During vertebrate embryo development, the body axis is subdivided into repeated structures, called somites. Somites bud off from an un-segmented tissue called the pre-somitic mesoderm (PSM) in a sequential and periodic manner, tightly controlled by an in built molecular clock, called the "segmentation clock". According to current understanding, the clock is comprised of: (i) an autonomous cellular oscillator consisting of an intracellular negative feedback loop of Her genes within the PSM cells, (ii) Delta-ligand and Notch-receptor coupling that facilitates synchronization of oscillators among the PSM cells, (iii) Tissue level waves of gene expression that emerge in the posterior PSM and move coherently towards anterior, leading to global arrest of oscillations in the form of somites. However, the movement of cellular oscillators within the PSM before the formation of somitic furrows, a prominent feature of the tissue as observed through this work has not been experimentally considered as a constituent of the segmentation clock so far. Our work aims to incorporate movement of cellular oscillators in the framework of the segmentation clock. It is well known from theoretical studies that the characteristics of relative motion of oscillators affect their synchronization properties and the patterns of oscillations they form. Particularly, theoretical studies by Uriu et al., PNAS (2010) suggest that cell movements promotes synchronization of genetic oscillations. Here, we established experimental techniques and image analysis tools to attain quantitative insight on (i) diffusion co-efficient of cellular oscillators, (ii) dynamics of a population of oscillators, within the PSM aiming towards concomitant understanding of the relationship between movement and synchronization of cellular oscillators. In order to quantitatively relate cellular oscillators and their motion within the PSM, I established imaging techniques that enabled visualization of fluorescenctly labeled nuclei as readouts of cell positions in live embryo, and developed dedicated segmentation algorithm and implemented tracking protocol to obtain nuclei positions over time in 3D space. Furthermore, I provide benchmarking techniques in the form of artificial data that validate segmentation algorithm efficacy and, for the first time proposed the use of transgenic embryo chimeras to validate segmentation algorithm performance within the context of in vivo live imaging of embryonic tissues. Preliminary analysis of our data suggests that there is relatively high cell mixing in the posterior PSM, within the same spatial zone where synchronous oscillations emerge at maximum speed. Also, there are indications of gradient of cell mixing along the anterior-posterior axis of the embryo. By sampling single cell tracks with the help of nuclei markers, we have also been able to follow in vivo protein oscillations at single cell resolution that would allow quantitative characterization of coherence among a population of cellular oscillators over time. Our image analysis work flow allows testing of mutant embryos and perturbation of synchrony dynamics to understand the cause-effect relationship between movement and synchronization properties at cellular resolution. Essentially, through this work, we hope to bridge the time scales of events and cellular level dynamics that leads to highly coordinated tissue level patterns and thereby further our understanding of the segmentation clock mechanism.

Indiana University-Purdue University Indianapolis (IUPUI) / This thesis presents a Field Programmable Gate Array (FPGA) based embedded system which is used to achieve high speed segmentation of 3D images. Segmenta- tion is performed using Expectation-Maximization with Maximization of Posterior Marginals (EM/MPM) Bayesian algorithm. In this system, the embedded processor controls a custom circuit which performs the MPM and portions of the EM algorithm. The embedded processor completes the EM algorithm and also controls image data transmission between host computer and on-board memory. The whole system has been implemented on Xilinx Virtex 6 FPGA and achieved over 100 times improvement compared to standard desktop computing hardware.

No description available.

No description available.

The visualization of a 3D image obtained from computerized tomography examinations has shown itself to be an important factor for increasing the quality of medical diagnoses and, consequently, treatment efficacy. There already exist on the market, several visualization softwares, which use different techniques to show the 3D tomography image. However, to show a high quality 3D image, sophisticated devices must be used to obtain slices, close to one another, thus increasing the incidence of X-ray given to the patient. An interpolation slice method which resulted from the TC examination produces good results, and is able to reduce the X-ray incidence upon the patient. This method must reconstruct the curvature from the patient s internal structures without using slices in close proximity. This work proposes a method of 3D image interpolation, composed of a juxtaposition of the slices from CT examination results. The goal of this method is to increase the quality of 3D visualization through the production of sharp and precise structure contours. This thesis proposes the division of the interpolation method into two steps. In the first step, the goal is to obtain an initial representation of the image in 3D, which is composed of real slices as well as virtual slices which are referred to in this work as initial virtual slices. In the second step, the empty spaces of the structure are recovered by the 3D image inpainting process. This work also proposes a method to obtain the initial virtual slice and two different methods for inpainting the 3D image. These inpainting methods are the transversal slice line prolongation method and the transportation and diffusion of information. Both methods use the differential equation theory. The transportation and diffusion of information method shows better results than other methods proposed in this work, besides this, this method presents better results than the linear interpolation and Goshtasby et al. [1] methods also implemented in this work. Visual and numerical comparisons are used to obtain this conclusion. The numerical measures used are statistical correlation, the PSNR and the Hausdorff distance [2]. The transportation and diffusion of information method shows itself able to produce better results than all the other tested methods. Besides this principal contribution, this work also developed a KIT to implement 2D and 3D CT visualize applications. / A visualização de imagens resultantes de exame de tomografia computadorizada (TC) em 3D ´e um fator importante para o aumento da precisão nos diagnósticos médicos e, consequentemente, na eficácia dos tratamentos. Atualmente existem diversos produtos no mercado, que fazem uso de várias técnicas existentes para apresentação de imagens tomográficas em 3D. Contudo, para se obter maior suavidade e precisão nos contornos das estruturas visualizadas em 3D, utiliza-se equipamentos capazes de produzir fatias paralelas do corpo humano muito próximas uma das outras, aumentando a exposição dos pacientes aos raios X. Um método de interpolação de fatias resultantes de exame de TC que forneça bons resultados, pode reduzir a incidência de raios X no paciente, pois esse método pode recuperar a curvatura das estruturas sem a necessidade de uma grande proximidade entre as fatias. Este trabalho propõe um método para a interpolação de imagem em 3D, formada pela justaposição de fatias de resultados de exames de tomografia computadorizada. O objetivo desse método ´e obter contornos suaves e precisos, melhorando os processos de visualização em 3D. Para isso, esta tese propõe a divisão do processo de interpolação em duas etapas. Na primeira etapa obtém-se uma representação inicial da imagem em 3D composta por fatias reais e por fatias denominadas de fatias virtuais iniciais e, na segunda etapa, restaura-se essas estruturas geradas com um processo de retoque de imagem em 3D. Este trabalho propõe também um método para obtenção da fatia virtual inicial e dois métodos diferentes para a realização do passo de retoque da imagem em 3D resultante da justaposição das fatias reais e virtuais iniciais. Esses métodos são o prolongamento de linhas nas fatias transversais e transporte e difusão de informações. Ambos os métodos utilizam a teoria de equações diferenciais. O método de transporte e difusão de informações demonstrou melhores resultados do que outro método proposto neste trabalho, além de obter melhores resultados do que os métodos de interpolação linear e Goshtasby e outros [1] implementados neste trabalho. Comparações visuais e comparações numéricas utilizando a correlação estatística, a PSNR e a distância de Haussdorff [2] foram realizadas para se obter essas conclusões. O método de transporte e difusão de informações é capaz de gerar contornos mais suaves e precisos que esses outros métodos testados. Além dessa contribuição principal, este trabalho também desenvolveu um KIT para a construção de aplicações visualizadoras de tomografias computadorizadas em 2D e em 3D. / Mestre em Ciências

This PhD study aimed to address the sustainability issues of the robotic systems from the environmental and social aspects. During the research, three approaches were developed: the first one an online programming-free model-driven system that utilises web-based distributed human-robot collaboration architecture to perform distant assembly operations. It uses a robot-mounted camera to capture the silhouettes of the components from different angles. Then the system analyses those silhouettes and constructs the corresponding 3D models.Using the 3D models together with the model of a robotic assembly cell, the system guides a distant human operator to assemble the real components in the actual robotic cell. To satisfy the safety aspect of the human-robot collaboration, a second approach has been developed for effective online collision avoidance in an augmented environment, where virtual three-dimensional (3D) models of robots and real images of human operators from depth cameras are used for monitoring and collision detection. A prototype system is developed and linked to industrial robot controllers for adaptive robot control, without the need of programming by the operators. The result of collision detection reveals four safety strategies: the system can alert an operator, stop a robot, move away the robot, or modify the robot’s trajectory away from an approaching operator. These strategies can be activated based on the operator’s location with respect to the robot. The case study of the research further discusses the possibility of implementing the developed method in realistic applications, for example, collaboration between robots and humans in an assembly line.To tackle the energy aspect of the sustainability for the human-robot production environment, a third approach has been developed which aims to minimise the robot energy consumption during assembly. Given a trajectory and based on the inverse kinematics and dynamics of a robot, a set of attainable configurations for the robot can be determined, perused by calculating the suitable forces and torques on the joints and links of the robot. The energy consumption is then calculated for each configuration and based on the assigned trajectory. The ones with the lowest energy consumption are selected. / <p>QC 20170223</p>

A level set-based segmentation procedure has been implemented to identify target object boundaries from 3D medical ultrasound images. Several test images (simulated, scanned phantoms, clinical) were subjected to various preprocessing methods and segmented. Two metrics of segmentation accuracy were used to compare the segmentation results to ground truth models and determine which preprocessing methods resulted in the best segmentations. It was found that by using an anisotropic diffusion filtering method to reduce speckle type noise with a 3D active contour segmentation routine using the level set method resulted in semi-automated segmentation on par with medical doctors hand-outlining the same images.

O estudo das propriedades de transporte do meio poroso é um tema importante para muitas áreas como a Ciência do Solo, onde o conhecimento dos processos que envolvem o movimento da água é de fundamental importância para o manejo e a conservação do mesmo. Nas últimas décadas, as técnicas não-invasivas e o processamento de imagens têm ajudado muito na modelagem e visualização da estrutura do meio, e têm sido aplicadas no estudo da distribuição dos fluidos com diferentes abordagens. Nesse trabalho é apresentado um novo método para análise do movimento da água, baseado na descrição da estrutura tridimensional da frente de molhamento no processo de infiltração vertical na região não-saturada do solo, considerando que a frente de molhamento tem informação relevante sobre os primeiros estágios da infiltração na interface líquido-sólido. O método proposto para a descrição da estrutura tridimensional da frente de molhamento compõe-se de dois principais módulos. O primeiro é responsável pela segmentação de imagens tomográficas para a detecção da frente de molhamento e cujo resultado é crucial para a análise da superfície resultante. O segundo módulo efetua a determinação de descritores da superfície obtida baseada na computação da variabilidade morfológica e a identificação de zonas de máxima adsorção através da análise da curvatura. As imagens usadas nos experimentos foram obtidas usando um tomógrafo de campo específico para estudos de solos, permitindo o processamento sem alterar a estrutura do solo. Os resultados preliminares são encorajadores e indicam que a abordagem utilizada consegue descrever o movimento da água usando informação da frente de molhamento no espaço tridimensional e no tempo. / The study of the transport properties in porous media is an important issue for many areas such as soil science, where knowledge about processes that involve the movement of water in the soil has fundamental importance to soil management and soil conservation. In recent decades noninvasive techniques and image processing algorithms have been very helpful in modeling and visualization of the structure medium and have been applied to study of the distribution of fluid with different approaches. This work present a new method to analysis of the movement of water based on the description of the three-dimensional wetting front structure in vertical infiltration process in unsaturated soil, whereas the wetting front structure has relevant information in the earliest stages of infiltration in liquid-solid interface. The proposed method for the description of the three-dimensional wetting front structure is comprised of two main modules. The first module is responsible of the three-dimensional image segmentation for the wetting front detection and its result is a very crucial step to analysis of the surface obtained. The second module compute features of the surface obtained to analysis based on morphological variability and maximal adsorption zones identification through the curvature. The image used in the experimental test were obtained using a tomograph of field specific to soil study, allowing the processing without changing of the soil structure. Our preliminary results are encouraging and indicate that our approach can describe the movement of water using information from the wetting front in three-dimensional space and time.

Imagens da anatomia interna são essenciais para as práticas médicas. Estabelecer correlação entre elas, é um importante procedimento para diagnóstico e tratamento. Nessa dissertação, é proposta uma abordagem para correlacionar dados multidimensionais de mesma modalidade de aquisição baseando-se somente nas informações de intensidade de pixels e voxels. O trabalho foi dividido em duas fases de implementação. Na primeira, foi explorado o problema de similaridade entre imagens médicas usando a perspectiva de análise de qualidade de imagem. Isso levou ao desenvolvimento de uma técnica de dois passos que estabelece um equilíbrio entre a velocidade de processamento e precisão de duas abordagens conhecidas. Avaliou-se a qualidade e aplicabilidade do algoritmo e, na segunda fase, o método foi estendido para analisar similaridade e encontrar a localização de uma imagem arbitrária (2D) em um volume (3D). A solução minimiza o número virtualmente infinito de possíveis orientações transversais e usa otimizações para reduzir a carga de trabalho e entregar resultados precisos. Uma visualização tridimensional volumétrica funde o volume (3D) com a imagem (2D) estabelecendo uma correspondência entre os dados. Uma análise experimental demonstrou que, apesar da complexidade computacional do algoritmo, o uso de amostragem, tanto na imagem quanto no volume, permite alcançar um bom equilíbrio entre desempenho e precisão, mesmo quando realizada com conjuntos de dados de baixa intensidade de gradiente. / Images of the inner anatomy are essential for clinical practice. To establish a correlation between them is an important procedure for diagnosis and treatment. In this thesis, we propose an approach to correlate within-modality 2D and 3D data from ordinary acquisition protocols based solely on the pixel/voxel information. The work was divided into two development phases. First, we explored the similarity problem between medical images using the perspective of image quality assessment. It led to the development of a 2-step technique that settles the compromise between processing speed and precision of two known approaches. We evaluated the quality and applicability of the 2-step and, in the second phase, we extended the method to use similarity analysis to, given an arbitrary slice image (2D), find the location of this slice within the volume data (3D). The solution minimizes the virtually infinite number of possible cross section orientations and uses optimizations to reduce the computational workload and output accurate results. The matching is displayed in a volumetric three-dimensional visualization fusing the 3D with the 2D. An experimental analysis demonstrated that despite the computational complexity of the algorithm, the use of severe data sampling allows achieving a great compromise between performance and accuracy even when performed with low gradient intensity datasets.

Les systèmes de fusion d'informations sont principalement composés, d'outils mathématiques permettant de réaliser la représentation et la combinaison des données. L'objectif de ces systèmes peut s'exprimer comme un problème de décision sur la vérité ou la vraisemblance d'une proposition étant donné une ou plusieurs informations issues de différentes sources. Les systèmes de fusion cherchent à exploiter au mieux les propriétés des sources de données en tenant compte de l'imperfection de l'information (imprécis, incomplet, ambigu, incertain, etc.) ainsi que l'aspect redondant, complémentaire et conflictuel des informations. Le système de fusion concerné par cette thèse a la capacité d'intégrer dans ses traitements de la connaissance experte. On le nomme système de fusion coopératif. Puisque ce système cherche à intégrer pleinement les experts dans son fonctionnement, il est important de mettre à disposition des utilisateurs des informations aidant à mieux comprendre la fusion réalisée. De tels systèmes disposent de nombreux paramètres à régler et ces derniers ont un impact important sur la qualité des résultats obtenus. Une des grandes problématiques liées à ces systèmes de fusion d'informations porte sur l'évaluation de leurs performances. L'évaluation doit permettre d'améliorer la qualité de la fusion, d'améliorer l'interaction expert/système et d'aider à mieux ajuster les paramètres du système. En général, l'évaluation de tels systèmes est réalisée en fin de chaîne par une évaluation globale du résultat. Mais, celle-ci ne permet pas de savoir précisément l'endroit de la chaîne qui nécessite une intervention. Une autre difficulté réside dans le fait qu'une vérité terrain complète sur le résultat n'est pas toujours disponible, ce qui complique la tâche d'évaluation de performances de ce type de systèmes. Le contexte applicatif de ce travail est l'interprétation d'images tridimensionnelles (images tomographiques, images sismiques, images synthétiques, ...). Dans ce contexte une évaluation locale des systèmes de fusion d'informations, a été mise en place. L'approche a montré son intérêt dans l'ajustement efficace des paramètres et dans la coopération avec l'expert. / Information fusion systems are mainly composed from mathematical tools allowing to realize data representation and combination. The aim of these systems can be expressed as a decision problem on the truth or plausibility of a proposition based on several information coming from different sources. Fusion try to manage the characteristics of the sources taking into account the information imperfection (inaccurate, incomplete, ambiguous, uncertain, etc.) and the redundant aspect, the complement and the conflictual aspect of information. Fusion systems concerned by this thesis have the ability to integrate the expert knowledge in their treatments. They are called cooperative fusion systems. Since these systems are trying to associate experts, it is important to provide to the users some informations that help them to better understand the fusion process. Such systems have many parameters that must be adjusted. These parameters have an important impact on the quality of the obtained results. One of the major problems associated to information fusion systems concerns the evaluation of their performance. A pertinent evaluation will allow to improve the quality of the fusion, to improve expert/system interaction and to better adjust the parameters of the system. Generally, the evaluation of such systems is made in the ouput of the processing chain by a global evaluation of the results. But it does not allow to know the precise subpart of the treatement chain that requires an adjustment of its parameters. Another difficulty releases in the fact that a complete ground truth of the result is not always available, which complicates the performance evaluation task. The application context of this work is the interpretation of 3D images (tomographic images, seismic images, synthetic images, ...). In this context, a local evaluation of the information fusion systems has been implemented. The approach has shown its interest in the efficient adjustment of parameters and the cooperation with expert.