It is known that a phase-perturbed object field from a fractal-like rough surface illuminated by a partially coherent beam generates speckle on the image plane. In this works, aberration effects on Gaussian speckle on the image plane in both perfectly and partially coherent systems are theoretically and experimentally investigated. Theory shows that the second order statistics of Gaussian laser speckle are independent of odd-functional aberrations, but they do affect Gaussian speckle contrast in a partially coherent system. Furthermore, it is theoretically derived that field statistics of Gaussian laser speckle generally become non-circular Gaussian due to aberrations, and an aberration effect is asymptotically ignorable for very weak or strong roughness. A brute force simulation method is introduced for non-Gaussian speckle in a partially coherent imaging system, where speckle irradiance is calculated from a quasi-monochromatic extended incoherent source. The source is modeled as a collection of independent point sources distributed on a regular grid. The partially coherent speckle pattern is calculated from the incoherent sum of coherent speckle patterns in the image plane generated from each point source. Speckle contrasts from a brute force model show good agreement with theoretical and experimental results. It is determined that non-Gaussian speckle contrast is strongly dependent on Hurst exponent of fractal rough surfaces using brute force simulations. The concept of a contributing object area at a fixed image point effectively explains the speckle contrast dependency. Measuring spherical aberrations using Gaussian laser speckle is discussed as one of applications and future works of the present study.

Tomography in soft X-ray microscopy is an emerging technique for obtaining quantitative 3D structural information about cells. One of its strengths, compared with other techniques, is that it can image intact cells in their near-native state at a few 10 nm’s resolution, without staining. However, the methods for reconstructing 3D-data rely on algorithms that assume projection data, which the images are generally not due to the imaging systems’ limited depth of focus. To bring out the full potential of tomography in soft X-ray microscopy an improved understanding of the image formation is desired. This Thesis reviews zone plate-based X-ray microscopy for biological imaging and the theory necessary for a numerical implementation of a 3D image formation model. Furthermore, a novel reconstruction approach is proposed that improves the overall resolution in a reconstruction of a tomographically imaged object. This is demonstrated by simulations and experiments. Finally, this Thesis covers work on the Stockholm X-ray microscope, including an upgrade of the X-ray source yielding unprecedented brightness for a compact system. With this upgrade it was possible to do high-quality imaging of cells in their near-native state with only 10 second exposures. / Tomografi i mjukröntgenmikroskopi är en ny teknik för att få ut kvantitativ strukturell 3D information om celler. Dess styrka jämfört med andra tekniker är att den kan avbilda intakta celler i deras nära naturliga tillstånd med ett par 10 nm upplösning, utan omfattande preparering. Dock är metoderna för att rekonstruera 3D-data beroende av algoritmer som antar projektionsdata, vilket bilderna i allmänhet inte är på grund av avbildningsystemens begränsade skärpedjup. För att få ut den fulla potentialen av tomografi i röntgenmikroskopi behövs en ökad förståelse för avbildningsprocessen. Denna avhandling behandlar zonplatte-baserad röntgenmikroskopi för biologisk avbildning och den nödvändiga teorin för en numerisk implementering av en avbildningsmodell i 3D. En ny rekonstruktionsmetod föreslås som förbättrar upplösningen i rekonstruktionen för ett tomografiskt avbildat objekt. Detta visas i simuleringar och experiment. Slutligen omfattar denna avhandling arbete på Stockholms mjukröntgenmikroskop, inklusive en uppgradering av röntgenkällan som ger oöverträffad ljusstyrka för ett kompakt system. Denna uppgradering möjliggör högkvalitativ avbildning av celler i deras nästan naturliga tillstånd med endast 10 sekunders exponering. / <p>QC 20160324</p>

A basic understanding of the hydrodynamic response behavior of the two-body system is important for a wide variety of offshore operations. This is a complex problem and model tests can provide data that in turn can be used to retrieve key information concerning the response characteristics of such systems. The current study demonstrates that the analysis of these data using a combination of statistical tools and system identification techniques can efficiently recover the main hydrodynamic parameters useful in design. The computation of the statistical parameters, spectral densities and coherence functions provides an overview of the general response behavior of the system. The statistical analysis also guides the selection of the nonlinear terms that will be used in the reverse multi-input / single-output (R-MI/SO) system identification method in this study. With appropriate linear and nonlinear terms included in the equation of motion, the R-MISO technique is able to estimate the main hydrodynamic parameters that characterize the offshore system. In the past, the R-MISO method was primarily applied to single body systems, while in the current study a ship moored to a fixed barge was investigated. The formulation included frequency-dependant hydrodynamic parameters which were evaluated from the experimental measurements. Several issues specific to this extension were addressed including the computation load, the interpretation of the results and the validation of the model. Only the most important cross-coupling terms were chosen to be kept based on the estimation of their energy. It is shown that both the heading and the loading condition can influence system motion behavior and that the impact of the wave in the gap between the two vessels is important. The coherence was computed to verify goodness-of-fit of the model, the results were overall satisfying.

Neste trabalho foram estudadas algumas formas de relação entre séries temporais multivariadas. Discutiu-se, inicialmente, a função de coerência, uma função análoga a função de correlação(que é dada no domínio do tempo) calculada no domínio da freqüência. Foram estudadas também as funções de coerência parcial e coerência parcial direcionada. A função de coerência parcial mede a relação entre duas componentes de uma série multivariada, isolados os efeitos de outra série. Em linhas gerais, a Coerência Parcial Direcionada pode ser interpredata como a decomposição da coerência parcial a partir de modelos autoregressivos multivariados. Esse conceito pode ser interpretado como uma representação do conceito de causalidade de Granger no domínio da freqüência. Finalmente, foram aplicadas as funções acima em dois conjuntos de dados: um modelo VAR(1) trivariado simulado e dados de medições de eletroencefalograma. / In this work we studied relationships between multivariate time series. We discussed the coherence function, a function similar to the correlation function(calculated in time domain) in frequency domain. Next, we discussed partial coherence and partial directed coherence. The partial coherence measures the relationship between two components of a multivariate time series, after removing the influence of another time series. Generally, the partial directed coherence can be interpreted as the decompositioin of the partial coherence from multivariate autoregressive models. We can interpret this function as a representation of the Granger causality concept in frequency domain. Finally, we applied these concepts in two situations: a simulated VAR(1) model and an electroencefalogram database.

Le contexte de cette thèse est l'étude de la cohérence partielle dans les faisceaux synchrotron produits par les anneaux de stockage de basse émittance, comme l’ESRF-EBS. L'objectif principal est la compréhension et l'application de la physique sous-jacente pour l'implémentation et le développement d'outils de calcul.Nous développons d’abord une théorie de l'optique-statistique pour les radiations émisses par des anneaux de stockage qui est basée sur le théorème de Kim et sur les contributions de Geloni et al. Nous utilisons ces formules d'une manière détaillée et légèrement différente. Nous insistons sur l'importance des paramètres stochastiques des faisceaux d'électrons pour décrire les propriétés de cohérence. Nous observerons que la longueur du paquet des électrons n’affecte pas les propriétés de la cohérence s’il y a un couplage faible entre la position longitudinal de l’électron et ses autres paramètres.Nous avons construit une description de l'optique statistique pour l’émission synchrotron liée aux modes de cohérence. Nous voyons qu'un ensemble est complètement cohérent si et seulement si ses modes de cohérences se réduisent a un seul mode. Geloni et al. mentionnent que l’émission d’un synchrotron est un processus stochastique gaussien. Nous ajoutons qu’il a une moyenne nulle et il est symétrique circulaire. En conséquence nous pouvons donner une interprétation physique au degré de cohérence spectrale en termes de densité de probabilité conditionnée de forme gaussienne.Nous avons développé et implémenté un algorithme qui calcule la décomposition de la densité spectrale en modes de cohérences. Il peut être appliqué à un faisceau d'électrons avec un paramètre Twiss-alpha fini et une dispersion d’énergie. Nous avons implémenté deux versions de l'algorithme. La première résout l'équation de Fredholm dans une base de fonctions constantes par morceaux. Les calculs pour les hautes harmoniques d'un onduleur et pour des émittances relativement larges demandent une trop grande mémoire pour être calculées. Pour réduire la mémoire requise, nous avons développé une méthode en deux pas. On résout d'abord l'équation pour un faisceau d'électron de divergence nulle, puis on ajoute les effets de la divergence dans un second temps.Nous présentons des tests approfondis qui incluent une distribution des électrons du type fonction delta, des champs électriques gaussiens dont les résultats analytiques sont connus, ainsi qu'une comparaison avec des résultats Monte Carlo produits par SRW.Nous appliquons cet algorithme sur un nombre de cas particuliers. Nous déterminons combien de modes sont nécessaires pour inclure 95% de la densité spectrale et comment le degré de cohérence spectrale change. Nous trouvons que la dispersion d'énergie ajoute des modes de cohérence. Cet effet est négligeable pour des anneaux courants mais pour l’ESRF-EBS elle ajoute des nouveaux modes. Des onduleurs plus courts et des plus hautes harmoniques augmentent le nombre de modes. Une comparaison entre un onduleur placée dans un point avec alpha fini et dans un point symétrique ne montre pas de différences significative. Une réduction artificielle de l’émittance du anneau ESRF-EBS montre un décroit du nombre de mode jusqu’à arriver à un seul mode.Nous avons simulé une ligne de lumière simplifiée focalisant 1:1. Une réduction de la taille de l'ouverture change les valeurs propres du spectre vers des modes de plus en plus petits ce qui entraine aussi une réduction du flux. Nous présentons une comparaison entre la densité spectrale calculée avec l’approximation Gauss-Shell, l’approximation analytique et l’approximation de la séparation. Bien qu'il n'y a pas d'erreurs négligeables entre le calcul exact et l'approximation de la séparation, nous concluons que cette dernière peut être une bonne et rapide solution permettant des calculs sur des ordinateur portables.Nous terminons cette thèse par une discussion/des idées sur de futures recherches. / The context of this thesis is the study of the partial coherence in synchrotron beams produced by ultra low emittance storage rings, like the ESRF-EBS ring under construction. As main objectives we had the understanding, application and development of the underlying physics and the implementation of computer tools able to calculate the relevant parameters.In the first part of this thesis we develop a theory for statistical optics for storage ring radiation. It is based on the brightness convolution theorem by Kim and on the subtle but very important theoretical contributions from Geloni et al. We derive their formulas in a slightly different way or in more a detailed form.We emphasize the importance of the description of the electron beam stochastic for the coherence properties of storage ring emission. We observe that for weak coupling of the longitudinal electron position to the other beam parameters the bunch length is a free parameter in view of coherence properties.We build our description of statistical optics around coherent modes. We show that an ensemble is completely coherent if and only if its coherent mode decomposition is a single mode. Geloni et al. mentioned that the synchrotron storage ring emission is a Gaussian random process. We add that the process has zero mean and is circularly-symmetric. In consequence we can give the spectral degree of coherence a physical interpretation in terms of Gaussian shaped conditional probability densities.We developed and implemented an algorithm that calculates the coherent mode decomposition of the cross spectral density for a given wavelength. It can be applied to electron beams with finite Twiss alpha and with energy spread. We implemented two algorithms. The first version solves the Fredholm equation in a two-dimensional step function basis set. Because of its memory requirements high undulator harmonics or current lattices with high emittances cannot be calculated. To reduce the memory requirements we developed the two-step method that solves the problem first for an electron beam with zero divergence and adds the effects of the divergence in a second step. The algorithms use the eigensolver library SLEPc. The implementations of the algorithms are open source.We present extensive tests of the algorithms. They include a delta-function shaped electron beam, a Gaussian single electron reference electric field, whose results are analytically known, and comparisons to SRW Monte Carlo samplings.We apply the algorithm to some particular cases. We determine how many modes are necessary to incorporate 95% of the spectral density and how the spectral degree of coherence changes. We find that the energy spread adds extra coherent modes. This effect is negligible for current lattices but for the ESRF-EBS lattice it accounts for a significant fraction of the total modes. Shorter undulators and higher harmonics increase the number of modes. A comparison between an undulator placed at a point with finite alpha and at a symmetry point shows no significant differences. A reduction of the ESRF-EBS beam parameters show a decrease of the mode numbers until they reach a single mode. We simulate a simple 1:1 imaging beamline with an aperture in the image plane. A reduction of the aperture size changes the eigenvalue spectrum to fewer and fewer modes that is paid with a decrease of flux. We present a comparison of the calculated cross spectral density with a Gaussian Schell-model, an analytic approximation and a separation approximation. Although there are not negligible errors between the exact calculation and the separation approximation we come to the conclusions that the separation approximation might be a good and quick approximation that allows the calculation on portable computers.We end the thesis with some ideas for future research.

Neste trabalho foram estudadas algumas formas de relação entre séries temporais multivariadas. Discutiu-se, inicialmente, a função de coerência, uma função análoga a função de correlação(que é dada no domínio do tempo) calculada no domínio da freqüência. Foram estudadas também as funções de coerência parcial e coerência parcial direcionada. A função de coerência parcial mede a relação entre duas componentes de uma série multivariada, isolados os efeitos de outra série. Em linhas gerais, a Coerência Parcial Direcionada pode ser interpredata como a decomposição da coerência parcial a partir de modelos autoregressivos multivariados. Esse conceito pode ser interpretado como uma representação do conceito de causalidade de Granger no domínio da freqüência. Finalmente, foram aplicadas as funções acima em dois conjuntos de dados: um modelo VAR(1) trivariado simulado e dados de medições de eletroencefalograma. / In this work we studied relationships between multivariate time series. We discussed the coherence function, a function similar to the correlation function(calculated in time domain) in frequency domain. Next, we discussed partial coherence and partial directed coherence. The partial coherence measures the relationship between two components of a multivariate time series, after removing the influence of another time series. Generally, the partial directed coherence can be interpreted as the decompositioin of the partial coherence from multivariate autoregressive models. We can interpret this function as a representation of the Granger causality concept in frequency domain. Finally, we applied these concepts in two situations: a simulated VAR(1) model and an electroencefalogram database.

This master’s thesis develops a novel method of digital holography, from recent studies known as Fresnel Incoherent Correlation Holography (FINCH). The method enables the reconstruction of the correlation records of three-dimensional objects, captured under quasi-monochromatic, incoherent illumination. The experimental system is based on an action of a Spatial Light Modulator, driven by computer generated holograms to create mutually correlated beams. Both optical and digital parts of the experiment can be carried out using procedures of classical holography, diffractive optics and digital holography. As an important theoretical result of the master’s thesis, a new computational model was proposed, which allows to describe the experiment completely with respect to its two basic phases. The proposed model allows to understood the method intuitively and can be used additionally for analysis and interpretation of the imaging parameters and the system optimalization. The theoretical part of the master’s thesis also presents a detailed description of the correlation imaging based on an appropriate reconstruction process. Computational models were developed for both monochromatic and quasi-monochromatic illumination. In experimental part, all theoretical results were verified. The imaging parameters were examined using standard resolution target tests and appropriate biological samples. As an original experimental result, spiral modification of the system resulting in a vortex imaging was proposed and realized. Here, a selective edge enhancement of three-dimensional objects is possible, resulting in a significant extension of possible applications of the method.

no / PURPOSE: To estimate refractive indices used by the Lenstar biometer to translate measured optical path lengths into geometrical path lengths within the eye. METHODS: Axial lengths of model eyes were determined using the IOLMaster and Lenstar biometers; comparing those lengths gave an overall eye refractive index estimate for the Lenstar. Using the Lenstar Graphical User Interface, we noticed that boundaries between media could be manipulated and opposite changes in optical path lengths on either side of the boundary could be introduced. Those ratios were combined with the overall eye refractive index to estimate separate refractive indices. Furthermore, Haag-Streit provided us with a template to obtain 'air thicknesses' to compare with geometrical distances. RESULTS: The axial length estimates obtained using the IOLMaster and the Lenstar agreed to within 0.01 mm. Estimates of group refractive indices used in the Lenstar were 1.340, 1.341, 1.415, and 1.354 for cornea, aqueous, lens, and overall eye, respectively. Those refractive indices did not match those of schematic eyes, but were close in the cases of aqueous and lens. Linear equations relating air thicknesses to geometrical thicknesses were consistent with our findings. CONCLUSION: The Lenstar uses different refractive indices for different ocular media. Some of the refractive indices, such as that for the cornea, are not physiological; therefore, it is likely that the calibrations in the instrument correspond to instrument-specific corrections and are not the real optical path lengths.

No description available.

Made available in DSpace on 2016-06-02T19:06:01Z (GMT). No. of bitstreams: 1 4845.pdf: 2916613 bytes, checksum: aa64366fdbe9befa8f14547fa4545763 (MD5) Previous issue date: 2012-08-18 / Multi-Electrode Array, MEA, was developed more than thirty years ago. This planar device of multiple microelectrodes has been used to detect local electric potential variations created by the ion movement through the protein channels that traverses the cell membranes in the near neighborhood. MEA offers the possibility of non invasive registering of the cell and their network s activities, allowing to know how the neurons start to connect through the synapses forming a network and generating spontaneous electrophysiological activities. In order to understand the neural network dynamics in face of the spontaneous activities and its evolution in dissociated hippocampal cell cultures, important properties in the synaptic plasticity, in this work it is proposed the analysis of the evolution and modeling of the hippocampal cell cultures in MEA using the theory of Partial Directed Coherence and Complex Networks. There were used the electrophysiological records obtained using MEA60 System, of the dissociated neurons of 18 days old Wistar rat embyo, in an experiment denoted as 371, realized at the University of Genoa, Italy. As the results obtained using the Partial Directed Coherence approach, it was verified that the method is capable to detect neuronal connectivity in the neuron cultures using MEA, even with the noisy signals. It was also verified that different time delays between signals during application of the PDC method do not affect directly on the results of the causality. PDC allowed to show that in MEA the amount of direct connections resulted is less than the amount of indirect connections, through the microelectrodes. This can indicate that the neurons prefer to communicate through existing connections than creating new connections. It was also observed that it is easier to lose direct connections than indirect connections between microelectrodes through the time. Through the experiments it can be observed that the culture in 25 DIV (Days In Vitro) developed more amount of connections between neighboring electrodes, with less overall connections than the culture in 46 DIV, that had more overall connections with less neighborhood connections. Since one of the PDC features is the directionality detection between connections, it was observed direction changes through the connections through the time, even though we do not know the physiological meaning of these changes in the cognitive process. It was also observed that the established connections do not follow random patterns, showing an indicative of a free scale network, although we used small statistical measures to characterize the networks. / Há mais de 30 anos a Matriz de microeletrodos (Multi-Electrode Array,MEA) foi desenvolvida. Este dispositivo planar de múltiplos microeletrodos tem permitido detectar as variações do potencial elétrico local que são criadas pelo movimento de íons através dos canais de proteínas que atravessam as membranas das células neuronais em sua vizinhança imediata. A MEA oferece a possibilidade de gravação não-invasiva da atividade das células e de redes de células, permitindo-nos conhecer como os neurônios se comunicam através de sinapses formando uma rede e disparando atividades eletrofisiológicas espontâneas evocadas. No sentido de poder entender melhor a dinâmica das redes neurais em termos de atividades espontâneas e sua evolução em culturas de células hipocampais dissociadas, que são as propriedades mais importantes na plasticidade sináptica, neste trabalho é proposta a análise da evolução e o modelamento de culturas de células hipocampais na MEA usando a teoria de Coerência Parcial Direcionada (PDC) e de Redes Complexas. Foram usados os registros eletrofisiológicos obtidos usando o sistema MEA60, de neurônios dissociados de embrião de rato Wistar, de 18 dias de vida em um experimento denotado como 371, realizado na Universidade de Gênova, Itália. Como resultados obtidos ao utilizar o método de Coerência Parcial Direcionada, verificou-se que o método é capaz de detectar conectividade neuronal nas culturas de neurônios da MEA, mesmo com sinais com presença de ruído. Também verificou-se que tempos de atraso diferentes na aplicação do PDC não tem uma influência direta nos resultados de causalidade. O PDC permitiu mostrar que na MEA a quantidade de conexões diretas estabelecidas foram sempre em menor quantidade do que as conexões indiretas, através de caminhos. Isso pode ser um indicativo de que os neurônios preferem estabelecer comunicações usando caminhos ja existentes do que criando novas conexões. Também observou-se que com o passar do tempo é mais fácil se perderem conexões diretas do que conexões intermediárias entre neurônios. Através dos experimentos realizados pode se obervar que a cultura no 25 DIV (dias in vitro) desenvolveu maior quantidade de conexões com nós vizinhos, possuindo menos conexões em total, do que a rede no 46 DIV que teve maior quantidade de conexões total mas menor quantidade de conexões com nós vizinhos. Como uma das características do PDC é a deteção da direcionalidade nas conexões, observouse mudanças no sentido das conexões ao longo do registro, embora não saibamos ainda o significado fisiológico dessas mudanças em processos cognoscitivos. Também observou-se que as conexões estabelecidas não seguiam um padrão aleatório, encontrando-se um indicativo de um comportamento de redes livres de escala, embora não possamos afirmar isso por ter utilizado poucas medidas estatísticas para caracterizar as redes.