Recently, with the escalating demands for optical communications, the need for bandwidth in optical communication network has increased. The technology fiber fabrication opens the possibility for fiber bandwidth form 1.3 to 1.6£gm. Cr4+:YAG double-clad crystal fiber (DCF) grown by the co-drawing laser-heated pedestal growth method has a strong spontaneous emission spectrum from 1.3 to 1.6£gm. Such fiber is therefore, eminently suitable for optical coherence tomography (OCT), broadband optical amplifier, amplifier spontaneous emission (ASE) light source, and tunable solid-state laser applications. In this thesis, multilayer dielectric thin films were directly deposited by E-gun coating onto the end faces of the Cr4+:YAG DCF. To improve thin-film quality, we can increase transmittance of laser output, and to design for the high power laser. For broadband optical amplifier in dual-pump and double-pass scheme, a 2.8-dB gross gain, a 1.6-dB insertion loss, and a 1.2-dB net gain at 1.4-£gm signal wavelength have been successfully developed with HR coating onto one of the Cr4+:YAG DCF end faces.

A polarization sensitive optical coherence tomography (PS-OCT) instrument is presented for the study of glaucoma. Glaucoma is the second leading cause of blindness worldwide and causes irreversible damage to the retina. This PS-OCT system was built to perform retinal imaging with a swept source laser providing a 28 kHz A-scan repetition rate. Thickness, phase retardation, birefringence and reflectance index measurements were taken from the primate eyes on a weekly or semi-weekly basis through the course of a 30 week study. Statistical analysis of these measurements indicates that the reflectance index is the earliest measured indicator of glaucomatous changes and a potential marker for early glaucoma diagnosis. / text

Purpose: The RTVue-100 is a new instrument for measuring retinal blood flow (RBF), but image quality needs to be optimized in order for valid blood flow results. The primary aim of this thesis was to assess the presence of learning effects with novice and experienced operators. Methods: Twelve upper-year optometric students from the University of Waterloo, School of Optometry and Vision Science, were trained in operating RTVue-100. Nine healthy participants, with a mean age (?? SD) of 25.7 ?? 3.8 years, underwent OCT imaging. Using the Doppler OCT of Retinal Circulation (DOCTORC) software, images were assessed by computer for various image quality parameters. Results: Paired samples t-tests showed significant statistical differences between the novice and experienced operators for the following image acquisition parameters: total acquisition time (TAT), number of attempts to complete total scan protocol, and number of valid images. Mean values for TAT and the number of attempts decreased, whereas the mean number of valid images increased from novice to experienced level. Conclusions: The results confirm that there are learning effects observed within the image acquisition process using the RTVue-100 SD-OCT.

Because of the ubiquitous use of contact lenses, there is considerable interest in better understanding the anatomy of the cornea, the part of the eye in contact with an exterior lens. The recent technology developments in high resolution Optical Coherence Tomography (OCT) devices allows for the in-vivo observation of the structure of the human cornea in 3D and at cellular level resolution. Prolonged wear of contact lenses, inflammations, scarring and diseases can change the structure and physiology of the human cornea. OCT is capable of in-vivo, non-contact, 3D imaging of the human cornea. In this research, novel image processing algorithms were developed to process OCT images of the human cornea, in order to determine the corneal optical scattering and transmission. The algorithms were applied to OCT data sets acquired from multiple subjects before, during and after prolonged (3 hours) wear of soft contact lenses and eye patches, in order to investigate the changes in the corneal scattering associated with hypoxia. Results from this study demonstrate the ability of OCT to measure the optical scattering of corneal tissue and to monitor its changes resulting from external stress (hypoxia).

Biofouling represents the main problem in membrane filtration systems. Biofouling arises when the biomass growth negatively impacts the membrane performance parameters (i.e. flux decrease and feed channel pressure drop). Most of the available techniques for characterization of biofouling involve membrane autopsies, providing information ex-situ destructively at the end of the process. OCT, is non-invasive imaging technique, able to acquire scans in-situ and non-destructively. The objective of this study was to evaluate the suitability of OCT as in-situ and non-destructive tool to gain a better understanding of biofouling behavior in membrane filtration systems. The OCT was employed to study the fouling behavior in two different membrane configurations: (i) submerged flat sheet membrane and (ii) spacer filled channel. Through the on-line acquisition of OCT scans and the study of the biomass morphology, it was possible to relate the impact of the fouling on the membrane performance. The on-line monitoring of biofilm formation on a flat sheet membrane was conducted in a gravity-driven submerged membrane bioreactor (SMBR) for 43 d. Four different phases were observed linking the variations in permeate flux with changes in biofilm morphology. Furthermore, the biofilm morphology was used in computational fluid dynamics (CFD) simulation to better understand the role of biofilm structure on the filtration mechanisms. The time-resolved OCT analysis was employed to study the biofouling development at the early stage. Membrane coverage and average biofouling layer thickness were found to be linearly correlated with the permeate flux pattern. An integrated characterization methodology was employed to characterize the fouling on a flat sheet membrane, involving the use of OCT as first step followed by membrane autopsies, revealing the presence of a homogeneous layer on the surface. In a spacer filled channel a 3D OCT time series analysis of biomass development under representative conditions for a spiral-wound membrane element was performed. Biomass accumulation was stronger on the feed spacer during the early stage, impacting the feed channel pressure drop more than the permeate flux. OCT biofilm thickness map was presented as new tool to evaluate the biofouling development in membrane filtration systems through the use of a false color scale.

Glaucoma is an ophthalmic pathology that is the second leading cause of blindness. The laboratory design of a Polarization Sensitive Spectral Domain Optical Coherence Tomographic System aims to detect early glaucoma symptoms and prevent vision loss that occurs due to late or no glaucoma diagnosis. In order to perform human clinical trials at partner hospitals across the country, a miniaturized and portable version of the laboratory system was developed. The system facilitates easy transportation and clinical testing of the otherwise voluminous laboratory system across different eye centers. Significant consideration was given for performance optimization, cost reduction, design improvements and providing a friendly user-patient interface. / text

Cette thèse porte sur la segmentation d'images OCT cutanées. Cette modalité d'imagerie permet de visualiser les structures superficielles avec une profondeur de l'ordre du millimètre. En dermatologie, elle permet d'explorer l'épiderme et sa jonction avec le derme. Cependant, les images OCT sont sévèrement affectées par le bruit speckle. Ce phénomène conjugué à la complexité inhérente aux structures de la peau rend l'interprétation des images difficile même pour des experts. L'approche classique consiste à filtrer le speckle avant de faire des traitements de segmentation. A l'inverse, dans cette thèse nous exploitons exclusivement le bruit comme information pour segmenter. Notre approche repose sur la modélisation statistique du speckle. La segmentation se fait par classification des paramètres de ce modèle probabiliste. Ainsi, - On montre que le speckle ne suit pas une loi Rayleigh, comme cela est établi analytiquement. - On ajuste plusieurs lois de probabilité à l'amplitude OCT; et on montre que celle-ci est distribuée selon la loi Gamma généralisée. - On établit que les paramètres de cette loi discriminent statistiquement les couches de la peau. - On conçoit une méthode de segmentation par classification des paramètres locaux du speckle. Les nombreuses expérimentations faites sur plusieurs corpus d'images in-vivo confirment la validité de notre approche. / This thesis deals with the segmentation of skin OCT images. This modality provides the means to visualize superficial structures down to a millimeter depth. In dermatology, it is used to examine the epidermis and its junction with the dermis. However, OCT images are severely affected by the speckle noise. This random phenomenon added to the complexity of human skin structures makes the visual interpretation of images very difficult. Classical image processing techniques filter this noise prior to any segmentation step. In this thesis, we rely exclusively on the properties of the speckle to perform segmentation. Our approach is based on the statistical modeling of the speckle. Images are segmented by classifying parameters of the statistical model. Therefore, - We show that speckle does not follow the Rayleigh distribution, as developed analytically in the literature. - We fit various probability laws to model OCT signal amplitude ; we show that Generalized Gamma has the best goodness of fit. - We establish that statistical parameters of this distribution discriminate skin layers with good variability. - We develop a segmentation method based on the classification of local statistical parameters. The various experimental results with a number of in-vivo images reported in the thesis confirm the validity of our approach

Objetivos: Avaliar as alterações retinianas em modelo experimental de hipóxia em coelhos aclimatizados em ambiente hipóxico-normobárico e investigar os efeitos do tratamento com bevacizumabe intravítreo (IV). Métodos: Vinte e dois coelhos New Zealand, com pesos entre 2,4 a 3,8 kg, foram divididos em quatro grupos. Os grupos S12% (n=5) e B12% (n=5) foram aclimatizados durante três dias consecutivos em concentrações de oxigênio (O2) a 12%. Os grupos S8% (n=5) e B8% (n=7) foram aclimatizados durante três dias consecutivos, com reduções graduais da concentração de O2, até atingir o nadir de 8%. Os olhos direitos (OD) foram mantidos como controle e os olhos esquerdos (OE) dos animais dos grupos S12% e S8% receberam injeção IV de 0,05 ml de solução salina balanceada (SSB), enquanto os OE dos grupos B12% e B8% receberam 0,05 ml (1,25 mg) de bevacizumabe IV. Foram realizados exames de tomografia de coerência óptica (OCT) para avaliação da espessura dos segmentos retinianos (SR) e coroidianos (SC), angiografia por fluoresceína sódica (AF) para observação da presença ou ausência de vasodilatação e tortuosidade da vasculatura retiniana e quantificação do Vascular Endothelial Growth Factor (VEGF) do humor aquoso e soro no primeiro dia (D0), antes do tratamento, no terceiro dia de hipóxia (D7) e no décimo primeiro dia (D11), utilizando-se a técnica do Luminex®. Após, os animais foram sacrificados e amostras do tecido retiniano foram avaliadas por histologia e imuno-histoquímica (IHQ). Resultados: Comparando-se os cortes horizontais dos OD (controle) nos períodos D0 e D7, notou-se redução de 8% (p<0,0001) e 10% (p<0,0001) da espessura do SR nas concentrações de O2 a 12% e 8%, respectivamente. Comparando-se os cortes verticais nos mesmos períodos, verificou-se redução da espessura do SR de 7%, tanto nas concentrações a 12% (p<0,0001) como a 8% (p<0,0001). Nos olhos tratados com bevacizumabe, a redução das médias das espessuras do SR para os cortes horizontais entre os períodos D0 e D7 foi de 6% (<0,0001) e 9% (<0,0001), para as concentrações de O2 a 12 e 8%, respectivamente. Enquanto que nos olhos tratados com SSB no mesmo período, observou-se redução de 8% (<0,0001) e 6% (<0,0001) para as concentrações de O2 a 12 e 8%, respectivamente, nos cortes horizontais. Nos cortes verticais, para os olhos tratados com bevacizumabe, houve redução de 5% (p=0,0005) e 8% (<0,0001) para concentrações de O2 a 12% e 8%, respectivamente; e para os olhos tratados com SSB foi encontrada redução de 7% (<0,0001) e 8% (<0,0001) nas concentrações de O2 a 12% e 8%, respectivamente. As espessuras dos SC não apresentaram alterações. O grupo B8 apresentou diferença estatisticamente significativa na análise da proporção dos olhos que não evidenciaram vasodilatação e tortuosidade dos vasos retinianos durante o período hipoxêmico, e não foram observados neovasos retinianos. A histologia e IHQ dos olhos tratados com SSB e bevacizumabe não demonstraram alterações quando comparados com os controles. Conclusões: A aclimatização de coelhos em ambiente hipóxico-normobárico resultou na redução da espessura do SR no terceiro dia de hipóxia. Notou-se, ainda, aumento da tortuosidade e vasodilatação. O bevacizumabe IV não inibiu a redução da espessura retiniana, mas sim a vasodilatação e tortuosidade vascular. / Objectives: Evaluate retinal changes in experimental model of hypoxia in rabbits acclimatized in normobaric-hypoxic environment and to investigate the effects of the treatment by intravitreal (IV) bevacizumab drug. Methods: Twenty two New Zealand rabbits weighing between 2,4 to 3,8 kg were divided into 4 groups. The groups S12 (n=5) and B12 (n=5) were acclimatized for 3 consecutive days in oxygen concentration (O2) to 12%. The groups S8 (n=5) and B8 (n=7) were acclimatized for 3 consecutive days with gradual reductions in O2 concentration until the nadir of 8%. The right eye (RE) were kept as controls and the left eye (LE) of the animals belonging to S12 and S8 groups received IV injection of 0,05 ml of balanced salt solution (BSS), while the LE belonging to groups B12 and B8 received 0,05 ml (1,25 mg) of bevacizumab IV. Optical coherence tomography (OCT) to evaluate the thickness of the retinal segments (RS) and choroidalsegments (CS), sodium fluorescein angiography (FA) for evaluation of the presence or absence of vasodilation and tortuosity of the retinal vasculature and quantification of VEGF in the aqueous fluid and peripheral blood sample were conducted at the first day (D0) before treatment, on the third day of hypoxia (D7) and day 11 (D11) using the Luminex® technique. After the animals were sacrificed, the retinal tissue samples were evaluated by histology and immunohistochemistry (IHC). Results: Comparing the horizontal sections of the RE (control) in D0 and D7 periods, a reduction of 8% (p<0,0001) and 10% (p<0,0001) the thickness of the RS in O2 concentration at 12% and 8%, respectively. Comparing the vertical cuts in the same period, there was reduced RS thickness of 7% in both concentrations to 12% (p<0,0001) and 8% (p<0,0001). In the eyes treated with bevacizumab, to reduce the average thickness of the retinal segment for horizontal cuts between D0 and D7 periods were 6% (<0,0001) and 9% (<0,0001) for O2 concentrations to 12 and 8%, respectively. While in the eyes treated with BSS in the same period, there was an 8% reduction (<0,0001) and 6% (<0,0001) for the O2 concentration at the 12% and 8%, respectively, in the horizontal cuts. In the vertical sections is observed for the eyes treated with bevacizumab, 5% reduction (p=0.0005) and 8% (<0,0001) O2 concentration at 12% and 8%, respectively; and BSS treated eyes was reduced by 7% (<0,0001) and 8% (<0,0001) in the O2 concentrations of 12% and 8%, respectively. The thickness of the CS did not show changes. The B8 group showed statistical difference in the analysis of the eyes that did not have vasodilation and tortuosity of the retinal vessels during the hypoxic period. Retinal neovascularization were not observed. Histology and IHC of the eyes treated with BSS and bevacizumab showed no changes compared to the control eyes. Conclusions: The acclimatization of the rabbits in normobaric-hypoxic environment has the effect of reducing the thickness RS on the third day of hypoxia. It is observed also increased tortuosity and vasodilation. The intravitreal bevacizumab does not inhibit retinal thickness decrease, but inhibits vasodilation and vascular tortuosity.

A Tomografia por Coerência Óptica (OCT) baseia-se na propriedade de retroespalhamento dos meios para construir imagens tomográficas do interior das amostras. De maneira similar, a técnica LIDAR (Light Detection and Range) faz uso desta propriedade para determinar as características da atmosfera, em especial o coeficiente de extinção do sinal. Explorar esta similaridade permitiu aplicar métodos de inversão utilizados na técnica LIDAR às imagens OCT, permitindo construir imagens de coeficiente de extinção, resultado inédito até o momento. Este trabalho teve o objetivo de estudar, propor, desenvolver e implementar algoritmos de métodos de inversão do sinal OCT para determinação do coeficiente de extinção em função da profundidade. Foram utilizados três métodos de inversão, da inclinação, do ponto de contorno e da profundidade óptica, com implementação em ambiente LABView&reg; . Estudo dos erros associados aos métodos de inversão foi realizado e, amostras reais (homogêneas e estratificadas) foram utilizadas para análises em uma e duas dimensões. As imagens de coeficiente de extinção obtidas pelo método da profundidade óptica claramente foram capazes de diferenciar o ar da amostra. As imagens foram estudadas empregando PCA e análise de clusters que avaliou a robustez da técnica em determinar o valor do coeficiente de extinção da amostra. Além disso, o método da profundidade óptica proposto foi empregado para estudar a hipótese de que existe correlação entre o coeficiente de extinção do sinal e a desmineralização de esmalte dental durante o processo cariogênico. Com a aplicação desta metodologia foi possível observar a variação do coeficiente de extinção em função da profundidade e sua correlação com a variação da microdureza, além de mostrar que em camadas mais profundas o valor do coeficiente de extinção valor tende ao de um dente sadio, comportando-se da mesma maneira que a microdureza do dente. / Optical Coherence Tomography (OCT) is based on the media backscatering properties in order to obtain tomographic images. In a similar way, LIDAR (Light Detection and Range) technique uses these properties to determine atmospheric characteristics, specially the signal extinction coeficient. Exploring this similarity allowed the application of signal inversion methods to the OCT images, allowing to construct images based in the extinction coeficient, original result until now. The goal of this work was to study, propose, develop and implement algorithms based on OCT signal inversion methodologies with the aim of determine the extinction coeficient as a function of depth. Three inversion methods were used and implemented in LABView&reg; : slope, boundary point and optical depth. Associated errors were studied and real samples (homogeneous and stratified) were used for two and three dimension analysis. The extinction coeficient images obtained from the optical depth method were capable to diferentiate air from the sample. The images were studied applying PCA and cluster analysis that established the methodology strength in determining the sample´s extinction coefficient value. Moreover, the optical depth methodology was applied to study the hipothesis that there is some correlation between signal extinction coeficient and the enamel teeth demineralization during a cariogenic process. By applying this methodology, it was possible to observe the variation of the extinction coefficient as depth function and its correlation with microhardness variation, showing that in deeper layers its values tends to a healthy tooth values, behaving as the same way that the microhardness.

A membrana amniótica é a camada interna das membranas fetais (placenta), amplamente utilizada em transplantes por ser um tecido que combina propriedades anti-inflamatórias, antimicrobianas e antifibróticas, além da limitada capacidade de provocar reações imunológicas. O uso da membrana fresca tem algumas limitações, como a necessidade de rápida utilização e a impossibilidade de obter total segurança diante de certas infecções. Qualquer tecido biológico utilizado para transplante deve ser estéril. A radioesterilização é uma alternativa para garantir a qualidade e segurança dos tecidos usados em transplantes e outras aplicações clínicas, a fim de minimizar os riscos de contaminação do receptor do tecido, porém a mesma pode causar alterações indesejáveis no tecido. No presente trabalho, foram testadas doses de 10, 15, 25 e 35 kGy, utilizando duas fontes de radiação ionizante: raios gama proveniente de fonte de Cobalto-60 e feixe de elétrons. Na análise qualitativa visual e táctil foi observado que, nas doses mais elevadas (a partir de 25 kGy) para ambas as fontes de radiação, as membranas irradiadas sofreram maior alteração de cor, tornando-se mais amareladas e com diminuição da elasticidade, deixando-as mais rígidas. A colorimetria sólida possibilitou minimizar a subjetividade da análise visual e a microscopia óptica foi essencial para avaliar as alterações histológicas comprovando, respectivamente, que a alteração de cor da membrana e o grau de degradação das camadas subjacentes do tecido tem relação direta com a dose de radiação empregada. Desse modo, as doses de 10-35 kGy podem ser aplicadas nas membranas amnióticas para sua utilização como bandagem biológica, porém, para as doses a partir de 25 kGy deve-se levar em consideração a alteração de coloração e condensação das camadas da membrana se estas forem destinadas para o uso oftálmico ou como substrato transportador para transplante de tecido cultivado in vitro. Com as técnicas de OCT, TG e ensaio de tração não foi possível avaliar as alterações biomecânicas encontradas na análise qualitativa, nas condições experimentais realizadas devido aos desvios-padrão obtidos para as cinco membranas testadas. / The amniotic membrane is the inner layer of the fetal membranes (placenta), widely used in transplantation as it is a tissue that combines properties anti-inflammatory and antifibrotic antimicrobial, and limited ability to induce immune reactions. The use of fresh membrane has some limitations such as the need for rapid deployment and not being completely safe against of certain infections. Any biological tissue used for transplantation should be sterile. The radiosterilization is an alternative to ensure the quality and safety of tissues used in transplants, and other clinical applications to minimize the risk of contamination of the tissue´s receptor, but it can cause undesirable changes in the tissue. In this study, we tested doses of 10, 15, 25 and 35 kGy, using two sources of ionizing radiation: gamma rays from cobalt-60 source and electron beam. In qualitative, visual and tactile analysis it has been observed that higher doses (25 kGy and up, to both sources of radiation) irradiated membranes had a greater color change, becoming yellowed and decreased elasticity, becoming more rigid. The solid colorimetry minimized the subjectivity of visual analysis and optical microscopy was essential to evaluate the histological changes showing, respectively, the color change of the membrane and the degree of degradation of the underlying layers of tissue is directly related to the dose of radiation employed. Thus, doses of 10-35 kGy can be applied in the amniotic membranes for application as a biological bandage, however doses from 25 kGy and up should take into account the changes in color and condensation of the layers of the membrane for ophthalmic use or as a carrier substrate for transplantation of cultured tissue in vitro. With the techniques of OCT, TG and tensile testing was not possible to evaluate the biomechanical findings in the qualitative analysis, the experimental conditions due to the standard-deviations obtained for the five membranes tested.