Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

La tomographie optique diffuse (TOD) est une modalité d’imagerie biomédicale 3D peu dispendieuse et non-invasive qui permet de reconstruire les propriétés optiques d’un tissu biologique. Le processus de reconstruction d’images en TOD est difficile à réaliser puisqu’il nécessite de résoudre un problème non-linéaire et mal posé. Les propriétés optiques sont calculées à partir des mesures de surface du milieu à l’étude. Dans ce projet, deux méthodes de reconstruction non-linéaire pour la TOD ont été développées. La première méthode utilise un modèle itératif, une approche encore en développement qu’on retrouve dans la littérature. L’approximation de la diffusion est le modèle utilisé pour résoudre le problème direct. Par ailleurs, la reconstruction d’image à été réalisée dans différents régimes, continu et temporel, avec des mesures intrinsèques et de fluorescence. Dans un premier temps, un algorithme de reconstruction en régime continu et utilisant des mesures multispectrales est développé pour reconstruire la concentration des chromophores qui se trouve dans différents types de tissus. Dans un second temps, un algorithme de reconstruction est développé pour calculer le temps de vie de différents marqueurs fluorescents à partir de mesures optiques dans le domaine temporel. Une approche innovatrice a été d’utiliser la totalité de l’information du signal temporel dans le but d’améliorer la reconstruction d’image. Par ailleurs, cet algorithme permettrait de distinguer plus de trois temps de vie, ce qui n’a pas encore été démontré en imagerie de fluorescence. La deuxième méthode qui a été développée utilise l’apprentissage machine et plus spécifiquement l’apprentissage profond. Un modèle d’apprentissage profond génératif est mis en place pour reconstruire la distribution de sources d’émissions de fluorescence à partir de mesures en régime continu. Il s’agit de la première utilisation d’un algorithme d’apprentissage profond appliqué à la reconstruction d’images en TOD de fluorescence. La validation de la méthode est réalisée avec une mire aux propriétés optiques connues dans laquelle sont inséres des marqueurs fluorescents. La robustesse de cette méthode est démontrée même dans les situations où le nombre de mesures est limité et en présence de bruit. / Abstract : Diffuse optical tomography (DOT) is a low cost and noninvasive 3D biomedical imaging technique to reconstruct the optical properties of biological tissues. Image reconstruction in DOT is inherently a difficult problem, because the inversion process is nonlinear and ill-posed. During DOT image reconstruction, the optical properties of the medium are recovered from the boundary measurements at the surface of the medium. In this work, two approaches are proposed for non-linear DOT image reconstruction. The first approach relies on the use of iterative model-based image reconstruction, which is still under development for DOT and that can be found in the literature. A 3D forward model is developed based on the diffusion equation, which is an approximation of the radiative transfer equation. The forward model developed can simulate light propagation in complex geometries. Additionally, the forward model is developed to deal with different types of optical data such as continuous-wave (CW) and time-domain (TD) data for both intrinsic and fluorescence signals. First, a multispectral image reconstruction algorithm is developed to reconstruct the concentration of different tissue chromophores simultaneously from a set of CW measurements at different wavelengths. A second image reconstruction algorithm is developed to reconstruct the fluorescence lifetime (FLT) of different fluorescent markers from time-domain fluorescence measurements. In this algorithm, all the information contained in full temporal curves is used along with an acceleration technique to render the algorithm of practical use. Moreover, the proposed algorithm has the potential of being able to distinguish more than 3 FLTs, which is a first in fluorescence imaging. The second approach is based on machine learning techniques, in particular deep learning models. A deep generative model is proposed to reconstruct the fluorescence distribution map from CW fluorescence measurements. It is the first time that such a model is applied for fluorescence DOT image reconstruction. The performance of the proposed algorithm is validated with an optical phantom and a fluorescent marker. The proposed algorithm recovers the fluorescence distribution even from very noisy and sparse measurements, which is a big limitation in fluorescence DOT imaging.

Thesis (MScEng (Mechanical and Mechatronic Engineering))--University of Stellenbosch, 2008. / A rapid measurement system is implemented using two digital video cameras, presenting a faster and less expensive solution to certain metrology problems. The cameras are calibrated from one stereo image-pair of a 3D calibration grid that allows an immediate assessment of the achievable metric accuracy of the system. Three different methods, using either laser tracking or structured light patterns, were developed and employed to solve the coordinate extraction and correspondence matching problems. Different image processing techniques were used to speed up the entire measurement process. All software development was accomplished using only freely distributed software packages. The system achieves calibration in less than a minute and accumulates point correspondences at 12 frames per second. Accuracies of greater than 0.4 mm are achieved for a 235 x 190 x 95 mm measurement volume using a single pair of images with 640 x 480 pixel resolution each.

The work reported in this thesis has been carried out in the following two areas of Optical metrology: 1. Measurement and correction of prism angles 2. Measurement of refractive indices using a spectrograph. The prism angles are conventionally tested by mechanical bevel protractors, autocol-limators (angle dekkors), simple interference techniques and interferometers. All these methods have their own limitations either in accuracy or in terms of cost. Mechanical methods are usually employed to measure the angles of prisms. Interference techniques and interferometers are also used but they need optically polished components. For both mechanical and simple interference methods of testing, it is essential to fabricate more than a single component in number. The process of building interferometers or purchasing interferometers, angle dekkors and standard angle gauges is not cost effective for many research laboratories, and medium scale industries. To overcome these difficulties simple and inexpensive methods without sacrificing the accuracy in the bargain are suggested for the measurement of prism angles, based on the principles of reflection of light. The refractive indices of prism materials for invisible and weaker spectral lines are usually determined from spectrograms using dispersion formulae and numerical interpolation techniques. In these methods, the accuracy of the results depends on the accuracy of determining the constants of the dispersion formulae. A simple experimental technique, using a spectrograph, is devised for the measurement of refractive indices of solids and liquids both for visible and invisible spectral lines (wavelengths). The thesis has been divided into six chapters. The first chapter starts with the general introduction. The second chapter presents the literature review of the existing methods for angle and refractive index measurements. The third chapter describes the proposed new techniques for prism angle measurements. The fourth chapter presents the experimental results of angle measurements, and the discussion of the accuracy of the results. This chapter also gives the scope for further research. The fifth chapter describes a newly proposed technique for measuring refractive indices and the experimental results. This chapter also gives the scope for further research. The summary of the results, conclusions, and suggestions for further work are presented in chapter six.

The optical touch pointer (OTP), a fluorescence spectroscopy based system, assists brain surgeons during guided brain tumor resection in patients with glioblastoma multiforme (GBM). After recording and analyzing the autofluorescence spectrum of the tissue, it is possible to distinguish malignant from healthy brain tissue. A challenge during the intraoperative measurements is the interference of blood. If it gets in contact with the laser pointer, the blood blocks the light transmission to and from the tissue. The purposes of the project were to study and categorize patterns of blood interference and to present possible solutions to avoid signal blocking by blood. To measure fluorescence and reflection two devices were used respectively, the OTP which has a spectrometer and a blue laser, and the diffused reflection spectroscopy system (DRS) which has a spectrometer and a white light source. Both operate independently from each other and are connected to a fiber optical probe. A similar scenario to the one in the operation theater was simulated in the lab. Fluorescence and diffuse reflection measurements with and without blood were realized on skin and on two different plastic fluorescent standards. The results were analyzed with the aid of MatLAB, and compared with data collected in the hospital during brain tumor resection. The highest autofluorescence of brain tissue and skin is reached at approximately 506 nm. Although skin and both plastic standards have different optical properties regarding color or rather fluorescence, all of them presented very similar curves when blood on them blocked partially or completely the light transmission. A blood layer of more than 0.1 mm thickness blocks the blue laser light. Blood absorption happens at 541 and 577 nm due to oxy-hemoglobin (HbO2) in both liquid and dried blood. When the fluorescence spectrum is available but weak, the reflection spectrum contains two dips (traces of HbO2 at 541 and 577 nm). In brain there were cases in which light absorption occurred additionally at other wavelengths than the absorption peaks of deoxyhemoglobin (Hb) and HbO2. Blood interference during the OP can be prevented if the probe rests in a saline solution after every measurement. In this way the fresh blood sticking on the probe dissolves in the solution. For dried or coagulated blood, additional manual cleansing is needed.

L'utilisation de fluides au comportement rhéologique complexe (seuil d'écoulement, thixotropie) est de plus en plus courante dans notre quotidien. Une description globale du comportement n'est pas suffisante et c'est pourquoi ce travail se focalise sur la détermination locale des propriétés de ces matériaux complexes. Pour cela nous nous appuyons sur des méthodes optiques pour obtenir des informations sur la contrainte et la vitesse de cisaillement. Nous avons choisi d'opter pour la PIV (Particle Image Velocimetry) pour l'obtention du gradient de vitesse et la photoélasticimétrie pour la mesure de contrainte. L'emploi de ces deux techniques de mesure oblige que les fluides étudiés soient transparents et biréfringents. Nous étudions alors une solution de Milling Yellow (fluide au comportement rhéologique simple) pour valider nos techniques de mesure et des suspensions de Laponite qui sont des fluides à seuil et thixotropes. La première étape de ce travail consiste à avoir une idée générale du comportement rhéologique des fluides d'où leur caractérisation à l'aide d'un rhéomètre. Ensuite, dans une géométrie où la répartition de contrainte est connue (géométrie à cylindres coaxiaux), nous déterminons les lois rhéo-optiques nous permettant de relier la contrainte dans le matériau à sa réponse optique. Enfin, dans une géométrie plan-plan, nous couplons les deux techniques de mesure optiques (PIV et photoélasticimétrie) afin de reconstruire un rhéogramme local des différents fluides étudiés pouvant être comparé à celui issu de mesures classiques de rhéométrie. / The use of fluids with a complex rheological behavior (yield stress, thixotropy) is becoming more common in our daily lives. However, a global description of this behavior is not satisfactory even if it is quickly and easily accessible. The aim of this work is to advance in the understanding of complex behaviors at a local scale. Optical methods are the best way to do that. In our case, we need to get information about the shear stress and the shear rate. So we need a measurement technique for each of these variables. A PIV (Particle Image Velocimetry) technique is used to obtain the shear rate and the shear stress is determined by photoelasticimetry. The use of these two techniques requires that the studied fluids are transparent and birefringent. Then, our measurement techniques are validated using a Milling Yellow solution (a simple rheological fluid) before studying Laponite suspensions which are thixotropic yield stress fluids. Firstly, a rheometer is used to have a general idea of the rheological behavior of our fluids. Secondly, in a geometry where the shear stress distribution is known (a coaxial cylinders geometry), rheo-optical laws connecting the shear stress within the material to its optical response are determined. Finally, in a plate-plate geometry, the two optical measurement techniques (PIV and photoelasticimetry) are coupled to reconstruct a local rheogram for the studied fluids that can be compared to the one obtained from conventional Rheometric measurements.

[pt] Projetistas de sistemas de comunicações ópticas necessitam estimar o coeficiente de PMD dos enlaces ópticos visando determinar a correspondente penalidade de potência do enlace. Os valores de PMD nas fibras variam aleatoriamente, conseqüentemente a determinação da PMD dos enlaces deverá ser calculada através de metodologias estatísticas. Esta dissertação contém um estudo sistemático da estimação do coeficiente de PMD das seções amplificadas de 02 backbones. Três 03 técnicas estatísticas: Técnica de Monte Carlo, Modelo Gama e Teorema do Limite Central Generalizado, recomendadas pelo Método 1 da norma TIA/EIA TSB 107 foram usadas e os resultados comparados com os valores medidos em campo destas seções. Os resultados das avaliações realizadas mostraram que a metodologia apresentada por esta recomendação induz a uma superestimação do coeficiente de PMD do enlace devido a limitação dos equipamentos de medição e conseqüentemente a uma superestimação da penalidade prevista. Esta superestimação deve-se ao fato da PMD das fibras estar abaixo do limite de sensibilidade dos equipamentos de medida comercialmente disponíveis. A estimação do coeficiente de PMD de enlaces requer então a utilização de equipamentos de medida mais precisos (ainda não disponíveis) ou corrigir esta metodologia de cálculo para a estimação da PMD dos enlaces ópticos com a utilização de fibras/cabos de maior comprimento. / [en] Optical system designers need to estimate the expected PMD coefficient of the links in order to calculate the corresponding power penalty. Fiber PMD values varies randomly, therefore the link PMD estimation shall be calculated by statistical methodologies. This thesis presents a systematic study of PMD estimation of the amplified spans of two backbones. Three statistical techniques: Monte Carlo Technique, Gamma Model and Generalized Central Limit Theorem, recommended by Method 1 from TIA/EIA TSB 107 Guideline were used and the results compared with the field measurement values of these spans. Evaluation results showed that this methodology cause an overestimation of the link PMD coefficient due to a limitation of the measurement eqquipments and consequently an overestimation of the power penalty. This overestimation is due to the fact that fiber PMD is bellow of the resolution limit of the commercially available measurement equipments. Link PMD coefficient estimation needs the use of more precise measurement equipment (Not available yet) or to correct this calculus methodology for the optical link PMD estimation with the use of longer fibers/cables.

This thesis focuses on one important component of the energy system - the window. Windows are installed in buildings mainly to create visual contact with the surroundings and to let in daylight, and should also be heat and sound insulating. This thesis covers four important aspects of windows: antireflection and switchable coatings, energy simulations and optical measurements. Energy simulations have been used to compare different windows and also to estimate the performance of smart or switchable windows, whose transmittance can be regulated. The results from this thesis show the potential of the emerging technology of smart windows, not only from a daylight and an energy perspective, but also for comfort and well-being. The importance of a well functioning control system for such windows, is pointed out. To fulfill all requirements of modern windows, they often have two or more panes. Each glass surface leads to reflection of light and therefore less daylight is transmitted. It is therefore of interest to find ways to increase the transmittance. In this thesis antireflection coatings, similar to those found on eye-glasses and LCD screens, have been investigated. For large area applications such as windows, it is necessary to use techniques which can easily be adapted to large scale manufacturing at low cost. Such a technique is dip-coating in a sol-gel of porous silica. Antireflection coatings have been deposited on glass and plastic materials to study both visual and energy performance and it has been shown that antireflection coatings increase the transmittance of windows without negatively affecting the thermal insulation and the energy efficiency. Optical measurements are important for quantifying product properties for comparisons and evaluations. It is important that new measurement routines are simple and applicable to standard commercial instruments. Different systematic error sources for optical measurements of patterned light diffusing samples using spectrophotometers with integrating spheres have been investigated and some suggestions are made for how to avoid such errors.

Les microalgues autotrophes sont une source prometteuse de biomasse pour des applications aussi variées que l'extraction de molécules, l'alimentation animale et humaine, la production énergétique ou la décontamination environnementale. La production de masse est donc en forte augmentation dans le monde. Cependant, les techniques actuelles pour caractériser l'état physiologique des cellules algales au cours de la croissance sont coûteuses en main d'œuvre et en temps, souvent basées sur du matériel de mesure générique répondant mal au cahier des charges. Elles sont inadaptées à la mesure en ligne.De nouveaux outils doivent donc être développés pour optimiser le pilotage des procédés de culture, en effectuant des mesures rapides de l'état physico-chimique des cellules. La spectroscopie visible (VIS) et proche infrarouge (NIR) se présente comme une solution pratique. De plus des travaux antérieurs ont démontrés que les propriétés spectrales d'absorption et de diffusion des cellules d'algues dans le domaine VIS-NIR sont très corrélées à leur caractéristiques chimiques (pigments) et physiques (tailles, densité des cellules). Les densités de cellules considérées en cultures denses sont très élevées (10^6-10^9 cellules/mL), rendant inévitables les phénomènes de multidiffusion. Cependant ces derniers ont été identifiés comme gênants pour l'extraction de données à partir des spectres mesurés, car ils rendent l'hypothèse de validité de la loi de Beer Lambert fausse. Dans cette thèse nous nous intéressons à l'extraction de données sur la physiologie des cellules algales à partir de mesures spectrales effectuées sur des échantillons denses, non-dilués, directement issus du milieu de culture. Notre approche se décline en plusieurs axes, correspondants aux différentes échelles de description du problème. D'abord, l'échelle de l'échantillon algal global est considérée. Nous en définissons les propriétés spectrales apparentes, et analysons le problème pratique de leur mesure. Nous avons utilisé un montage à double sphères d'intégration et développé un protocole de mesure complet, que nous décrivons. Ensuite, les propriétés spectrales linéaires intrinsèques au milieu algal sont abordées, et nous cherchons à les reliées aux propriétés apparentes de l'échantillon. Pour cela nous utilisons le formalisme de l'équation de transfert radiatif (ETR) donnant une modélisation rigoureuse des phénomènes de multidiffusion à l'œuvre dans les milieux turbides. En pratique, résoudre l'ETR ne peut se faire que par une approximation ou la simulation. Dans nos travaux nous examinons la méthode Adding-Doubling et son inverse, utilisées avec succès par d'autres équipes sur des échantillons turbides de tissus biologiques. En troisième lieu, l'échelle de description de la cellule d'algue individuelle est abordée. AlgaSim, un programme de simulation basé sur la théorie de Mie étendue, a été développé au cours de cette thèse pour modéliser les spectres d'absorption et de diffusion d'une cellule algale décrite par ses paramètres physiologiques, tels que la taille et le poids sec, les proportions des différents matériaux cellulaires, la quantité et la composition des pigments. Ainsi, les liens entre propriétés physiques et chimiques de la cellule et ses propriétés spectrales sont étudiés. Enfin, une méthode complète est proposée pour articuler toutes les échelles de description précédemment examinées. Les liens entre propriétés intrinsèques du milieu algal et les propriétés optiques individuelles des cellules sont cherchés. Les paradigmes développés aux différentes échelles sont ensuite mis bout à bout pour relier la description physiologique des cellules d'algue aux propriétés spectrales apparentes mesurées sur un échantillon donné. La méthode est testée sur des échantillons algaux réels. Les premiers résultats sont prometteurs, démontrant le potentiel opérationnel de la spectroscopie VIS-NIR pour le suivi de procédés de culture dense de microalgues. / Autotrophic microalgae are seen as a promising source of biomass for various applications such as chemicals extraction, animal and human food, energy production and environment cleaning. Consequently, the global mass production of microalgae has largely increased over the last decade. However, the current techniques used for the characterization of the algal cells all along the growth process require time-consuming sample preparation, a large amount of costly, standard instrumentation and cannot usually be performed in situ.New tools are needed to optimize the monitoring of the cultivation process by providing a faster measurement of the microalgal cells physical and chemical states. For this purpose, utilizing visible (VIS) and near infrared (NIR) spectroscopy is looked as a promising solution. Moreover, previous studies demonstrated that the spectral absorption and scattering properties of microalgal suspensions in the VIS-NIR domain depend heavily on the chemical characteristics (pigments) and physical characteristics of the cells (size, density of the cells). In a context of cultivation process, cell density in the culture medium is very high (10^6-10^9 cell/mL) which makes the multi-scattering phenomena significant. However, recent studies have showed that the data extraction from spectroscopic measurements performed on turbid samples is highly complicated by the influence of the scattering phenomena on the spectra, making the classical processing methods based on the assumption of Beer law irrelevant. This thesis addresses the issue of retrieving information about the physiological state of microalgal cells from spectral measurements performed on non-diluted, dense bulk culture media. For this purpose, our approach includes successive guidelines, corresponding to different scales of description. First, the scale of the bulk algal aliquot is considered: the apparent spectral properties are defined, and the practical issue of measuring them with an adapted setup is investigated. In particular, a double-integrating sphere setup, as well as a complete measurement protocol are implemented. Second, the intrinsic linear spectral properties of the dense algal medium are defined, and the links between the intrinsic and apparent spectral properties are investigated. The formalism of the radiative transport equation (RTE) is used for this purpose, as it rigorously models the physical phenomena due to multiple scattering. Solving the RTE must be implemented in practice with an approximation or simulation method. In this work, we investigate in particular the Adding-Doubling method and its inverse, which have been proved to be adapted to the case of highly turbid organic tissues and materials. Third, the scale of an individual algal cell is considered. In this thesis we have developed a simulation program called AlgaSim based of the extended Mie theory, which makes it possible to simulate the spectral absorption and scattering properties of an algal cell described by its physiological characteristics, such as its mean size and dry weight, proportions of different cell materials and pigment quantity and composition. The links between the chemical and physical properties of an algal cell and its spectral properties are thus investigated.Finally, a complete method is proposed to link all the scales of description. In particular, the links between the intrinsic spectral properties of an algal medium and the individual properties of the constitutive cells are considered. By organizing all the paradigms previously investigated, it is possible to implement a complete model linking the physiological description of the constitutive algal cells to the apparent spectral properties measured on a dense culture sample. The method and its inverse are tested on real algal samples. They show promising primary results, proving the operational potential of VIS-NIR spectroscopy for the monitoring of dense algal cultures.

Nanotechnology offers great promise for the development of nanodevices. Hence it becomes important to study the mechanical behavior of nanostructures for their use in such systems. MEMS (Micro ElectroMechanical Systems) provide an effective and precise method for testing nanostructures. Consequently this study focuses on the development of a MEMS thermal nanotensile tester to investigate the mechanical behavior of one-dimensional nanostructures. Extensive characterization of these MEMS devices (structural, electrical and thermal behavior) was performed using experimental as well as finite element methods. Tensile testing of nanostructures requires manipulation of individual nanostructures on the MEMS device. The study involves the development of an efficient methodology for the manipulation of nanowires and nanobeams for nanoscale testing. Furthermore, two different sensing schemes for the developed devices, namely capacitive and resistive, have been extensively investigated and the advantages and various issues related to both have been discussed. Nanocrystalline (nc) Ni nanobeams (typical dimensions of 500 nm x 200 nm x 20 µm) have been tested to failure using the MEMS devices. Improvements in the design for the MEMS nanotensile tester have been suggested to significantly enhance the device performance and to resolve the various issues involved with nano scale tests. Differential capacitive sensing for stress-strain measurements has been suggested to improve the accuracy of strain measurements.