A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation. / May 2007

3D modeling of real objects has an increasing importance in numerous areas. Although many methods and solutions are already proposed for 3D data acquisition, research continuing in this area is still intense. However, a crucial drawback about 3D data extraction algorithms is their testing and validation difficulty. Additionally, obtaining calibrated 2D and 3D imaging systems is troublesome due to their high effort demand for calibration and high cost. In this thesis, a 2D/3D Imaging Simulator is proposed in order to ease development and testing of 3D data interpretations of different methods and also to generate synthetic images for miscellaneous use. Furthermore, an example application on FRGC database is explained in detail.

A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation.

It is well established that acquiring large amounts of range data with vision sensors can quickly lead to important data management challenges where processing capabilities become saturated and pre-empt full usage of the information available for autonomous systems to make educated decisions. While sub-sampling offers a naïve solution for reducing dataset dimension after acquisition, it does not capitalize on the knowledge available in already acquired data to selectively and dynamically drive the acquisition process over the most significant regions in a scene, the latter being generally characterized by variations in depth and surface shape in the context of 3D imaging. This thesis discusses the development of two formal improvement measures, the first based upon surface meshes and Ordinary Kriging that focuses on improving scene accuracy, and the second based upon probabilistic occupancy grids that focuses on improving scene coverage. Furthermore, three selection processes to automatically choose which locations within the field of view of a range sensor to acquire next are proposed based upon the two formal improvement measures. The first two selection processes each use only one of the proposed improvement measures. The third selection process combines both improvement measures in order to counterbalance the parameters of the accuracy of knowledge about the scene and the coverage of the scene. The proposed algorithms mainly target applications using random access range sensors, defined as sensors that can acquire depth measurements at a specified location within their field of view. Additionally, the algorithms are applicable to the case of estimating the improvement and point selection from within a single point of view, with the purpose of guiding the random access sensor to locations it can acquire. However, the framework is developed to be independent of the range sensing technology used, and is validated with range data of several scenes acquired from many different sensors employing various sensing technologies and configurations. Furthermore, the experimental results of the proposed selection processes are compared against those produced by a random sampling process, as well as a neural gas selective sensing algorithm.

The application of 3D laser scanning to the analysis of human skeletal remains provides the opportunity for new methodological approaches, including for the assessment of age at death. The focus of this new perspective revolves around the question of whether morphological development of skeletal features can be captured with quantitative measurements taken from 3D scanned representations of physical specimens, with the aims of adding an increased level of accuracy and precision over currently employed age estimations methods that focus on visual, and often subjective, assessments based comparisons with plaster casts and written descriptions. The current research was conducted to determine if specific morphological features of the pubic symphysis could be isolated and quantified on 3D models, and whether these measurements captured the general age related trends of symphyseal development. Using CAD software, each symphyseal face was divided into half and quadrant specific sections in an attempt to better capture the development of symphyseal morphology. A sample of left male pubic symphyses (n = 40) scanned from a well-documented collection of known-age individuals (Coimbra Identified Skeletal Collection) was selected for this study. Seven symphyseal features were identified from the Suchey-Brooks method unisex age phase descriptions. Eight measurements were generated to quantify these features. The data for each feature was subjected to linear regression analyses to test for statistical correspondence to known chronological age at death. Rim completeness, billowing height and area, and depth of symphyseal face depression demonstrated the strongest relationships with chronological age, while curvature of the ventral rampart and the angle of the dorsal aspect, showed significant but weak relationships with known age. Degree of dorsal lipping and dorsal rampart curvature showed no relationship with age. The results of the study suggest that quantitative assessments of morphological changes at the pubic symphysis are possible and therefore can potentially add further insights into age at death estimations based on the pubic symphysis, as measurements taken within CAD software are far more precise than traditional measuring implements. This study illustrates the potential for 3D imaging to improve the methods of osteological analyses applied particularly in the fields of bioarchaeology and forensic anthropology. / Graduate

A robotic microscope was designed using a microcontroller to take time-lapse digital photographs of developing salamander embryos. The microcontroller operated three stepper motors to control three-axis movement accurately, and two six mega-pixel digital cameras to capture through-focus time-lapse digital pictures of six views of Ambystoma mexicanum embryos (axolotl, a salamander). The device is designed to take images every five minutes for 80 hours of early development, from fertilization to stage 20, when the neural tube closes to form the brain and spinal column. Techniques to enhance the embryo images were investigated including image fusion to get in-focus views from a stack of images. In the early embryo surface epithelial cells differentiate to form neural tissue and external skin tissue. Observing the whole embryo surface at cellular level will give a better idea of the stress and strain each cell undergoes and what physical forces are involved in cell differentiation.

This study investigated arch dimension changes associated with growth and tooth wear in Australian Aboriginals aged from age 8 to 15 years using 2D and 3D digital imaging systems. Serial dental casts of Australian Aboriginals from Yuendumu were used in the study. The sample comprised 25 females and 24 males for whom casts were available at ages of 8, 12 and 15 years ( a total of 294 dental study casts). The primary method of data acquisition involved obtaining digital photographs and digitizing the images using an Apple IIGS computer and customised software program. A subset of 40 dental stone models (5 individuals at ages 8, 12, 15 and 18 years) were duplicated and scanned using the Minolta Vivid 900 laser surface scanner at the DSIRO Laboratories, National University Singapore. The 3-D images were digitised using the Rapidform software package (Inus, technology, Seoul, Korea). Study variables included mesiodistal crown diameters, arch widths, arch depths and arch lengths. Mesiodistal crown dimensions in males tended to be larger than those in females. All arch dimensions were significantly larger in males than females. Upper and lower Intercanine width increased from age 8 to age 12 years but did not change thereafter. Upper and lower intermolar widths increased with age from 8 years to 15 years while arch depth decreased. No significant reduction in arch lengths was found from age 12 to 15 years. The two imaging systems were comparable in their measurement reliability, although the 2D method provided consistently larger crown diameters than the 3D method. Changes in arch dimensions with age in the Aboriginal sample were similar to those reported for other populations. However, no measurable change was detected in arch length over time, even though the Aboriginals had abrasive diets that would be expected to contribute to interproximal wear. It was concluded that the 2D and 3D imaging methods were suitable for clinical use but would require further refinement for research projects aimed at assessing minor changes in arch lengths associated with interproximal wear. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1347947 / Thesis (D.Clin.Dent.) -- University of Adelaide, School of Dentistry, 2008

Dans cette thèse, nous présentons un système complet permettant de sauvegarder un processus destructif tel qu'une dissection anatomique. Nous proposons une méthode depuis l'acquisition 3D des données jusqu'à la visualisation interactive et immersive, dans le but de créer une vérité terrain. L'acquisition 3D regroupe l'acquisition de la géométrie par scanner laser (maillage) ainsi que de l'information de couleur par le biais d'un appareil photo haute résolution (texture). Ce processus d'acquisition et répété au cours de la dissection du spécimen. Les différentes acquisitions du spécimen sont représentées par des surfaces 3D texturées. Elles sont ensuite recalées entre elles. Un expert anatomiste peut alors explorer ces différentes étapes de dissections modélisées dans une visualisation immersive en utilisant du matériel d'interaction (bras haptique). Un outil d'étiquetage permet une segmentation manuelle précise de régions d'intérêt visibles sur chacune des surfaces 3D. Un objet tridimensionnel peut ensuite être reconstruit et proposé à l'utilisateur sur la base des zones d'intérêt étiquetées. Le but étant de créer des vérité terrains afin de confronter des résultats issus de modalités d'acquisition volumiques (IRM). Nous montrons l'application de la méthode à la reconstruction de faisceaux de fibres blanches humaine dans le but de valider des résultats de tractographie. / In this thesis, we present a system to keep track of a destructive process such as a medical specimen dissection, from data acquisition to interactive and immersive visualization, in order to build ground truth models. Acquisition is a two-step process, first involving a 3D laser scanner to get a 3D surface, and then a high resolution camera for capturing the texture. This acquisition process is repeated at each step of the dissection, depending on the expected accuracy and the specific objects to be studied. Thanks to fiducial markers, surfaces are registered on each others. Experts can then explore data using interaction hardware in an immersive 3D visualization. An interactive labeling tool is provided to the anatomist, in order to identify regions of interest on each acquired surface. 3D objects can then be reconstructed according to the selected surfaces. We aim to produce ground truths which for instance can be used to validate data acquired with MRI. The system is applied to the specific case of white fibers reconstruction in the human brain.

Biofilms are microbial communities developing at the interface between two phases, usually solidliquid, where the micro-organisms are nested in a self-secreted polymer matrix. The biofilm mode of growth is predominant in nature (for e.g. the slimy matter forming on rocks at river bottoms, the viscous deposit in water pipes or even dental plaque) and confers a suitable environment for the development of the micro-organisms. This is particularly the case for porous media which provide favourable substrates given their significant surface to volume ratio. The multi-physical framework of biofilms in porous media is highly complex where the mechanical, chemical and biological aspects interacting at different scales are poorly understood and very partially controlled. An example is the feedback mechanism between flow, spatial distribution of the micro-organisms and the transport of nutrient (by diffusion and advection). Biofilms developing in porous media are a key process of many engineering applications, for example biofilters, soil bio-remediation, CO2 storage and medical issues like infections. Progress in this domain is substantially hindered by the limitations of experimental techniques in metrology and imaging in opaques structures. The main objective of this thesis is to propose robust and reproducible experimental methodologies for the investigation of biofilms in porous media. An experimental workbench under controlled physical and biological conditions is proposed along with a validated 3D imaging protocol based on X-ray micro-tomography (XR MT) using a novel contrast agent (barium sulfate and agarose gel) to quantify the spatial distribution of the biofilm. At first, the XR MT-based methodology is compared to a commonly used techniques for biofilm observation: one or multiple photon excitation fluorescence microscopy, here two-photon laser scanning microscopy (TPLSM). This comparison is performed on Pseudomonas Aeruginosa biofilms grown in transparent glass capillaries which allows for the use of both imaging modalities. Then, the study of uncertainty associated to different metrics namely volume, 3D surface area and thickness, is achieved via an imaging phantom and three different segmentation algorithms. The quantitative analysis show that the protocol enables a visualisation of the biofilm with an uncertainty of approximately 17% which is comparable to TPLSM (14%). The reproducibility and robustness of the XR MT-based methodology is demonstrated. The last step of this work is the achievement of a novel bioreactor elaborated by additive manufacturing and controlled by a high-performance micro-fluidic system. The experimental workbench that we have designed enables to monitor in real-time the evolution of transport properties (effective permeability), O2 concentrations and biofilm detachment by spectrophotometry, all under controlled hydrodynamical conditions. Our methodology allows to investigate the influence of biophysical parameters on the colonisation of the porous medium, for example, the influence of flow rate or nutrient concentration on the temporal development of the biofilm. In conclusion, the thesis work proposes a robust and reproducible experimental methodology for the controlled growth and 3D imaging of biofilms in porous media; while providing versatility in the control of the substrate’s micro-architecture as well as on the flow and biochemical culture conditions. To our knowledge, the scientific approach followed, along with the experimental apparatus, form the most complete methodology, at this time, for the study of biofilms in porous media.

Orientador: Cecilia Amelia de Carvalho Zavaglia / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Mecanica / Made available in DSpace on 2018-08-12T19:23:25Z (GMT). No. of bitstreams: 1 Oliveira_MarceloFernandesde_M.pdf: 4714169 bytes, checksum: 6873bf558bc7f4069005075b60b3b470 (MD5) Previous issue date: 2008 / Resumo: A Prototipagem Rápida (PR), ao longo dos últimos 20 anos, vem provendo inovação, redução de tempo e custo nas mais diversas aplicações, propiciando o surgimento de novos paradigmas, em diferentes setores de atividades. A PR tem como recurso principal a capacidade de construir rapidamente formas físicas complexas, difíceis ou mesmo impossíveis de serem construídas pelas tecnologias estabelecidas há mais tempo. O presente trabalho avalia a aplicação da prototipagem rápida em 40 projetos de pesquisa, distribuídos em 18 áreas e subáreas do conhecimento. Essa avaliação, de caráter qualitativo é construída a partir dos pareceres dos proponentes desses projetos e da experiência do autor com as tecnologias PR utilizadas neste trabalho. Foram avaliados os benefícios do emprego da PR e o desempenho dos materiais em quatro classes de aplicações dos projetos: prototipagem visual (PV), prototipagem funcional (PF), ferramental rápido (FR) e manufatura rápida (MR). A capacidade da PR em construir formas complexas é o grande benefício trazido aos projetos de pesquisa. Esse benefício é corroborado pelo bom desempenho das peças construídas com os materiais nylon/SLS, gesso/3DP e ABS/FDM, dentro das classes de aplicações. Para as necessidades apresentadas, relativas ao corpo e superfície das peças, é discutido o emprego de técnicas de pós-processamento. Para PV, a necessidade maior é evitar o amarelamento da superfície do nylon/SLS. Para PF, são necessidades o reforço mecânico das peças de nylon/SLS e ABS/FDM para solicitações dinâmicas e, também, reforço mecânico para peças de pequenas dimensões. É necessária também a planarização das superfícies para peças utilizadas em escoamento hidrodinâmico. Em FR, o uso dos três materiais foi aplicado em ferramental indireto ao invés do direto. Finalmente, nylon/SLS e ABS/FDM foram usados com sucesso em MR e isto, por si só, significa uma superação nas aplicações desses materiais / Abstract: Over the last 20 years, Rapid Prototyping (RP) has provided innovation, time and cost reduction in diverse applications, enabling the emergence of new paradigms in different sectors. RP has as main feature the ability to quickly build complex physical forms which are difficult or even impossible to build using previous established technologies. This study evaluates the application of rapid prototyping in 40 research projects, in 18 areas and subareas of knowledge. This qualitative assessment is based on the point of view of both the proponents of the projects and the author who has experience in the RP technologies employed in this work. The benefits of using RP and the materials performance were evaluated distributing the projects into four classes according to their applications defined by author: visual prototyping (VP), functional prototyping (FP), rapid tooling (RT) and rapid manufacturing (RM). The RP ability of building complex forms was pointed out as the great benefit to all analyzed research projects. This benefit is confirmed by the good performance due to the application of the pieces built with nylon/SLS, gypsum/3DP and ABS/FDM within the classes of application. In this study we discuss the employment of post-processing techniques to solve some needs presented and regarding the pieces surface and body. For VP, the main need was to avoid the yellowing on nylon/SLS surfaces. For FP, the needs point to the mechanical strength of the nylon/SLS and ABS/FDM pieces for dynamic requests, as well as the mechanical strength of pieces of small dimension. In the analysis of FP projects, also, the planarization of the surfaces has been requested for hydrodynamic flow. Regarding RT, the three materials was employed as indirect RT instead direct RT. Finally, nylon/SLS and ABS/FDM were successfully used in RM, and this fact alone represents an overcome of the application of these materials / Mestrado / Materiais e Processos de Fabricação / Mestre em Engenharia Mecânica