Dans cette thèse, nous nous intéressons à la restauration d'image tridimensionnelle de microscopie de fluorescence. Deux difficultés majeures dans ce système d'imagerie sont traitées. La première est le flou variable en profondeur qui est dû aux aberrations induites par la variation des indices de réfraction dans le système optique et le spécimen imagé. La deuxième est le bruit qui est principalement dû au processus de comptage de photons. L'objectif de cette thèse est de réduire ces distorsions afin de fournir aux biologistes une image de meilleure qualité possible. Dans la première partie de cette thèse, nous étudions les modèles d'approximation du flou variable en profondeur et nous choisissons un modèle adéquat au problème d'inversion. Dans ce modèle, la réponse impulsionnelle (RI) variable en profondeur est approchée par une combinaison convexe d'un ensemble de RIs invariables spatialement. Nous développons pour ce modèle deux méthodes rapides de restauration non-aveugle par minimisation d'un critère régularisé, chacune d'elles est adaptée au type de bruit présent dans les images de microscopie confocale ou à champ large. Dans la deuxième partie, nous abordons le problème de restauration aveugle et proposons deux méthodes dans lesquelles le flou variable en profondeur et l'image sont conjointement estimés. Dans la première méthode, la RI est estimée en chaque voxel du volume considéré afin de laisser une grande liberté sur la forme de la RI, tandis que dans la deuxième méthode, la forme de la RI est contrainte par une fonction gaussienne afin de réduire le nombre de variables inconnues et l'espace des solutions possibles. Dans ces deux méthodes d'estimation aveugle, l'effet des aberrations optiques n'est pas efficacement estimé en raison du manque d'information. Nous améliorons ces méthodes d'estimation en alternant des contraintes dans les domaines fréquentiel et spatial. Des résultats sont montrés en simulation et sur des données réelles. / In this thesis, we focus on the restoration of three-dimensional image of fluorescence microscopy. Two major difficulties in this imaging system are considered. The first one is the depth-variant blur due to aberrations induced by the refractive index variation in the optical system and the imaged specimen. The second difficulty is the noise due to the photon counting process. The goal of this thesis is to reduce these distortions in order to provide biologists with a better image quality. In the first part of this thesis, we study the approximation models of the depth-variant blur and choose an appropriate model for the inversion problem. In that model, the depth-variant point spread function (PSF) is approximated by a convex combination of a set of space-invariant PSFs. We then develop for that model two fast non-blind restoration methods by minimizing a regularized criterion, each of these methods is adapted to the type of noise present in images of confocal or wide field microscopy. In the second part, we address the problem of blind restoration and propose two methods where the depth-variant blur and the image are jointly estimated. In the first method, the PSF is estimated at each voxel in the considered volume in order to allow high degree of freedom on the PSF shape while in the second method, the shape of the PSF is constrained by a Gaussian function in order to reduce the number of unknown variables and the space of possible solutions. In both blind estimation methods, the effect of optical aberrations is not effectively estimated due to the lack of information. We thus improve these estimation methods by alternating some constraints in the frequency and spatial domains. Results on simulated and real data are shown.

Vision research has uncovered computational principles that generalize across species and brain area. However, these biological mechanisms are not frequently implemented in computer vision algorithms. In this thesis, models suitable for application in computer vision were developed to address the benefits of two biologically-inspired computational principles: multi-scale sampling and active, space-variant, vision. The first model investigated the role of multi-scale sampling in motion integration. It is known that receptive fields of different spatial and temporal scales exist in the visual cortex; however, models addressing how this basic principle is exploited by species are sparse and do not adequately explain the data. The developed model showed that the solution to a classical problem in motion integration, the aperture problem, can be reframed as an emergent property of multi-scale sampling facilitated by fast, parallel, bi-directional connections at different spatial resolutions. Humans and most other mammals actively move their eyes to sample a scene (active vision); moreover, the resolution of detail in this sampling process is not uniform across spatial locations (space-variant). It is known that these eye-movements are not simply guided by image saliency, but are also influenced by factors such as spatial attention, scene layout, and task-relevance. However, it is seldom questioned how previous eye movements shape how one learns and recognizes an object in a continuously-learning system. To explore this question, a model (CogEye) was developed that integrates active, space-variant sampling with eye-movement selection (the where visual stream), and object recognition (the what visual stream). The model hypothesizes that a signal from the recognition system helps the where stream select fixation locations that best disambiguate object identity between competing alternatives. The third study used eye-tracking coupled with an object disambiguation psychophysics experiment to validate the second model, CogEye. While humans outperformed the model in recognition accuracy, when the model used information from the recognition pathway to help select future fixations, it was more similar to human eye movement patterns than when the model relied on image saliency alone. Taken together these results show that computational principles in the mammalian visual system can be used to improve computer vision models.

No description available.

The finite element method (FEM) has been widely applied to various medical imaging applications over the past two decades. The remarkable progress in high-resolution imaging techniques has allowed FEM to draw great research interests in computing trabecular bone (TB) stiffness from three-dimensional volumetric imaging. However, only a few results are available in literature on applying FEM to multi-row detector CT (MDCT) imaging due to the challenges posed by limited spatial resolution. The research presented here develops new methods to preserve TB structure connectivity and to generate high-quality mesh representation for FEM from relatively low resolution images available at MDCT imaging. Specifically, it introduced a space-variant hysteresis algorithm to threshold local trabecular structure that preserves structure connectivity. Also, mesh generation algorithms was applied to represent TB micro-architecture and mesh quality was compared with that generated by traditional methods. TB stiffness was computed using FEM simulation on micro-CT (µ-CT) and MDCT images of twenty two cadaveric specimens of distal tibia. Actual stiffness of those specimens were experimentally determined by mechanical testing and its correlation with computed stiffness was analyzed. The observed values of linear correlation (r2) between actual bone stiffness and computed stiffness from µ-CT and MDCT imaging were 0.95 and 0.88, respectively. Also, reproducibility of the FEM-based computed bone stiffness was determined from repeat MDCT scans of cadaveric specimens and the observed intra-class correlation coefficient was a high value of 0.98. Experimental results demonstrate the feasibility of application of FEM with high sensitivity and reproducibility on MDCT imaging of TB at distal tibia under in vivo condition.

This thesis analyzes the process of deblurring of degraded images generated by space-variant nonlinear image systems with Gaussian observation noise. The restoration of blurred images is performed by using two methods / a modified version of the Optimum Decoding Based Smoothing Algorithm and the Bootstrap Filter Algorithm which is a version of Particle Filtering methods. A computer software called MATLAB is used for performing the simulations of image estimation. The results of some simulations for various observation and image models are presented.

A wide range of applications currently utilize conventional optical elements to individually transform the phase, polarization, and spectral transmission/reflection of the incident radiation to realize the desired system level function. The material properties and the feasibility of fabrication primarily impact the device and system functionality that can be realized. With the advancement in micro/nano patterning, growth, deposition and etching technology, devices with novel and multiplexed optical functionalities have become feasible. As a result, it has become possible to engineer the device response in the near and far field by controlling the phase, polarization or spectral response at the micro scale. One of the methods that have been explored to realize unique optical functionalities is by varying the structural properties of the device as a function of spatial location at the sub-micron scale across the device aperture. Spatially varying the structural parameters of these devices is analogous to local modifications of the material properties. In this dissertation, the optical response of interference transmission filters, guided mode resonance reflection filters, and diffraction gratings operated in Littrow condition with strategically introduced spatial variation have been investigated. Spatial variations in optical interference filters were used to demonstrate wavelength tunable spatial filters. The effect was realized by integrating diffractive and continuous phase functions on the defect layer of a one-dimensional photonic crystal structure. Guided mode resonance filters are free space optical filters that provide narrow spectral reflection by combining grating and waveguide dispersion effects. Frequency dependent spatial reflection profiles were achieved by spatially varying the grating fill fraction in designed contours. Diffraction gratings with space variant fill fractions operating in Littrow condition were used to provide graded feedback profiles to improve the beam quality and spatial brightness of broad area diode lasers. The fabrication of space variant structures is challenging and has been accomplished primarily by techniques such as ruling, electron beam writing or complex deposition methods. In order to vary the desired structural parameter in a designed manner, a novel technique for the fabrication of space variant structures using projection lithography with a fidelity that rivals any of the current technologies was also developed as a part of this work. The devices exhibit wavelength dependent beam shaping properties in addition to spatial and spectral filtering and have potential applications in advanced imaging systems, graded reflectivity laser mirrors, and engineered illumination. The design, modeling, microfabrication and experimental characterization of space variant micro optical elements with novel optical functionalities are presented.

Ce travail consiste en l'étude de phénomènes optomécaniques en d'interaction spin-orbite de la lumière, en utilisant des milieux inhomogènes et anisotropes comme systèmes modèles, différents types de systèmes matériels étant considérés en pratique. En particulier,nous avons utilisé des défauts de cristaux liquides nématiques pour lesquels nous avons identifié expérimentalement d'un couple optique de nature spin-orbite conduisant à des modifications de champ d'orientation moléculaire du cristal liquide. Aussi, grâce à l'utilisation de verres nanostructurés artificiellement permettant un contrôle de l'interaction spin-orbite à la demande,nous mettons en évidence un phénomène de couple optique inverse qui est l'analogue angulaire des forces optiques dites négatives. Cet effet optomécanique contre-intuitif est démontré expérimentalement, d'une manière indirecte, grâce à la mise en place de diverses expériences de décalage en fréquence Doppler associées aux degrés de liberté de rotation. Enfin, nous présentons nos tentatives en vue de réaliser expérimentalement l'observation directe d'un couple optique inverse. Plusieurs options sont envisagées, qui comprennent à la fois des approches à base de matériaux métalliques ou diélectriques. De manière générale, cela implique la miniaturisation des systèmes considérés, ce qui est effectué à la fois à l'échelle millimétrique et micrométrique. / This work focuses on angular optomechanics driven by the spin-orbit interaction of light, using inhomogeneous and anisotropic media as model systems and different kinds of such material systems are considered in practice. In particular, we use nematic liquid crystal defects and report on the direct experimental observation of spin-orbit optical radiation torque that leads to distortion of molecular orientation pattern of the defects. Then, by using solid-state spin-orbit couplers of arbitrary order made of artificially nanostructured glasses, we unveil an optical torque reversal phenomenon that is the angular counterpart of so-called optical negative forces. This counterintuitive optomechanical effect is experimentally retrieved, in an indirect manner, via rotational Doppler frequency shift experiments. Finally, we report on our attempts to build up an experimental framework allowing the direct observation of optical torque reversal. Several options are considered, which include both metallic and dielectric approaches and involve sample miniaturization that has been explored at the millimeter and micrometer scale.

Approved for public release, distribution is unlimited / In this thesis, the ocean was modeled as a waveguide with an ideal pressure - release surface, and an ideal rigid bottom. The ocean waveguide was then treated as a linear, time - invariant, space - variant (TISV) filter or communication channel. The filter is time - invariant because no motion was modeled and because the properties of the ocean were assumed to be constant. The filter is space - variant because of the presence of the two boundaries, that is, the ocean surface and ocean bottom. This thesis investigates the ocean as a linear TISV filter by evaluating 1) the complex frequency response, 2) the impulse response, and 3) the transfer function of the ocean with respect to depth. It is shown that the TISV impulse response of the ocean contains information that can be used to help localize a target in range and whether the target is above or below the receiver. Computer simulation results were obtained by evaluating the three filter functions for several different test cases. / Ensign, United States Navy