The following work explores the role of 3D printing in biological anthropology. A case study approach is used to provide an understanding of two different applications for 3D printing and to identify a potential methodology for creating 3D models. Case study one looks at the application of 3D printing to reconstruction projects using a flowerpot to test the reconstruction methodology. The second case study uses both laser surface and CT scanning to create a replica of a human skeleton. The two methods of data acquisition are evaluated for advantages and limitations in creating the virtual model. This work shows that there is a role for 3D printing in biological anthropology, but that data acquisition and processing issues are the most significant limiting factors in producing skeletal replicas.

The waterborne pathogen Batrachochytrium dendrobatidis (Bd), amphibian chytrid, is implicated as being the causative agent for global amphibian declines. The fungus attacks the keratinized skin of adult and postmetamorphic animals and the keratinized mouthparts of tadpoles. Postmetamorphic animals seem to be more susceptible to Bd than tadpoles and adult frogs. Hypotheses exist that the origin of the fungus is in Africa. During the study different aspects of Bd infections in South African frogs were examined including the distribution of Bd, cultivation of Bd, preservation of cultures, the morphology of Bd as an infection as well as in culture and finally differences in host defense. Positive and negative localities for Bd were identified through surveys conducted in South Africa. These data will be contributed to the Bd Mapping Project and the African Bd Database in order to determine whether chytrid has any environmental preferences. Cultures obtained from the positive localities were maintained and cryopreserved for use in numerous experiments. In a future study, DNA extractions from the cultures will be analyzed using multilocus sequence typing in order to determine the sequence type of South African strains in comparison with global strains. This will provide important epidemiological information concerning the origin and control of Bd. The morphology of Bd was also examined using scanning electron microscopy and laser scanning confocal microscopy. Damage due to Bd infections was more severe on the larval mouthparts of Amietia vertebralis than that of Hadromophryne natalensis. The adverse effect of Bd is therefore not limited to postmetamorphic animals. Confocal microscopy uses fluorescent stains and lasers to examine specific structures within organisms. An especially effective stain used during confocal microscopy on Bd is Calcofluor White M2R. Due to its specificity this stain can be used as an effective screening tool for Bd in tissue. The role of antimicrobial skin peptides as a defense against Bd was also examined. A. vertebralis experiences die-offs due to chytrid, while H. natalensis does not experience the same effect in the presence of Bd. H. natalensis possess more antimicrobial skin peptides against Bd with a higher effectiveness than peptides extracted from A. vertebralis. This may explain the observed susceptibility of A. vertebralis to Bd. The relevance of this study is in order to identify areas in South Africa in which the probability of finding Bd is high. This will help in the surveillance of Bd and in the identification of susceptible species to be monitored and protected against the fungus. The effect of Bd on frog species can also be determined by means of exposure experiment using cultures isolated during this study. Through the identification of peptides effective against Bd, predictions can be made with regard to the susceptibility of different frogs to Bd, improving our ability to protect the amphibian biodiversity in South Africa. With the use of confocal microscopy in the examination of Bd, we became the first group to use the method. By the identification of a stain with a high potential as a screening tool, we also contributed to the more efficient identification of Bd in tissue. Keywords: Batrachochytrium dendrobatidis, Bd, amphibian chytrid, distribution, cultivation, antimicrobial skin peptides, laser scanning confocal microscopy, Amietia vertebralis, Hadromophryne natalensis, South Africa / Thesis (M. Environmental Science)--North-West University, Potchefstroom Campus, 2009.

The following work explores the role of 3D printing in biological anthropology. A case study approach is used to provide an understanding of two different applications for 3D printing and to identify a potential methodology for creating 3D models. Case study one looks at the application of 3D printing to reconstruction projects using a flowerpot to test the reconstruction methodology. The second case study uses both laser surface and CT scanning to create a replica of a human skeleton. The two methods of data acquisition are evaluated for advantages and limitations in creating the virtual model. This work shows that there is a role for 3D printing in biological anthropology, but that data acquisition and processing issues are the most significant limiting factors in producing skeletal replicas.

Made available in DSpace on 2014-06-11T19:30:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2007-03-29Bitstream added on 2014-06-13T18:40:49Z : No. of bitstreams: 1 galvanin_eas_dr_prud.pdf: 5173646 bytes, checksum: aae51c2e230277eff607da015efe8a65 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / As metodologias para a extração automática de telhados desempenham um papel importante no contexto de aquisição de informação espacial para Sistemas de Informação Geográficas (SIG). Neste sentido, este trabalho propõe uma metodologia para extração automática de contornos de telhado de edifícios utilizando dados de varredura a laser. A metodologia baseiase em duas etapas principais: 1) Extração de regiões altas (edifícios, árvores etc.) de um Modelo Digital de Elevação (MDE) gerado a partir dos dados laser; 2) Extração das regiões altas que correspondem a contornos de telhados. Na primeira etapa são utilizadas as técnicas de divisão recursiva, via estrutura quadtree e de fusão Bayesiana de regiões considerando Markov Random Field (MRF). Inicialmente a técnica de divisão recursiva é usada para particionar o MDE em regiões homogêneas. No entanto, devido a ligeiras diferenças de altura no MDE, nesta etapa a fragmentação das regiões pode ser relativamente alta. Para minimizar essa fragmentação, a técnica de fusão Bayesiana de regiões é aplicada nos dados segmentados. Utiliza-se para tanto um modelo hierárquico, cujas alturas médias das regiões dependem de uma média geral e de um efeito aleatório, que incorpora a relação de vizinhança entre elas. A distribuição a priori para o efeito aleatório é especificada como um modelo condicional auto-regressivo (CAR). As distribuições a posteriori para os parâmetros de interesse foram obtidas utilizando o Amostrador de Gibbs. Na segunda etapa os contornos de telhados são identificados entre todos os objetos altos extraídos na etapa anterior. Levando em conta algumas propriedades de telhados e as medidas de alguns atributos (por exemplo, área, retangularidade, ângulos entre eixos principais de objetos) é construída uma função de energia a partir do modelo MRF. / Methodologies for automatic building roof extraction are important in the context of spatial information acquisition for geographical information systems (GIS). Thus, this work proposes a methodology for automatic extraction of building roof contour from laser scanning data. The methodology is based on two stages: 1) Extraction of high regions (buildings, trees etc.) from a Digital Elevation Model (DEM) derived from laser scanning data; 2) Building roof contour extraction. In the first stage is applied the recursive splitting technique using the quadtree structure followed by a Bayesian merging technique considering Markov Random Field (MRF) model. The recursive splitting technique subdivides the DEM into homogeneous regions. However, due to slight height differences in the DEM, in this stage the region fragmentation can be relatively high. In order to minimize the fragmentation, a region merging technique based on the Bayesian framework is applied to the previously segmented data. Thus, a hierarchical model is proposed, whose height values in the data depend on a general mean plus a random effect. The prior distribution for the random effects is specified by the Conditional Autoregressive (CAR) model. The posterior probability distributions are obtained by the Gibbs sampler. In the second stage the building roof contours are identified among all high objects extracted previously.

De nombreux travaux ont montré le potentiel de la télédétection parscanner laser aéroporté pour caractériser les massifs forestiers.Cependant, l'application aux forêts complexes de montagne reste encorepeu documentée. On se propose donc de tester les deux principalesméthodes permettant d'extraire des paramètres forestiers sur desdonnées acquises en zone montagneuse et de les adapter aux contraintesspéci fiques à cet environnement. En particulier on évaluera d'unepart l'apport conjoint de la régression à vecteurs de support et de laréduction de dimension pour l'estimation de paramètres de peuplement,et d'autre part l'intérêt d'un apprentissage non supervisé pour ladétection d'arbres. / Numerous studies have shown the potential of airborne laser scanningfor the mapping of forest resources. However, the application of thisremote sensing technique to complex forests encountered in mountainousareas requires further investigation. In this thesis, the two mainmethods used to derive forest information are tested with airbornelaser scanning data acquired in the French Alps, and adapted to theconstraints of mountainous environments. In particular,a framework for unsupervised training of treetop detection isproposed, and the performance of support vector regression combinedwith dimension reduction for forest stand parameters estimation isevaluated.

Submitted by Lucas Jamiro Barbosa (eng.lucasjb@gmail.com) on 2018-02-21T18:50:52Z No. of bitstreams: 1 barbosa_lj_me_prud.pdf: 5180173 bytes, checksum: 561a235397d5860ed83f8776cc40f6a4 (MD5) / Approved for entry into archive by ALESSANDRA KUBA OSHIRO ASSUNÇÃO (alessandra@fct.unesp.br) on 2018-02-21T19:37:41Z (GMT) No. of bitstreams: 1 barbosa_lj_me_prud.pdf: 5180173 bytes, checksum: 561a235397d5860ed83f8776cc40f6a4 (MD5) / Made available in DSpace on 2018-02-21T19:37:41Z (GMT). No. of bitstreams: 1 barbosa_lj_me_prud.pdf: 5180173 bytes, checksum: 561a235397d5860ed83f8776cc40f6a4 (MD5) Previous issue date: 2017-04-28 / Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) / O Sensoriamento Remoto tem-se mostrado, nos últimos anos, uma excelente ferramenta na aquisição de informações da cobertura da Terra. Dentre os diversos sensores remotos, o sistema de aquisição de dados por varredura LASER (Light Amplification by Stimulated Emission of Radiation) se apresenta como uma ferramenta poderosa na coleta de informações tridimensionais. A tecnologia lidar (Light Detection And Ranging), quando a bordo de aeronaves, pode ser denominada como Airborne Laser Scanning (ALS), diferente dos sistemas aerofotogramétricos de imageamento tradicionais, permite coletar, simultaneamente, pontos com coordenadas 3D sobre copas de árvores, bem como o terreno abaixo dela, em função da capacidade de registro de múltiplos retornos e da divergência do pulso. Por esta razão, esta tecnologia tem sido utilizada em diversas aplicações florestais, como manejo e recuperação florestal, silvicultura, exploração madeireira, dentre outras. Diversas pesquisas têm mostrado a possibilidade de utilização dos dados lidar na extração e delimitação de indivíduos arbóreos e, portanto, na estimativa de variáveis dendrométricas. Desta forma, o desenvolvimento de técnicas que proporcionem a automatização no delineamento das copas das árvores e na estimativa destas informações é de grande interesse. Contudo, grande parte das pesquisas relacionadas à detecção de árvores, delimitação de copa e estimativa de algumas variáveis são desenvolvidas considerando cenários homogêneos e específicos, onde a vegetação é caracterizada pela presença de árvores coníferas e/ou deciduais, ou florestas de exploração madeireira. Portanto, o objetivo desta pesquisa foi a implementação e avaliação de uma técnica que permita detectar indivíduos arbóreos e aglomerados, considerando um cenário urbano heterogêneo e complexo; e, destes indivíduos, estimar variáveis dendrométricas como área da copa; altura da árvore; e raio médio da copa. A metodologia proposta é realizada em três etapas e se baseia no uso do método de crescimento de regiões, aplicado à nuvem de pontos originais, ordenados quanto à altura. Além disso, são usados polígonos convexos visando a extração de indivíduos arbóreos e aglomerados. Para isso, são utilizados três parâmetros: distância mínima, buffer e perímetro comum. Foram realizados experimentos considerando dados reais e cenários diferentes em uma área urbana, para diferentes conjuntos de parâmetros utilizados no processo de delimitação das copas. Os mesmos foram avaliados quanto a acurácia temática, completeza e F-Score, calculados em função de referências obtidas de forma manual. Na delimitação de indivíduos arbóreos e aglomerados, simultaneamente, o maior valor de F-Score foi de 54% e na delimitação de indivíduos e aglomerados, em separado, o melhor resultado obtido foi 74% e 39%, respectivamente. Embora melhorias possam ser feitas visando aumentar estes indicadores, principalmente para aglomerados, pode-se considerar que o método proposto tem potencial de aplicação, sobretudo quando se tem por objetivo a extração de árvores individuais em ambiente urbano. / Remote Sensing has shown to be, in the last years, an excellent way of acquiring Earth’s surface data. Among all remote sensors, the system of data acquisition by LASER (Light Amplification by Stimulated Emission of Radiation) scanning has been presented as a powerful tool for three-dimensional information collection. lidar (Light Detection And Ranging) technology, when onboard of airplanes can be named Airborne Laser Scanning (ALS) and, differently from traditional photogrammetric techniques, allows the collection of simultaneously 3D points over tree crowns, as well as the ground underneath it, due to the recording capacity of multiple echoes arising from the divergence of the pulse. For this reason, this technology has been used in many different forest applications, as management and forest recovery, forestry, logging and others. Some researchers have shown the possibility of using lidar data on tree extraction and crown delineation and, therefore, on the estimation of their dendrometric variables. In this way, the development of techniques that can provide the automation of tree crowns delineation and estimation of this information has increased. However, most of the researches performed ever related to tree detection, canopy delineation and estimation of some dendrometric variables are developed considering homogeneous and specific scenarios where the vegetation is characterized by the presence of coniferous and/or deciduous trees. For this purpose, the objective of this research was the implementation and evaluation of a technique capable of detecting individual trees and clumps, considering a heterogeneous urban scenario. Additionally, from those individual trees some dendrometric variables such as crown area; tree height and average crown radius were estimated. Experiments were conducted considering different study areas in an urban environment varying the parameters used in the crown delineation process. Those experiments were evaluated in terms of thematic accuracy, completeness and F-Score, computed based on reference values obtained manually. When the simultaneous delimitation of arboreal individuals and agglomerates was performed the best F-Score was 54%. For independent processing, the best result was 74% and 39%, respectively, for individuals and agglomerates. Although improvements can be performed aiming to improve those indicators, mainly to clumps, it is possible to consider that the proposed method has potential, especially when the objective is the extraction of individual trees in an urban environment.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Estudos em animais experimentais evidenciaram associações significativas entre esquistossomose mansoni e hipercolesterolemia. Estudos in vitro e in vivo já demonstraram que o colesterol é essencial para Schistosoma mansoni, embora este não tenha capacidade de sintetizá-lo. A captação é realizada a partir do ambiente (cultivo ou hospedeiro) através do tegumento. O colesterol está envolvido nos mecanismos de evasão do helminto contra a resposta imunológica, além de poder participar na modulação da sinalização celular e reprodução, estimulando os órgãos reprodutores dos helmintos adultos como observado na fase aguda da infecção experimental. Este trabalho tem como objetivo avaliar se o mesmo fenômeno ocorre na fase crônica. Os helmintos foram recuperados de dez camundongos submetidos à dieta hiperlipídica ou padrão (controle) foram corados pelo carmin cloridrico e montados, individualmente, em lâmina histológica com bálsamo do Canadá. A preparação foi analisada por microscopia de campo claro nos seguintes caracteres: tegumento e o sistema reprodutor nos vermes machos (lobos testiculares, vesícula seminal, lobos testiculares supranumerários e canal ginecóforo) e, nas fêmeas (ovário, oótipo, útero, ovo, glândulas vitelínicas e espermateca). Posteriormente, algumas lâminas foram separadas para visualização pela microscopia confocal dos órgãos do sistema reprodutores acima descritos. Apesar de ter sido observado uma maior quantidade de espermatozoides, uma maior quantidade de oócitos sendo liberados no grupo da dieta, não houve diferença estatística significativa (p>0,05) entre os grupos analisados. Houve um aumento na oogênese como observado na fase aguda. Dessa forma, o colesterol pode estar relacionado com a estimulação na atividade dos órgãos reprodutores dos helmintos adultos na fase crônica da infecção. / Studies in experimental animals showed significant associations between with schistosomiasis and hypercholesterolemia. In vitro and in vivo studies have demonstrated that cholesterol is essential for Schistosoma mansoni, although this is not able to synthesize it. The capture is carried out from the environment (cultivation or host) through the tegument. The capture is carried out from the middle (cultivation or host) through the tegument. Cholesterol is involved in the helminth evasion mechanisms against the immune response, and can participate in the modulation of cell signaling and reproduction of worms by stimulating the reproductive organs of adult worms as observed in the acute phase of experimental infection. This study aims to evaluate whether the same phenomenon occurs in the chronic phase. Helminthes recovered from ten mice subjected to high fat diet or standard (control) were stained with hydrochloric carmine and mounted individually on histological slide with Canada balsam. The preparation was analyzed by bright field microscopy the following characteristics: oral sucker and ventral sucker, tubercles on tegument and the reproductive system in male worms (lobes testicular, seminal vesicles, supernumerary testicular lobes and gynaecophoric canal), and in females (ovary, ootype, uterus, egg, vitelline glands and spermatheca). Subsequently, some slides were separated for confocal microscopy for visualization of the organs of the reproductive system described above. Despite having been observed a higher amount of sperm, a larger number of oocytes are released in the diet group, there was no statistically significant difference (p> 0.05) between the groups. There was an increase in oogenesis as observed in the acute phase. Thus, cholesterol may be related to the stimulation of the activity of the reproductive organs of adult helminths in the chronic phase of infection.

Mobile laser scanning systems automate the acquisition of 3D point clouds of environments. The mapping systems are commonly mounted on cars or ships. This paper presents a flexible mapping solution mounted on an underground vehicle that is able to map underground mines in 3D in walking speeds. A clever choice of hard- and software enables the system to generate 3D maps without using GPS (global positioning system) information and without relying on highly expensive IMU (inertial measurement unit) systems.

La préparation d'interventions de maintenance dans les installations industrielles a dorénavant recours à des outils d'étude, de modélisation et de simulation basés sur l'exploitation de modèles virtuels 3D des installations. L'acquisition de ces modèles tridimensionnels s'effectue à partir de nuages de points mesurés, depuis plusieurs points de vue, par balayage angulaire horizontal et vertical d'un faisceau laser par scanner laser terrestre. L'expression dans un repère commun de l'ensemble des données acquises est appelée consolidation, au cours de laquelle les paramètres de changement de repères entre les stations sont calculés. L'objectif de cette thèse est d'améliorer la méthode d'acquisition de données laser en environnements industriels. Celle-ci doit, au final, garantir la précision et l'exactitude nécessaires des données tout en optimisant le temps et les protocoles d'acquisition sur site, en libérant l'opérateur d'un certain nombre de contraintes inhérentes au relevé topographique classique. Nous examinons, dans un premier temps, l'état de l'art des moyens et méthodes mis en œuvre lors de l'acquisition de nuages de points denses de scènes d'intérieurs complexes (Partie I). Dans un deuxième temps, nous étudions et évaluons les données utilisables pour la consolidation: données laser terrestres, algorithmes de reconstruction de primitives et systèmes de géolocalisation d'intérieur (Partie II). Dans une troisième partie, nous formalisons et expérimentons ensuite un algorithme de recalage basé sur l'utilisation de primitives appariées, reconstruites dans les nuages de points (Partie~III). Nous proposons finalement une approche probabiliste de l'appariement de primitives permettant l'intégration des informations et incertitudes a priori dans le système de contraintes utilisé pour le calcul des poses (Partie IV). / Many pre-maintenance operations of industrial facilities currently resort on to three-dimensional CAD models. The acquisition of these models is performed from point clouds measured by Terrestrial Laser Scanning (TLS). When the scenes are complex, several viewpoints for scanning, also known as stations, are necessary to ensure the completeness and the density of the survey data. The generation of a global point cloud, i.e. the expression of all the acquired data in a common reference frame, is a crucial step called registration. During this process, the pose parameters are estimated. If the GNSS systems are now a solution for many outdoor scenes, the registration of indoor TLS data still remains a challenge. The objective of this thesis is to improve the acquisition process of TLS data in industrial environments. The aim is to guarantee the precision and accuracy of acquired data, while optimizing on-site acquisition time and protocols by, as often as possible, freeing the operator from the constraints inherent to conventional topographic surveys. In a first part, we consider the state of the art of the means and methods used during the acquisition of dense point clouds of complex interior scenes (Part I). In a second part, we study and evaluate the data available for the registration: terrestrial laser scanner data, primitive reconstruction algorithms in point clouds and indoor geolocation systems (Part II). In the third part, we then formalize and experiment a registration algorithm based on the use of matched primitives, reconstructed from per station point clouds (Part III). We finally propose a probabilistic approach for matching primitives, allowing the integration of a priori information and uncertainty in the constraints system used for calculating poses (Part IV).

During the past two decades, many researchers have developed methods for the detection of structural defects at the early stages to operate the aerospace vehicles safely and to reduce the operating costs. The Surface Response to Excitation (SuRE) method is one of these approaches developed at FIU to reduce the cost and size of the equipment. The SuRE method excites the surface at a series of frequencies and monitors the propagation characteristics of the generated waves. The amplitude of the waves reaching to any point on the surface varies with frequency; however, it remains consistent as long as the integrity and strain distribution on the part is consistent. These spectral characteristics change when cracks develop or the strain distribution changes. The SHM methods may be used for many applications, from the detection of loose screws to the monitoring of manufacturing operations. A scanning laser vibrometer was used in this study to investigate the characteristics of the spectral changes at different points on the parts. The study started with detecting a load on a plate and estimating its location. The modifications on the part with manufacturing operations were detected and the Part-Based Manufacturing Process Performance Monitoring (PbPPM) method was developed. Hardware was prepared to demonstrate the feasibility of the proposed methods in real time. Using low-cost piezoelectric elements and the non-contact scanning laser vibrometer successfully, the data was collected for the SuRE and PbPPM methods. Locational force, loose bolts and material loss could be easily detected by comparing the spectral characteristics of the arriving waves. On-line methods used fast computational methods for estimating the spectrum and detecting the changing operational conditions from sum of the squares of the variations. Neural networks classified the spectrums when the desktop – DSP combination was used. The results demonstrated the feasibility of the SuRE and PbPPM methods.