CNPq; CAPES / A termografia permite a visualização de valores de temperatura de um corpo por meio de imagens. Na área médica, encontra aplicações em oncologia, análise de queimaduras, doenças vasculares, doenças respiratórias, doenças de pele e como forma geral de verificação da vitalidade dos tecidos. A termografia 3D consiste de uma malha 3D com uma textura térmica projetada em sua superfície, oferecendo uma visualização mais precisa dos padrões de temperatura das estruturas anatômicas. Propõe-se, por meio do presente trabalho, um sistema capaz de combinar imagens termográficas 2D com sua malha 3D correspondente e, como resultado, entregar uma imagem termográfica 3D para aplicações médicas. Para isso foram utilizadas as técnicas de Otimização por Enxame de Partículas (PSO) e de reconstrução 3D Structure from Motion (SfM). Diferentemente de outros trabalhos na literatura, a malha 3D e as imagens térmicas não precisam ser adquiridas simultaneamente, não sendo necessário um arranjo mecânico dedicado. A malha 3D pode ter origem em um scanner 3D ou em uma imagem de ressonância magnética, por exemplo. Para avaliar os resultados, um phantom, isto é, um objeto estático de avaliação, com propriedades conhecidas, foi construído. Para tal, uma técnica inédita, utilizando placas de circuito impresso foi desenvolvida. Como resultado, comparações entre a saída do método proposto e o phantom, apresentaram um erro máximo de 3,73 mm e médio de 1,41 mm, com desvio padrão de 0,74 mm, em um phantom de 100 x 150 x 103,2 mm. / Thermography is an imaging method that allows temperature visualization of various regions of an object. In medicine, it finds applications related to oncology, burn trauma, vascular, respiratory and skin diseases, and as a general tissue vitality checking tool. 3D thermography adds tridimensional information to the conventional 2D thermography. It is made from a 3D mesh wrapped by thermal texture, enabling a more precise visualization of thermal patterns of anatomical structures. We propose a system capable of combining 2D thermal images with their corresponding 3D mesh, delivering a 3D thermogram for medical applications as a result. We used Particle Swarm Optimization (PSO) for mesh alignment and Structure from Motion (SfM) for 3D reconstruction in the present method. In contrast to most research found in the literature, the 3D mesh and the thermal images do not need to be acquired simultaneously, and a mechanical support for the thermal camera and the 3D scanner is not required. The 3D mesh may be acquired, for instance, from a 3D scanner or a magnetic resonance imaging machine. In order to evaluate the results, a phantom, that is, a static assessment object of known properties has been built. For this purpose, a novel technique using printed circuit boards has been developed. As a result, comparison between the output of the method and the phantom shows a maximum error of 3.73 mm and a mean error of 1.41 mm with 0.74 mm of standard deviation in phantom of 100 x 150 x 103.2 mm. / 5000

We present a variational method for unfolding of the cortex based on a user-chosen point of view as an alternative to more traditional global flattening methods, which incur more distortion around the region of interest. Our approach involves three novel contributions. The first is an energy function and its corresponding gradient flow to measure the average visibility of a region of interest of a surface from a given viewpoint. The second is an additional energy function and flow designed to preserve the 3D topology of the evolving surface. This latter contribution receives significant focus in this thesis as it is crucial to obtain the desired unfolding effect derived from the first energy functional and flow. Without it, the resulting topology changes render the unconstrained evolution uninteresting for the purpose of cortical visualization, exploration, and inspection. The third is a method that dramatically improves the computational speed of the 3D topology-preservation approach by creating a tree structure of the triangulated surface and using a recursion technique.

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.

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.

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

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) / 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) / Advancements in human genomics have simultaneously enhanced our basic understanding of the human body and ability to combat debilitating diseases. Historically, research has shown that there have been many hindrances to realizing this medicinal revolution. One hindrance, with particular regard to the kidney, has been our inability to effectively and routinely delivery genes to various loci, without inducing significant injury. However, we have recently developed a method using hydrodynamic fluid delivery that has shown substantial promise in addressing aforesaid issues. We optimized our approach and designed a method that utilizes retrograde renal vein injections to facilitate widespread and persistent plasmid and adenoviral based transgene expression in rat kidneys. Exogenous gene expression extended throughout the cortex and medulla, lasting over 1 month within comparable expression profiles, in various renal cell types without considerably impacting normal organ function. As a proof of its utility we by attempted to prevent ischemic acute kidney injury (AKI), which is a leading cause of morbidity and mortality across among global populations, by altering the mitochondrial proteome. Specifically, our hydrodynamic delivery process facilitated an upregulated expression of mitochondrial enzymes that have been suggested to provide mediation from renal ischemic injury. Remarkably, this protein upregulation significantly enhanced mitochondrial membrane potential activity, comparable to that observed from ischemic preconditioning, and provided protection against moderate ischemia-reperfusion injury, based on serum creatinine and histology analyses. Strikingly, we also determined that hydrodynamic delivery of isotonic fluid alone, given as long as 24 hours after AKI is induced, is similarly capable of blunting the extent of injury. Altogether, these results indicate the development of novel and exciting platform for the future study and management of renal injury.