L'imagerie ultrasonore est une modalité d'acquisition privilégiée en imagerie médicale en raison de son innocuité, sa simplicité d'utilisation et son coût modéré d'utilisation. Néanmoins, la résolution limitée et le faible contraste limitent son utilisation dans certaines d'applications. C'est dans ce contexte que différentes techniques de post-traitement visant à améliorer la qualité de telles images sont proposées dans ce manuscrit. Dans un premier temps, nous proposons d'aborder le problème conjoint de la déconvolution et de la segmentation d'images ultrasonores en exploitant l'interaction entre ces deux problèmes. Le problème, énoncé dans un cadre bayésien, est résolu à l'aide d'un algorithme MCMC en raison de la complexité de la loi a posteriori des paramètres d'intérêt. Dans un second temps, nous proposons une nouvelle méthode rapide de super-résolution fondée sur la résolution analytique d'un problème de minimisation l2-l2. Il convient de remarquer que les deux approches proposées peuvent être appliquées aussi bien à des images ultrasonores qu'à des images naturelles ou constantes par morceaux. Enfin, nous proposons une méthode de déconvolution aveugle basée sur un modèle paramétrique de la réponse impulsionelle de l'instrument ou du noyau de flou. / In the field of medical image analysis, ultrasound is a core imaging modality employed due to its real time and easy-to-use nature, its non-ionizing and low cost characteristics. Ultrasound imaging is used in numerous clinical applications, such as fetus monitoring, diagnosis of cardiac diseases, flow estimation, etc. Classical applications in ultrasound imaging involve tissue characterization, tissue motion estimation or image quality enhancement (contrast, resolution, signal to noise ratio). However, one of the major problems with ultrasound images, is the presence of noise, having the form of a granular pattern, called speckle. The speckle noise in ultrasound images leads to the relative poor image qualities compared with other medical image modalities, which limits the applications of medical ultrasound imaging. In order to better understand and analyze ultrasound images, several device-based techniques have been developed during last 20 years. The object of this PhD thesis is to propose new image processing methods allowing us to improve ultrasound image quality using postprocessing techniques. First, we propose a Bayesian method for joint deconvolution and segmentation of ultrasound images based on their tight relationship. The problem is formulated as an inverse problem that is solved within a Bayesian framework. Due to the intractability of the posterior distribution associated with the proposed Bayesian model, we investigate a Markov chain Monte Carlo (MCMC) technique which generates samples distributed according to the posterior and use these samples to build estimators of the ultrasound image. In a second step, we propose a fast single image super-resolution framework using a new analytical solution to the l2-l2 problems (i.e., $\ell_2$-norm regularized quadratic problems), which is applicable for both medical ultrasound images and piecewise/ natural images. In a third step, blind deconvolution of ultrasound images is studied by considering the following two strategies: i) A Gaussian prior for the PSF is proposed in a Bayesian framework. ii) An alternating optimization method is explored for blind deconvolution of ultrasound.

Espectros Raman de super-redes &#948-dopadas, na geometria de retro¬espalhamento, mostram uma estrutura na região do fônon LO que é alargada e deslocada em relação à correspondente linha observada no material intrínseco. Neste trabalho, este fenômeno é teoricamen¬te explicado através do acoplamento de um fônon LO de momento q, propagando-se ao longo da super-rede, com as excitações eletrônicas desse sistema. O deslocamento e o alargamento da linha são obtidos através do cálculo da auto-energia desse fônon, a qual pode ser expressa em termos da função resposta densidade-densidade do gás de elétrons modulado. Efeitos da interação elétron-elétron são tratados através da aproximação das fases aleatórias (RPA). / The Raman spectra of &#948-doping superlattice, in backscattering ge¬ometry, show a structure in the region of the LO phonon which is broadened and shifted in comparison whit the same structure in the intrinsic material. In this work, this phenomena is interpreted as consequence of the coupling of LO xne-phonon of momentum q, along the axis of the superlattice, whit the excitations of the modulate electron gas, that exists in this system. The shift and the broadening of the phonon are calculated as the real and imagi¬nary parts of the phonon self-energy, which in turn is related to the density-density response function of modulate electron gas. Effects of electron-electron interaction are calculated within the Random Phase Approximation (RPA).

Segmentação de imagens é ainda uma etapa desafiadora do processo de reconhecimento de padrões. Entre as abordagens de segmentação, muitas são baseadas em particionamento em grafos, as quais apresentam alguns inconvenientes, sendo um deles o tempo de processamento muito elevado. Com as recentes pesquisas na teoria de redes complexas, as técnicas de reconhecimento de padrões baseadas em grafos melhoraram consideravelmente. A identificação de grupos de vértices pode ser considerada um processo de detecção de comunidades de acordo com a teoria de redes complexas. Como o agrupamento de dados está relacionado com a segmentação de imagens, esta também pode ser abordada através de redes complexas. No entanto, a segmentação de imagens baseado em redes complexas apresenta uma limitação fundamental, que é o número excessivo de nós na rede. Neste trabalho é proposta uma abordagem de redes complexas para segmentação de imagens de grandes dimensões que é ao mesmo tempo precisa e rápida. Para alcançar este objetivo, é incorporado o conceito de Super Pixels, visando reduzir o número de nós da rede. Os experimentos mostraram que a abordagem proposta produz segmentações de boa qualidade em baixo tempo de processamento. Além disso uma das principais contribuições deste trabalho é a determinação dos melhores parâmetros, uma vez que torna o método bastante independente dos parâmetros, o que não fora alcançado antes em nenhuma pesquisa da área / Image segmentation is still a challenging stage of the pattern recognition process. Amongst the various segmentation approaches, some are based on graph partitioning, many of which show some drawbacks, such as the high processing times. Recent trends on complex network theory have contributed considerably to the development of graph-based pattern recognition techniques. The identification of group of vertices can be considered a community detection process according to complex network theory. Since data clustering is closely related to image segmentation, image segmentation tasks can also be tackled by complex networks. However, complex network-based image segmentation poses a very important limitation: the excessive number of nodes of the underlying network. In this work we propose a approach based on complex networks suitable for the segmentation of image with large dimensions that is accurate and yet fast. To accomplish that, we have incorporated the concept of Super Pixels aiming at reducing the number of the nodes in the network. The results have shown that the proposed approach delivered accurate image segmentation within low computational times. Another contribution worth mentioning is the determination of the best values for the parameters needed by the underlying graphbased segmentation and community detection algorithms, which enabled the proposed approach to become less dependent on the parameters. To the best of our knowledge, this is a new contribution to the field

O presente estudo teve como objetivo avaliar o efeito de níveis crescentes de inclusão de polpa cítrica na dieta de equinos, através da avaliação da palatabilidade, digestibilidade aparente e características físico-químicas das fezes. As dietas foram compostas por 60% da energia proveniente do volumoso (feno de Coast Cross) e 40% do concentrado, com níveis crescentes de inclusão de polpa cítrica (0, 7, 14, 21 e 28%). Para a realização do experimento, foram realizados dois testes. O primeiro ensaio consistiu na determinação da palatabilidade dos concentrados, através do teste de preferência. Para isso foram utilizados 15 equinos, por um período de 10 dias, totalizando 150 observações, em delineamento inteiramente casualizado. As variáveis observadas foram primeira ação, primeira escolha e razão de ingestão. Para a realização do ensaio de digestibilidade e características físico-químicas das fezes, foram utilizados cinco equinos, em delineamento quadrado latino 5x5. Avaliou-se a digestibilidade aparente dos nutrientes e as características de cor, consistência, pH, concentração e relação entre ácidos graxos de cadeia curta e capacidade tamponante a pH 5 e a pH 6, das fezes. Observou-se efeito da inclusão da polpa cítrica (P<0,001) sobre a primeira ação, sendo que 66,91% dos animais cheiraram os concentrados, enquanto 33,09% comeram, e também para a primeira escolha (P<0,001),onde os tratamentos 0, 7 e 14% apresentaram maior preferência. Para a razão de ingestão, também houve diferença (P<0,001) entre os tratamentos, sendo que o concentrado controle o mais consumido. Não foi observado efeito (P>0,05) dos níveis de inclusão de polpa cítrica sobre a digestibilidade aparente dos nutrientes. Para as características das fe zes não houve efeito de tratamento (P>0,05) na consistência e cor. A coloração se manteve esverdeada, e a consistência foi classificada como normal (escore 3).Não houve efeito de tratamento (P>0,05) para o pH, concentração e relação entre ácidos graxos de cadeia curta e capacidade tamponante das fezes. O valor médio observado de pH foi de 6,62, e a capacidade tamponante a pH 5 e pH 6 foi de 16,53 e 5,13 mmol/L, respectivamente. Os cavalos têm a capacidade de identificar a presença da polpa cítrica nos concentrados, e preferem concentrados sem a inclusão. A adição de polpa cítrica em até 28% não afeta negativamente a digestibilidade dos concentrados e as características físico-químicas das fezes, sendo uma alternativa de ingrediente na formulação de dietas para equinos. / The purpose of this study was to evaluate the citrus pulp inclusion in horses diet, through evaluation of palatability, apparent digestibility and feces physicochemical characteristics. The diets were composed of 60% of the energy from roughage (Coast Cross hay) and 40% from concentrate with increasing levels of citrus pulp (0, 7, 14, 21 and 28%).To perform the experiment, there were two distinct tests. The first experiment consisted in determining the concentrates palatability. Fifteen horses were used, for a 10-day period, totaling 150 observations, in a randomized design. The variables were first action, first choice and intake rate. For the digestibility test and feces physicochemical characteristics, five horses were used in 5x5 Latin square design. Were evaluated the nutrients digestibility and the feces characteristics of color, consistency, pH, concentration and relation between short-chain fatty acids, and buffering capacity at pH 5 and pH 6. There was an effect of the citrus pulp inclusion (P<0.001) on the first action, 66.91% of the animals smelled the concentrates, while 33.09% ate. For the first choice there was also significant difference (P<0.001) and 0, 7 and 14% treatments had a higher preference. For the intake rate there were differences (P<0.001) between treatments, being the control concentrate the most consumed. There was no effect (P>0.05)of the citrus pulp levels on nutrient digestibility. For feces characteristics there were no treatment effect (P>0.05) in consistency and color. The color remained green, and consistency were classified as normal (score 3). There was no treatment effect (P>0.05) for pH, concentration and relation between short-chain fatty acids, and buffering capacity of the feces, the mean pH value observed was 6.62, and the buffering capacity at 5 and 6 was 16.53 and 5.13 mmol / L respectively. Horses have the ability to identify the citrus pulp presence in concentrates, but they prefer the concentrates without citrus pulp inclusion. Addition of citrus pulp does not adversely affect the concentrates digestibility or the feces physicochemical characteristics, being an alternative ingredient in the horses diets formulation.

Este trabalho consiste de três partes: Teoremas de coordenatização de Wedderburn e de Zorn, O problema de Nathan Jacobson e Teoremas de Fatorização de Kronecker para as superálgebras alternativas. Na primeira parte apresentamos os teoremas de coordenatização de Wedderburn e de Zorn e suas aplicações na teoria de representações das álgebras associativas e alternativas. Na segunda parte resolvemos um problema de longa data que foi anunciado por Nathan Jacobson sobre a descrição das álgebras alternativas que contém M&#8322(F ) (álgebra associativa de matrizes 2 × 2) com o mesmo elemento identidade. Na terceira parte damos uma prova independente que é válida em qualquer característica do clássico Teorema de Fatorização de Kronecker de Nathan Jacobson. Generalizamos esse resultado e provamos um teorema de Fatorização de Kronecker para as superálgebras alternativas cuja parte par contém O com o mesmo elemento identidade. Além disso, provamos um Teorema de Fatorização de Kronecker para as superálgebras alternativas que contêm a superálgebra associativa M(1|1)(F ) com o mesmo elemento identidade. Como Corolário desse resultado, respondemos a um análogo do problema de Jacobson para as superálgebras alternativas, isto é, descrevemos as superálgebras alternativas que contêm à superálgebra associativa M(1|1)(F ) com o mesmo elemento identidade. Finalmente, estudamos as representações das superálgebras alternativa simples O(4,4) e O[u]. Classificamos os bimodules sobre essas superálgebras e provamos alguns análogos do Teorema de Fatorização de Kronecker para as superálgebras alternativas que contenham O(4|4) ou O[u] com o mesmo elemento identidade / This work consists of three parts: Wedderburn and Zorn coordinatizations theorems, Nathan Jacobsons problem and Kroneckers Factorization theorems for alternative superalgebras. In the first part we present Wedderburn and Zorn coordinatizations theorems and their applications in the theory of representations of associative and alternative algebras. In the second part we solve a long standing problem that was announced by Nathan Jacobson on the description of alternative algebras containing M&#8322(F ) (associative matrix algebra 2 × 2) with the same identity element. In the third part we give an independent proof that is valid in any characteristic of Nathan Jacobsons classic Kronecker Factorization Theorem. We generalize this result and prove a Kronecker Factorization Theorem for alternative superalgebras whose even part contains O with the same identity element. In addition, we prove a Kronecker Factorization Theorem for alternative superalgebras containing the associative superalgebra M(1|1)(F ) with the same identity element. As a corollary of this result, we respond to an analogue of Jacobsons problem for alternative superalgebras, that is, we describe the alternative superalgebras containing the associative superalgebra M(1|1)(F ) with the same identity element. Finally, we study the representations of the simple alternative superalgebras O(4|4) e O[u]. We classify the bimodules on these superalgebras and prove some analogues of the Kronecker Factorization Theorem for alternative superalgebras containing O(4|4) or O[u] with the same identity element

Este trabalho apresenta uma possibilidade de leitura do espaço geográfico por meio das histórias em quadrinhos do gênero super-heróis - com ênfase em Batman - levando em conta a importância destes ícones e da linguagem quadrinhística no mundo moderno. Ao verificarmos como a paisagem é retratada nas aventuras dos super-heróis, buscamos interpretar as representações do espaço - e se possível os espaços de representação - e como elas ratificam e/ou legitimam os valores e idéias da sociedade que, direta ou indiretamente, as geraram: a sociedade americana/capitalista. A contribuição mais evidente da pesquisa consiste no fato de abordar uma temática ainda pouco explorada dentro dos estudos geográficos e ao mesmo tempo, estabelecer uma possível ponte interdisciplinar com a área de conhecimento da Comunicação / This paper provides a way to interpret geographic space trough the use of super-hero comics - mainly Batman - highlighting the importance of cultural icons and the comic book language in the modern world. We attempted to demonstrate that the landscape itself, as well as what this landscape represents, confirms or legitimizes the values and ideas of american/capitalist society which, directly or indirectly, generates them. The most important contribution of this paper lies in its application of the little used theme of super-hero comics in geographic studies. In addition, this study facilitates the establishment of an interdisciplinary bridge to the area of Communication studies

Différentes études précédentes ont démontré que IL-1β et PKA peuvent réduire la transmission synaptique inhibitrice dans la LAMINA II de la moelle épinière, en contribuent de cette manière au développement de douleur chronique de tipe inflammatoire. Au niveau des sites post-synaptiques, les changements dans la transmission synaptique (par exemple suivant le relâchement de IL-1β ou après l’activation de PKA), reflètent donc des changements dans les propriétés et/ou dans le nombre des molécules présentes au niveau de la synapse. Au cours de mon doctorat, j’ai pu profiter des techniques basés sur l’imagerie des molécules uniques afin d’étudier les effets de PKA et IL-1β sur la dynamiques et le nombre absolu de GlyR dans les synapses de la moelle épinière. Mes résultats ont montré que PKA et Il-1β peuvent déplacer les GlyR des sites inhibitoires post-synaptiques ciblent différentes sous-unités α du récepteur de la glycine. Comme les sous-unités GlyRα ne se lient pas directement à la géphyrine, ces effets sont vraisemblablement le résultat d’un changement de conformation du GlyR dépendant de la sous-unité. Pendant mon projet, j’ai utilisé la technique de microscopie de super-résolution PALM pour développer une méthode pour déterminer la stœchiométrie des GlyR et le nombre absolu de récepteurs et des molécules d’échafaudage au niveau des synapse de la moelle épinière. Mes résultats décrivent que les GlyR se composent de 3 sous-unités α et de 2 sous-unités β, et proposent qu’une synapse de la moelle épinière contient en moyenne 80 GlyR et 250 molécules de géphyrine. Ces résultats sont essentiels pour mettre en relation l’ampleur des mécanismes de régulation et de plasticité agissant sur la transmission synaptique, avec les changements en nombre de molécules présentes dans les synapses de la moelle épinière. Sur la base de mes découvertes on pourra maintenant étudier les mécanismes structuraux impliqués dans la régulation de la fonction et la dynamique des GlyR dépendantes des sous-unités α que j’ai démontré. / IL-1β and PKA impair glycine receptor-mediated synaptic transmission in the lamina II of the spinal cord, contributing to the development of inflammatory types of chronic pain. At post-synaptic sites, the strength of synaptic transmission depends on the biophysical properties and on the absolute number of receptors expressed. Consequently, changes in synaptic transmission (i.e. following the release of IL-1β or the activation of PKA), reflect changes in the properties and/or number of molecules present at the synapse. During my PhD I have taken advantage of single-molecule based imaging techniques to study the effects of IL-1β and PKA on the dynamics and absolute numbers of GlyRs at spinal cord synapses.My results show for the first time that both Il-1β and PKA displace GlyRs from inhibitory post-synaptic sites, targeting different α-subunit of GlyRs. Specifically, IL-1β reduces GlyR α-containing receptors at spinal cord synapse, whereas PKA affects GlyR α3L subunit. Given that the GlyR α subunits do not bind to the gephyrin scaffold, these effects likely reflect an α-subunit dependent change in GlyR conformation that decreases the affinity of the GlyR subunits for gephryrin. Glycine receptors are composed of α- and β- subunits that assemble into heteropentameric complexes with an unclear stoichiometry. Using super resolution PALM microscopy I have developed a single-molecule counting approach to determine the stoichiometry of GlyRs and the absolute number of receptor and scaffold molecules at spinal cord synapses. According to my results GlyRs is composed by 3 α and 2 β-subunits, and an average spinal cord synapse contains around 80 GlyRs and 250 scaffold molecules. These data are fundamental to relate the magnitude of regulatory and plasticity mechanisms acting on glycinergic transmission, with quantitative changes in molecule numbers at spinal cord synapses. My research has shown how absolute quantitative approaches can help achieve a more detailed insight into the organization of complex molecular assemblies and their dynamic regulation.

Le Calcul des Variations et son interprétation géométrique ont toujours joué un rôle crucial en Physique Mathématique, que ce soit par le formalisme lagrangien, ou à travers les équations hamiltoniennes.Le formalisme multisymplectique permet une description géométrique de dimension finie des théories de champ classiques (qui correspondent à des problèmes variationnels avec plusieurs variables spatio-temporelles) vues d’un point de vue hamiltonien. La géométrie multisymplectique joue un rôle similaire à celui de la géométrie symplectique dans la description de la mécanique hamiltonienne classique. De plus, l’approche multisymplectique fournit un outil pour construire une structure symplectique sur l’espace des solutions de la théorie des champs et pour l’étudier.Dans cette thèse, je m’intéresse principalement au formalisme multisymplectique pour construire des théories de champs de premier ordre et j’espère pouvoir donner deux principales contributions originales :– Je montre que, dans certaines situations, la structure symplectique de l’espace des phases covariant peut en effet dépendre du choix de la topologie du découpage de l’espace-temps en l’espace et en le temps;– Je construis une extension du formalisme multisymplectique aux théories de super-champs. En tant que «sous-produit», je présente une autre contribution que j’espère intéressante :– Je définie des formes fractionnaires sur des supervariétés avec leur calcul de Cartan. Ces formes fractionnaires se révèlent utiles pour construire le formalisme multisymplectique pour les théories de super-champs.Les ingrédients principaux du formalisme que j'utilise sont : l’espace des multimoments de dimension finie P et son extension aux théories de super-champs que je définie ; la superforme lagrangienne, le superhamiltonien et la superforme multisymplectique. Dans la thèse je montre aussi un théorème de comparaison qui permets de clarifier les relations existant entre les théories dites en composantes et les théories de superchamps. J’explique comment le formalisme supermultisymplectique peut être utilisé pour définir des super crochets de Poisson pour les superchamps. Je donne une version "super" du premier théorème de Noether valable pour l'action de supergroupes de symétrie et je propose une extension « super » de l'application multimoment. Enfin je présente quelques exemples montrant comment toute la théorie peut être mise en œuvre : en particulier j'étudie la superparticule libre et le modèle sigma 3-dimensionnel. / The Calculus of Variations and its geometric interpretation always played a key role in Mathematical Physics, either through the Lagrangian formalism, or through the Hamiltonian equations.The multisymplectic formalism allows a finite dimensional geometric description of classical field theories seen from an Hamiltonian point of view. Multisymplectic geometry plays the same role played by symplectic geometry in the description of classical Hamiltonian mechanics. Moreover the multisymplectic approach provides a tool for building a symplectic structure on the space of solutions of the field theory and for investigating it.In this thesis I use the multisymplectic formalism to build first order field theories and I hope to give two main original contributions:– I show that, in some situations, the symplectic structure on the covariant phase space may indeed depend from the choice of splitting of spacetime in space and time;– I extend the multisymplectic formalism to superfield theories.As a "byproduct", I present another contribution:– I define fractional forms on supermanifolds with their relative Cartan Calculus. These fractional forms are useful to build the multisymplectic formalism for superfield theories.The main ingredients of the formalism I use are: the finite dimensional multimomenta phase space P and its extension to super field theories, which I give; the Lagrangian superform; the super-Hamiltonian, the multisymplectic superform.In my thesis I also prove a Comparison Theorem which allows to clarify the relations existing between the so called components theories and the so called superfield theories. I explain how the supermultisymplectic formalism can be used to define super Poisson brackets for super fields. I give a "super" version of the first Noether theorem valid for the action of supergroups of symmetry and I propose a “super” extension of the multimomentum map.Finally I present some examples showing how all the theory can be implemented: I study the free superparticle and the 3-dimensional sigma-model.

Chez les bactéries, les pôles cellulaires servent de domaines subcellulaires impliqués dans plusieurs processus cellulaires. Chez l’agent pathogène du choléra, Vibrio cholerae, en forme de bâtonnet incurvé, le pole contenant l’unique flagelle est impliqué dans la virulence. La protéine d’ancrage polaire HubP interagit avec plusieurs ATPases telles que ParA1 (ségrégation des chromosomes), ParC (localisation polaire du système de chimiotaxie) et FlhG (biosynthèse des flagelles), organisant ainsi l'identité polaire de V. cholerae. Cependant, les mécanismes moléculaires exacts de cet ancrage polaire doivent encore être élucidés. L’objectif de cette thèse est d’établir une vue d'ensemble de l'organisation de pôle cellulaire ce qui implique le mécanisme d’orchestration des différentes fonctions cellulaires par l’identification de l’ensemble des partenaires d'interaction de HubP ainsi que la cartographie fine du pôle cellulaire par microscopie à super résolution (PALM). Afin d’identifier de nouveaux partenaires d'interaction de HubP, j'ai étudié la différence de composition en protéines polaires entre les contextes HubP+ et HubP-. La composition en protéines polaires a été quantifiée de manière relative et absolue en ajoutant des Tag isobares aux protéines extraites de mini-cellules. Ces mini-cellules correspondent des petits compartiments cellulaires issus d’un évènement de division anormal proche du pole et sont enrichies en protéines polaires. Parmi ~800 protéines identifiées, ~ 80 protéines ont été considérées comme enrichies en contexte HubP+ incluant de nombreuses protéines attendues (FlhG, ParC et en aval des protéines de chimiotaxie). J'ai étudié la localisation de 14 protéines par microscopie à fluorescence et pu révéler 4 nouvelles protéines présentant une localisation polaire dépendant de HubP : VbrX, VbrY, et 2 protéines hypothétiques MotV et MotW. La délétion de motV et motW provoque un défaut significatif de propagation dans une gélose molle suggérant une implication dans la chimiotaxie et/ou la motilité. Alors que la microscopie électronique a montré que les deux mutants ont bien un flagelle polaire unique, le suivi-vidéo de leur déplacement a révélé que les deux mutants présentaient des défauts de nage assez distincts: ∆motV est plutôt affecté dans le changement de direction et ∆motW dans la vitesse de déplacement. Des expériences de microscopie fluorescente ont montré que MotV, MotW et HubP présentaient des dynamiques de localisation polaire distinctes au cours du cycle cellulaire. Pour une observation fine du pôle cellulaire par PALM, de nouveaux outils d’analyse d’image à haut débit étaient exigés. La précision des contours des petites cellules bactériennes faiblement contrastées n’est pas suffisante par l’observation en fond clair, j'ai développé une nouvelle technique de marquage avec des protéines fluorescentes photo-activables pour un tracé précis de la membrane interne ou du périplasme. En outre, nous avons créé un logiciel utilisant Matlab appelé Vibio qui intègre le contour de cellule et la liste des molécules obtenues par microscopie à super résolution. La capacité d’analyse à haut débit du logiciel permet d’étudier la distribution des molécules de l’échelle de la cellule unique à une population en orientant les cellules par leur courbure longitudinale. J’ai pu révéler que HubP est principalement localisé du côté convexe du pôle de la cellule, tandis que ses partenaires se situaient principalement au milieu du pôle. Mon travail de thèse a révélé avec succès de nouveaux partenaires d'interaction de HubP et la fonction de certaines protéines dans la motilité cellulaire. J'ai développé une nouvelle technique de microscopie pour une localisation subpolaire précise qui fonctionne bien pour l'analyse d'images PALM dans Vibio. J’ai ainsi pu faire progresser les connaissances de l’orchestration des fonctions polaires chez V. cholerae. / In rod shaped bacteria, cell poles serve as important subcellular domains involved in several cellular processes including motility, chemotaxis, protein secretion, antibiotic resistance, and chromosome segregation. In the cholera pathogen Vibrio cholerae, vibrioid rod shape and single polarized flagellum involve in the virulence. Polar landmark protein HubP was shown to interact with multiple ATPases, such as ParA1 (chromosome segregation), ParC (polar localization of chemotaxis apparatus), and FlhG (flagella biosynthesis), thus organizing the polar identity of V. cholerae by tethering proteins to cell pole. However, the exact molecular mechanisms are yet to be elucidated. In this thesis, I tackled to unveil comprehensive view of the cell pole organization which implies the orchestration of different cellular functions, by identifying further interaction partners of HubP as well as drawing conceivable picture of the cell pole by super-resolution photoactivated localization microscopy. To identify new interaction partners of HubP, I used minicells in which cell poles were enriched as they derived from cell division near the cell pole. Difference in protein composition between HubP+ and HubP- minicells were examined by isobaric tags for relative and absolute quantitation. Among ~800 proteins identified, ~80 proteins were considered to be enriched in HubP+ minicells including many expected proteins (FlhG, ParC and downstream chemotaxis proteins). I chose 14 proteins to investigate their subcellular localization with fluorescent microscopy. In conclusion, I discovered 4 proteins that showed polar localization in a HubP-dependent manner. These proteins are VbrX, VbrY, and 2 hypothetical proteins MotV and MotW. ∆motV and ∆motW showed significant defect in a diameter of travel in soft agar plate that suggesting the possible involvement in chemotaxis and/or motility. Whereas electron microscopy showed that both mutants possess intact monotrichous flagellum, video-tracking revealed that the two mutants showed rather distinct defects during swimming: MotV is rather turning mutant while MotW is a speed mutant. Fluorescent microscopy experiments indicated that MotV, MotW and HubP showed distinct polar dynamics over cell cycle. For fine-scale observation of the cell pole by PALM, it was appreciated that novel tools for high-throughput analysis was demanded. Since brightfield images are not sufficient to have accurate contours of small and low contrast bacterial cells, I developed new labeling technique with photoactivatable fluorescent proteins for precise outlining at either inner membrane or periplasm. Furthermore, we created Matlab-based software called Vibio which integrates cell outline and the list of molecules obtained by super-resolution microscopy. High-throughput capability of the software enabled to analyze distribution of detected molecules from single cell to whole bunch of cells in a manner that cells are oriented by cell curvature. These allowed me to discover that HubP is mostly lopsided at the convex side of the cell pole, while its partners mostly located middle of the pole. Altogether, I successfully unveiled 4 novel interaction partners of HubP. I revealed of the function of hypothetical proteins that are involved in cell motility. I developed new labeling technique for precise polar localization that works well for PALM image analysis in Vibio. Therefore, I observed precise polar localization of HubP and other polar proteins.

La reconstruction 3D multi-vue atteint désormais un niveau de maturité industrielle : des utilisateurs non-experts peuvent produire des modèles 3D large-échelle de qualité à l'aide de logiciels commerciaux. Ces reconstructions utilisent des capteurs haut de gamme comme des LIDAR ou des appareils photos de type DSLR, montés sur un trépied et déplacés autour de la scène. Ces protocoles d'acquisition sont mal adaptés à l’inspection d’infrastructures de grande taille, à géométrie complexe. Avec l'évolution rapide des capacités des micro-drones, il devient envisageable de leur confier ce type de tâche. Un tel choix modifie les données d’acquisition : on passe d’un ensemble restreint de photos de qualité, soigneusement acquises par l’opérateur, à une séquence d'images à cadence vidéo, sujette à des variations de qualité image dues, par exemple, au bougé et au défocus.Les données vidéo posent problème aux logiciels de photogrammétrie du fait de la combinatoire élevée engendrée par le grand nombre d’images. Nous proposons d’exploiter l’intégralité des images en deux étapes. Au cours de la première, la reconstruction 3D est obtenue en sous-échantillonnant temporellement la séquence, lors de la seconde, la restitution haute résolution de texture est obtenue en exploitant l'ensemble des images. L'intérêt de la texture est de permettre de visualiser des détails fins du modèle numérisé qui ont été perdus dans le bruit géométrique de la reconstruction. Cette augmentation de qualité se fait via des techniques de Super Résolution (SR).Pour atteindre cet objectif nous avons conçu et réalisé une chaîne algorithmique prenant, en entrée, la séquence vidéo acquise et fournissant, en sortie, un modèle 3D de la scène avec une texture sur-résolue. Cette chaîne est construite autour d’un algorithme de reconstruction 3D multi-vues de l’état de l’art pour la partie géométrique.Une contribution centrale de notre chaîne est la méthode de recalage employée afin d’atteindre la précision sub-pixellique requise pour la SR. Contrairement aux données classiquement utilisées en SR, nos prises de vues sont affectées par un mouvement 3D, face à une scène à géométrie 3D, ce qui entraîne des mouvements image complexes. La précision intrinsèque des méthodes de reconstruction 3D est insuffisante pour effectuer un recalage purement géométrique, ainsi nous appliquons un raffinement supplémentaire par flot optique. Le résultat de cette méthode de restitution de texture SR est d'abord comparée qualitativement à une approche concurrente de l’état de l’art.Ces appréciations qualitatives sont renforcées par une évaluation quantitative de qualité image. Nous avons à cet effet élaboré un protocole d’évaluation quantitatif de techniques de SR appliquées sur des surfaces 3D. Il est fondé sur l'utilisation de mires fractales binaires, initialement proposées par S. Landeau. Nous avons étendu ces idées au contexte de SR sur des surfaces courbes. Cette méthode est employée ici pour valider les choix de notre méthode de SR, mais elle s'applique à l'évaluation de toute texturation de modèle 3D.Enfin, les surfaces spéculaires présentes dans les scènes induisent des artefacts au niveau des résultats de SR en raison de la perte de photoconsistence des pixels au travers des images à fusionner. Pour traiter ce problème nous avons proposé deux méthodes correctives permettant de recaler photométriquement nos images et restaurer la photoconsistence. La première méthode est basée sur une modélisation des phénomènes d’illumination dans un cas d'usage particulier, la seconde repose sur une égalisation photométrique locale. Les deux méthodes testées sur des données polluées par une illumination variable s'avèrent effectivement capables d'éliminer les artefacts. / Multi-view 3D reconstruction techniques have reached industrial level maturity : non-expert users are now able to use commercial software to produce quality, large scale, 3D models. These reconstructions use top of the line sensors such as LIDAR or DSLR cameras, mounted on tripods and moved around the scene. Such protocols are not designed to efficiently inspect large infrastructures with complex geometry. As the capabilities of micro-drones progress at a fast rate, it is becoming possible to delegate such tasks to them. This choice induces changes in the acquired data : rather than a set of carefully acquired images, micro-drones will produce a video sequence with varying image quality, due to such flaws as motion blur and defocus. Processing video data is challenging for photogrammetry software, due to the high combinatorial cost induced by the large number of images. We use the full image sequence in two steps. Firstly, a 3D reconstruction is obtained using a temporal sub-sampling of the data, then a high resolution texture is built from the full sequence. Texture allows the inspector to visualize small details that may be lost in the noise of the geometric reconstruction. We apply Super Resolution techniques to achieve texture quality augmentation. To reach this goal we developed an algorithmic pipeline that processes the video input and outputs a 3D model of the scene with super resolved texture. This pipeline uses a state of the art 3D reconstruction software for the geometric reconstruction step. The main contribution of this pipeline is the image registration method used to achieve the sub-pixel accuracy required for Super Resolution. Unlike the data on which Super Resolution is generally applied, our viewpoints are subject to relative 3D motion and are facing a scene with 3D geometry, which makes the motion field all the more complex. The intrinsic precision of current 3D reconstruction algorithms is insufficient to perform a purely geometric registration. Instead we refine the geometric registration with an optical flow algorithm. This approach is qualitatively to a competing state of the art method. qualitative comparisons are reinforced by a quantitative evaluation of the resulting image quality. For this we developed a quantitative evaluation protocol of Super Resolution techniques applied to 3D surfaces. This method is based on the Binary Fractal Targets proposed by S. Landeau. We extended these ideas to the context of curved surfaces. This method has been used to validate our choice of Super Resolution algorithm. Finally, specularities present on the scene surfaces induce artefacts in our Super Resolution results, due to the loss of photoconsistency among the set of images to be fused. To address this problem we propose two corrective methods designed to achieve photometric registration of our images and restore photoconsistency. The first method is based on a model of the illumination phenomena, valid in a specific setting, the second relies on local photometric equalization among the images. When tested on data polluted by varying illumination, both methods were able to eliminate these artefacts.