu par<p>la région de Bruxelles Capitale. Les cellules de flux doivent permettre l'observation et la reconnaissance des micro-organismes vivants dans une large gamme de dimensions (de quelques microns à 1mm) avec la microscopie holographie digitale.<p>La problématique d'observation et de manipulation des microorganismes en flux est liée au clogging (bouchage) et à la sédimentation qui limitent la durée de vie des cellules d'observation. Ce projet de thèse s'inscrit dans cette problématique et propose deux axes d'étude pour limiter l'interaction entre organismes et canaux, la focalisation hydrodynamique, basée sur le guidage de flux, et la focalisation acoustique, basée sur la manipulation des particules.<p><p>La focalisation hydrodynamique est une technique basée sur l'injection différentiée de l'échantillon à observer et d'un fluide support. La différence des vitesses d'injection des flux permet de contrôler la dispersion des particules afin d'optimiser leur observation. Dans le cadre de cette thèse, un prototype à bas-coût a été développé et construit, permettant de focaliser les particules dans un faisceau jusqu'à 4% de leur faisceau incident.<p><p>La focalisation acoustique utilise la création d'une onde acoustique stationnaire afin de regrouper les particules en suspension au centre du canal. Au cours de cette thèse, plusieurs prototypes ont été réalisés, mettant en évidence la formation de motifs tridimensionnaux. Un model numérique a été spécialement développé afin d'étudier les conditions de génération de ces motifs, et de nombreuses expériences ont été menées afin de s'assurer de leur reproductibilité. Une bonne adéquation entre la position des particules mesurée et calculée numériquement a été démontrée. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Radiofrequency ablation (RFA) is a minimally invasive treatment for either hepatocellular carcinoma or metastasis liver carcinoma. In order to resect large lesions, the surgeon has to perform multiple time-consuming destruction cycles and reposition the RFA needle for each of them. The critical step in handling a successful ablation and preventing local recurrence is the correct positioning of the needle. For small tumors, the surgeon places the middle of the active needle tip in the center of the tumor under intra-operative ultrasound guidance. When one application is not enough to cover the entire tumor, the surgeon needs to repeat the treatment after repositioning of the needle, but US guidance is obstructed by the opacity stemming from the first RFA application. In this case the surgeon can only rely on anatomical knowledge and the repositioning of the RFA needle becomes a subjective task limiting the treatment accuracy. We have developed a computer assisted surgery guidance application for this repositioning procedure. Our software application handles the complete process from preoperative image analysis to tool tracking in the operating room. Our framework is mostly used for this RFA procedure, but is also suitable for any other medical or surgery application. / Doctorat en Sciences de l'ingénieur / info:eu-repo/semantics/nonPublished

Ce manuscrit de thèse de doctorat présente la conception et la réalisation d’un système d’imageriepour le diagnostic précoce des pathologies de la peau. Un diagnostic précoce permet de réduire lesactes chirurgicaux inutiles. Il est important de mettre en avant que seulement 20% des pathologiesfaisant office d’une opération chirurgicale, sont malignes. De plus, les pronostics de l’année 2015avançaient trois millions de nouveaux cas de cancer de la peau diagnostiqués aux ´ Etats-Unis. Basésur la tomographie par cohérence optique à balayage en longueur d’onde et une configuration pleinchamp et multi-canaux, le système d’imagerie médicale est capable d’imager en volume les couchesinternes de la peau et donc de fournir un diagnostic médical pour le professionnel de santé. Pourune fabrication en série du système portatif, les composants optiques sont micro-fabriqués sur dessubstrats et assemblés verticalement. Ces micro-composants optiques requièrent une caractérisationspécifique. Pour cela, deux systèmes ont ainsi été développés pour estimer leurs performancesoptiques. Ce travail a été réalisé dans le cadre du projet Européen VIAMOS (Vertically IntegratedArray-type Mirau-based OCT System). / The manuscript concerns the optical design and the development of a non-invasive new imagingsystem for the early diagnosis of skin pathologies. Indeed, an early diagnosis can make the differencebetween malignant and benign skin lesion in order to minimize unnecessary surgical procedure.Furthermore, prognosis for the year 2015 was that more than three millions new skin cancer caseswill be diagnosed in the United States. Based on the swept source optical coherence tomographytechnique in full-field and multiple channels configuration, the imaging system is able to perform avolumetric image of the subsurface of the skin, and thus can help in taking a better medical decision.Furthermore, for a batch-fabrication of the hand-held device, micro-optical components were made atwafer-level and vertically assembled using multi-wafer bonding. This miniaturized system requiresspecific characterization. Thus, two systems were also developed for imaging quality evaluation ofmicro-optical elements. This work has been supported by the VIAMOS (Vertically Integrated ArraytypeMirau-based OCT System) European project.

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Indiana University-Purdue University Indianapolis (IUPUI) / Mammographic density is an important risk factor for breast cancer, detecting and screening at an early stage could help save lives. To analyze breast density distribution, a good segmentation algorithm is needed. In this thesis, we compared two popularly used segmentation algorithms, EM-MPM and K-means Clustering. We applied them on twenty cases of synthetic phantom ultrasound tomography (UST), and nine cases of clinical mammogram and UST images. From the synthetic phantom segmentation comparison we found that EM-MPM performs better than K-means Clustering on segmentation accuracy, because the segmentation result fits the ground truth data very well (with superior Tanimoto Coefficient and Parenchyma Percentage). The EM-MPM is able to use a Bayesian prior assumption, which takes advantage of the 3D structure and finds a better localized segmentation. EM-MPM performs significantly better for the highly dense tissue scattered within low density tissue and for volumes with low contrast between high and low density tissues. For the clinical mammogram, image segmentation comparison shows again that EM-MPM outperforms K-means Clustering since it identifies the dense tissue more clearly and accurately than K-means. The superior EM-MPM results shown in this study presents a promising future application to the density proportion and potential cancer risk evaluation.

Indiana University-Purdue University Indianapolis (IUPUI) / We present a novel, variational and statistical approach for model-based segmentation. Our model generalizes the Chan-Vese model, proposed for concurrent segmentation of multiple objects embedded in the same image domain. We also propose a novel shape descriptor, namely the Multi-Compartment Distance Functions or mcdf. Our proposed framework for segmentation is two-fold: first, several training samples distributed across various classes are registered onto a common frame of reference; then, we use a variational method similar to Active Shape Models (or ASMs) to generate an average shape model and hence use the latter to partition new images. The key advantages of such a framework is: (i) landmark-free automated shape training; (ii) strict shape constrained model to fit test data. Our model can naturally deal with shapes of arbitrary dimension and topology(closed/open curves). We term our model Active Geometric Model, since it focuses on segmentation of geometric shapes. We demonstrate the power of the proposed framework in two important medical applications: one for morphology estimation of 3D Motor Neuron compartments, another for thickness estimation of Henle's Fiber Layer in the retina. We also compare the qualitative and quantitative performance of our method with that of several other state-of-the-art segmentation methods.

Indiana University-Purdue University Indianapolis (IUPUI) / The sympathetic nervous system strongly modulates the contractile and electrical function of the heart. The anatomical underpinnings that enable a spatially and temporally coordinated dissemination of sympathetic signals within the cardiac tissue are only incompletely characterized. In this work we took the first step of unraveling the in situ 3D microarchitecture of the cardiac sympathetic nervous system. Using a combination of two-photon excitation fluorescence microscopy and computer-assisted image analyses, we reconstructed the sympathetic network in a portion of the left ventricular epicardium from adult transgenic mice expressing a fluorescent reporter protein in all peripheral sympathetic neurons. The reconstruction revealed several organizational principles of the local sympathetic tree that synergize to enable a coordinated and efficient signal transfer to the target tissue. First, synaptic boutons are aligned with high density along much of axon-cell contacts. Second, axon segments are oriented parallel to the main, i.e., longitudinal, axes of their apposed cardiomyocytes, optimizing the frequency of transmitter release sites per axon/per cardiomyocyte. Third, the local network was partitioned into branched and/or looped sub-trees which extended both radially and tangentially through the image volume. Fourth, sub-trees arrange to not much overlap, giving rise to multiple annexed innervation domains of variable complexity and configuration. The sympathetic network in the epicardial border zone of a chronic myocardial infarction was observed to undergo substantive remodeling, which included almost complete loss of fibers at depths >10 µm from the surface, spatially heterogeneous gain of axons, irregularly shaped synaptic boutons, and formation of axonal plexuses composed of nested loops of variable length. In conclusion, we provide, to the best of our knowledge, the first in situ 3D reconstruction of the local cardiac sympathetic network in normal and injured mammalian myocardium. Mapping the sympathetic network connectivity will aid in elucidating its role in sympathetic signal transmisson and processing.

Indiana University-Purdue University Indianapolis (IUPUI) / Object segmentation, quantification, and shape modeling are important areas inmedical image processing. By combining these techniques, researchers can find valuableways to extract and represent details on user-desired structures, which can functionas the base for subsequent analyses such as feature classification, regression, and prediction. This thesis presents a new framework for building a three-dimensional (3D) hippocampal atlas model with subfield information mapped onto its surface, with which hippocampal surface registration can be done, and the comparison and analysis can be facilitated and easily visualized. This framework combines three powerful tools for automatic subcortical segmentation and 3D surface modeling. Freesurfer and Functional magnetic resonance imaging of the brain's Integrated Registration and Segmentation Tool (FIRST) are employed for hippocampal segmentation and quantification, while SPherical HARMonics (SPHARM) is employed for parametric surface modeling. This pipeline is shown to be effective in creating a hippocampal surface atlas using the Alzheimer's Disease Neuroimaging Initiative Grand Opportunity and phase 2 (ADNI GO/2) dataset. Intra-class Correlation Coefficients (ICCs) are calculated for evaluating the reliability of the extracted hippocampal subfields. The complex folding anatomy of the hippocampus offers many analytical challenges, especially when informative hippocampal subfields are usually ignored in detailed morphometric studies. Thus, current research results are inadequate to accurately characterize hippocampal morphometry and effectively identify hippocampal structural changes related to different conditions. To address this challenge, one contribution of this study is to model the hippocampal surface using a parametric spherical harmonic model, which is a Fourier descriptor for general a 3D surface. The second contribution of this study is to extend hippocampal studies by incorporating valuable hippocampal subfield information. Based on the subfield distributions, a surface atlas is created for both left and right hippocampi. The third contribution is achieved by calculating Fourier coefficients in the parametric space. Based on the coefficient values and user-desired degrees, a pair of averaged hippocampal surface atlas models can be reconstructed. These contributions lay a solid foundation to facilitate a more accurate, subfield-guided morphometric analysis of the hippocampus and have the potential to reveal subtle hippocampal structural damage associated.

Indiana University-Purdue University Indianapolis (IUPUI) / The positive identification of human remains that are decomposed, burnt, or otherwise disfigured can prove especially challenging in forensic anthropology, resulting in the need for specialized methods of analysis. Due to the unique morphological characteristics of the frontal sinus, a positive identification can be made in cases of unknown human remains, even when remains are highly cremated or decomposed. This study retrospectively reviews 3D CBCT images of a total of 43 Caucasian patients between the ages of 20-38 from the Indiana University School of Dentistry to quantify frontal sinus differences between adult males and females and investigate the usefulness of frontal sinus morphology for forensic identification. Digit codes with six sections and eleven-digit numbers were created to classify each individual sinus. It was shown that 3D CBCT images of the frontal sinus could be used to make a positive forensic identification. Metric measurements displayed a high degree of variability between sinuses and no two digit codes were identical. However, it was also shown that there were almost no quantifiable and significant sexually dimorphic differences between male and female frontal sinuses. This study confirms that sex determination should not be a primary goal of frontal sinus analysis and highlights the importance of creating a standard method of frontal sinus evaluation based on metric measurements.