Dans le cadre d'une thèse financée par la région Bretagne, nous nous sommes attachés à mettre en évidence la possibilité d'utiliser la polarimétrie de Mueller comme outil d'investigations biomédicales. Cette technique, utilisant les propriétés de la polarisation de la lumière, permet une exploration non invasive des tissus biologiques en s'appuyant sur des agents de contraste naturels. La première partie de notre étude a été le développement du polarimètre, montage expérimental complet permettant la mesure de la matrice de Mueller du milieu d'étude. Après avoir choisi les éléments optiques adéquats (polariseurs en verre dichroïque, lames de phase entrainées en rotation par des moteurs pas à pas) ainsi que la source (diode laser à 808 nm) et le détecteur (caméra CCD 795x596 pixels avec objectif de 28 mm), nous nous sommes concentrés à optimiser le système d'acquisition de la matrice de Mueller. En effet, lors de la mesure, des perturbations qui constituent le " bruit expérimental " viennent limiter la précision du système. Nous distinguons deux sources d'incertitude distinctes : les erreurs aléatoires, inhérentes à l'expérience, et les erreurs systématiques, liées à la qualité intrinsèque des composants optiques et à leurs défauts de positionnement. En interférant avec le signal étudié, ces erreurs de mesure justifient l'importance d'un étalonnage rigoureux du polarimètre. Nous avons alors appliqué différentes méthodologies permettant de réduire grandement les effets néfastes de ces erreurs de mesure. D'un côté, une méthode de surdétermination du système (64 mesures d'intensités en réalisant 64 combinaisons angulaires des orientations des lames quart d'onde) permet de minimiser les erreurs aléatoires. Ces 64 combinaisons angulaires ont été judicieusement choisies grâce à la minimisation du nombre de conditionnement associé à la matrice de passage du système. Pour atténuer l'influence des erreurs systématiques, nous avons réalisé un repérage des axes neutres des lames quart d'onde précis au millième de degré près. Puis, nous avons utilisé une méthode de recherche des paramètres réels des lames de phase (retard et ellipticité). Pour pouvoir estimer les incertitudes de mesure liées à une matrice de Mueller expérimentale, nous pouvons mettre sous la forme d'une matrice de Mueller les écarts type statistiques mesurés pour chacune des 64 intensités. Nous pouvons alors évaluer les matrices de Mueller des erreurs aléatoires et systématiques. En réduisant au maximum ces matrices d'erreurs lors d'une mesure de la matrice de Mueller du système à vide, nous pouvons considérer notre polarimètre comme étant correctement étalonné. La dernière étape de ce travail a consisté à implanter un système imageur sur notre polarimètre. Grâce à des systèmes de mise en forme du faisceau (système de diaphragme et d'un couple de lentilles convergentes) et de réduction du bruit de speckle (film diffuseur homogène sur disque tournant), nous pouvons alors utiliser notre polarimètre en imagerie afin de pouvoir caractériser des milieux biologiques. La deuxième partie de notre étude s'est portée sur l'analyse et l'interprétation de la matrice de Mueller. Une fois celle-ci mesurée, il faut introduire des techniques d'extraction de l'information polarimétrique. Pour cela, nous utilisons la technique de décomposition de la matrice de Mueller en éléments simples de polarisation. L'information de polarisation contenue dans la matrice est alors modélisée en termes de dichroïsme (modifications d'amplitude du champ électrique), de biréfringence (modifications de phase du champ électrique) et de dépolarisation (action non déterministe). Pour l'étude de milieux complexes que sont les tissus biologiques, il est impératif d'utiliser une décomposition qui modélise au mieux les propriétés du milieu (configuration expérimentale, nombre et ordre des effets optiques simples) et qui minimise l'influence des erreurs de mesure. Nous avons pour cela introduit une procédure de génération de bruit pseudo expérimental afin de pouvoir inspecter, sur des matrices théoriques et expérimentales, la propagation des erreurs sur les paramètres polarimétriques calculés grâce aux quatre algorithmes existants (classique, inverse, normal et symétrique). Notre étude a alors montré qu'aucune de ces décompositions n'étaient adapté à l'étude de milieux diffusants en rétrodiffusion (configuration expérimentale choisie pour l'étude des tissus biologiques). Nous avons alors opté pour l'utilisation d'une nouvelle décomposition dite " hybride " qui permet à la fois de modéliser parfaitement la géométrie des milieux biologiques et de propager les erreurs expérimentales de manière satisfaisante. Cet algorithme hybride nous a également permis de mettre au point une procédure de détermination de la décomposition adéquate. En effet, si cet algorithme permet de traiter tous les systèmes physiques, il peut également servir à identifier le nombre et l'ordre des effets optiques élémentaires et ainsi minimiser l'influence des incertitudes expérimentales en utilisant des décompositions plus simples (classique et inverse). La troisième et dernière partie de notre étude s'est donc attachée à l'étude polarimétrique de tissus biologiques. Dans un premier temps, nous nous sommes intéressés à l'étude du syndrome cutané d'irradiation aiguë. Les différentes études ont montré que le phénomène d'irradiation engendrait une baisse de la dépolarisation ainsi qu'une perte de son caractère anisotrope, phénomènes constatés lors d'altérations des fibres de collagène. Nous avons également mis en évidence la dépendance de la réponse polarimétrique à la longueur d'étude. En effet, la discrimination entre échantillon sain et échantillon irradié (même faiblement) se fait plus efficacement en utilisant des hautes longueurs d'onde (λ > 800 nm). En revanche, pour discriminer les échantillons irradiés suivant la dose reçue, une investigation plus en surface (λ < 600 nm) semble donner des résultats plus satisfaisants. Enfin, nous avons utilisé l'imagerie polarimétrique pour l'étude de la fibrose hépatique. L'interprétation statistique des images acquises a permis de montrer que la polarimétrie de Mueller semble permettre la discrimination des différents stades de fibrose. Les paramètres de dépolarisation semblent permettre la discrimination entre le foie sain et les premiers stades de fibrose (F1-F2). L'information de dispersion sur les paramètres de retard (retardance et azimut associé) permet la discrimination entre échantillons cirrhosés (F4) et non cirrhosés (F0 à F3).

<p> </p><p> </p><p> </p><p><p>The main</p><p>objective of this thesis is to study the polarization effects of the beetle <em>Cetonia aurata </em>using Mueller-matrix ellipsometry. The outer shell of the beetle consists of complex microstructures which control the polarization of the reflected light. It has metallic appearance which originates from helicoidal structures. When these microstructures are exposed to polarized or unpolarized light, only left-handed circularly polarized light is reflected. Moreover, the exo-skeleton of the beetle absorbs right-handed polarized light. Multichannel Mueller-matrix ellipsometer or dual rotating compensator ellipsometer, called RC2, from J.A.Woollam is used to measure the polarization caused by different parts of beetle’s body. The 16 Mueller matrix elements are measured in the spectral range 400-800 nm at multiple angles of incidencein the range 40⁰-70⁰. An Optical model is developed to help us understand the nature and type of microstructure which only reflects the green colour circularly polarized light. With the help of multiparametric modeling, we were able to find optical properties and structural parameters. The parameters are: the number of layers, the numbers of sub-layers, their thicknesses, and the orientation with respect to optical axes. This optical model describes the nanostructures which provide the reflection properties similar to the nanostructure found in the beetle <em>Cetonia aurata. </em>The model is also useful for analysis of the optical response data of different materials with multilayer structures.</p></p><p> </p>

The main objective of this thesis is to study the polarization effects of the beetle Cetonia aurata using Mueller-matrix ellipsometry. The outer shell of the beetle consists of complex microstructures which control the polarization of the reflected light. It has metallic appearance which originates from helicoidal structures. When these microstructures are exposed to polarized or unpolarized light, only left-handed circularly polarized light is reflected. Moreover, the exo-skeleton of the beetle absorbs right-handed polarized light. Multichannel Mueller-matrix ellipsometer or dual rotating compensator ellipsometer, called RC2, from J.A.Woollam is used to measure the polarization caused by different parts of beetle’s body. The 16 Mueller matrix elements are measured in the spectral range 400-800 nm at multiple angles of incidencein the range 400-700. An Optical model is developed to help us understand the nature and type of microstructure which only reflects the green colour circularly polarized light. With the help of multiparametric modeling, we were able to find optical properties and structural parameters. The parameters are: the number of layers, the numbers of sub-layers, their thicknesses, and the orientation with respect to optical axes. This optical model describes the nanostructures which provide the reflection properties similar to the nanostructure found in the beetle Cetonia aurata. The model is also useful for analysis of the optical response data of different materials with multilayer structures.

The focus of this thesis is the improvement of acquisition and processing of Mueller matrix polarimetry using a confocal scanning laser ophthalmoscope (CSLO) and the application of Mueller matrix polarimetry to image the retina. Stepper motors were incorporated into a CSLO to semi-automate Mueller matrix polarimetry and were used in retinal image acquisition. Success rates of Fourier transform based edge detection filters, designed to improve the registration of retinal images, were compared. The acquired polarimetry images were used to reassess 2 image quality enhancement techniques, Mueller matrix reconstruction (MMR) and Stokes vector reconstruction (SVR), focusing on the role of auto-contrasting or normalization within the techniques and the degree to which auto-contrasting or normalization is responsible for image quality improvement of the resulting images. Mueller matrix polarimetry was also applied to find the retardance image of a malaria infected retinal blood vessel imaged in a confocal scanning laser microscope (CSLM) to visualize hemozoin within the vessel. Image quality enhancement techniques were also applied and image quality improvement was quantified for this blood vessel. The semi-automation of Mueller matrix polarimetry yielded a significant reduction in experimental acquisition time (80%) and a non-significant reduction in registration time (44%). A larger sample size would give higher power and this result might become significant. The reduction in registration time was most likely due to less movement of the eye, particularly in terms of decreased rotation seen between registered images. Fourier transform edge detection methods increased the success rate of registration from 73.9% to 92.3%. Assessment of the 2 MMR images (max entropy and max signal-to-noise ratio (SNR)) showed that comparison to the best CSLO images (not auto-contrasted) yielded significant average image quality improvements of 158% and 4% when quantified with entropy and SNR, respectively. When compared to best auto-contrasted CSLO images, significant image quality improvements were 11% and 5% for entropy and SNR, respectively. Images constructed from auto-contrasted input images were of significantly higher quality than images reconstructed from original images. Of the 2 other images assessed (modified degree of polarization (DOPM) and the first element of the Stokes vector (S0)), DOPM and S0 yielded significant average image quality improvements quantified by entropy except for the DOPM image of the RNFL. SNR was not improved significantly when either SVR image was compared to the best CSLO images. Compared to the best auto-contrasted CSLO images, neither DOPM nor S0 improved average image quality significantly. This result might change with a larger number of participants. When MMR were applied to images of malaria infected retinal slides, image quality was improved by 19.7% and 15.3% in terms of entropy and SNR, respectively, when compared to the best CSLO image. The DOPM image yielded image quality improvements of 8.6% and -24.3% and the S0 image gave improvements of 9.5% and 9.4% in entropy and SNR, respectively. Although percent increase in image quality was reduced when images were compared to initial auto-contrasted CSLO images, the final image quality was improved when auto-contrasting occurred prior to polarimetry calculations for max SNR and max entropy images. Quantitative values of retardance could not be found due to physical constraints in the CSLM that did not allow for characterization of its polarization properties and vibrational noise. Mueller matrix polarimetry used to find the retardance image of a malaria infected retina sample did yield visualization of hemozoin within the vessel but only qualitatively. In conclusion, improvements in the acquisition and registration of CSLO images were successful in leading to considerably shorter experimentation and processing times. In terms of polarimetric image quality improvement techniques, when compared to the best CSLO image. A large proportion of the improvement was in fact due to partially or completely stretching the pixel values across the dynamic range of the images within the algorithm of each technique. However, in general the image quality was still improved by the Mueller matrix reconstruction techniques using both entropy and SNR to generate the CSLO retinal images and the CSLM imaged malaria infected sample. In the malaria sample, retinal blood vessel visualization was also qualitatively improved. The images yielded from Mueller matrix polarimetry applied to a malaria infected retinal sample localized hemozoin within the blood vessel, but a quantitative image of the phase retardance could not be achieved.

The polarization behaviour for six species of Scarab beetles from the Chrysina genus is investigated with Mueller Matrix Spectroscopic Ellipsometer (MMSE). The m41 element of the matrix, which is related to the circular polarization behaviour, is analysed. The ellipticity, degree of polarization and azimuth angle are also presented to get a better understanding of the polarization effect. The measurements were done with a dual rotating compensator ellipsometer. The measured wavelength region was from 240 to 1000 nm and the angle of incidence from 25° to 75° in most of the cases. In general very high ellipticities (near circular) are reported. All specimens studied reflect both right- and left-handed polarized light. Depending on the species, two general types of polarization behaviour were observed. Chrysina macropus and Chrysina peruviana showed m41 values close to 0. Green stripes on Chrysina gloriosa showed similar polarization behaviour whereas gold stripes on the same beetle had much more pronounced m41 variations. Large m41 variations were also observed for Chrysina argenteola, Chrysina chrysargyrea and Chrysina resplendens. Four specimens of Chrysina resplendens show different m41 patterns suggesting differences in their structures.

Light reflected from the scarab beetles Cetonia aurata (C. aurata) and Chrysina gloriosa (C. gloriosa) has left-handed polarization. In this work the polarizing properties and structural characteristics of the cuticles of these two beetles are investigated with two different techniques: scanning electron microscopy (SEM) and Mueller-matrix spectroscopic ellipsometry (MMSE). SEM is used to get cross section images of the epicutucle and the endocuticle. Thicknesses around 18 μm were measured for both layers for C. aurata and between 12 and 16 μm for C. gloriosa. A layered structure is observed in both beetles. In addition, a cusp-like structure is also observed in C. gloriosa. MMSE showed left-handed near-circular polarization of light reflected on both beetles. For C. aurata this is observed in a narrow wavelength range (500-600 nm) and for C. gloriosa in a wider wavelength range (400-700 nm) when measured on golden areas of the cuticle. C. gloriosa also has green areas where the reflected light was linearly polarized. The results are used in regression modelling. A good model approximation was found for C. aurata for angles up to 60 whereas a good starting point for future work was reached for C. gloriosa.

The 711-acre Mueller development is located just three miles northeast of downtown on the former site of the Robert Mueller Municipal Airport. Planned as one of Austin’s major transit-oriented New Urbanist developments, Mueller contains a pattern of pedestrian and bike friendly streets to encourage a range of transportation options for residents and visitors. Mueller is 30% complete and provides housing and jobs to over 3000 residents and 3000 employees. This MDS seeks to understand how current residents, employees, and visitors use the bike lanes, sidewalks, and roads in the Mueller community. To evaluate the transportation infrastructure, the author designed and coded a custom Google Maps survey that asked residents to draw common routes, points of interest, and points of concern related to their transportation choices. The results of this study then influenced a future urban design of the undeveloped portion of Mueller. / text

The focus of this thesis is the improvement of acquisition and processing of Mueller matrix polarimetry using a confocal scanning laser ophthalmoscope (CSLO) and the application of Mueller matrix polarimetry to image the retina. Stepper motors were incorporated into a CSLO to semi-automate Mueller matrix polarimetry and were used in retinal image acquisition. Success rates of Fourier transform based edge detection filters, designed to improve the registration of retinal images, were compared. The acquired polarimetry images were used to reassess 2 image quality enhancement techniques, Mueller matrix reconstruction (MMR) and Stokes vector reconstruction (SVR), focusing on the role of auto-contrasting or normalization within the techniques and the degree to which auto-contrasting or normalization is responsible for image quality improvement of the resulting images. Mueller matrix polarimetry was also applied to find the retardance image of a malaria infected retinal blood vessel imaged in a confocal scanning laser microscope (CSLM) to visualize hemozoin within the vessel. Image quality enhancement techniques were also applied and image quality improvement was quantified for this blood vessel. The semi-automation of Mueller matrix polarimetry yielded a significant reduction in experimental acquisition time (80%) and a non-significant reduction in registration time (44%). A larger sample size would give higher power and this result might become significant. The reduction in registration time was most likely due to less movement of the eye, particularly in terms of decreased rotation seen between registered images. Fourier transform edge detection methods increased the success rate of registration from 73.9% to 92.3%. Assessment of the 2 MMR images (max entropy and max signal-to-noise ratio (SNR)) showed that comparison to the best CSLO images (not auto-contrasted) yielded significant average image quality improvements of 158% and 4% when quantified with entropy and SNR, respectively. When compared to best auto-contrasted CSLO images, significant image quality improvements were 11% and 5% for entropy and SNR, respectively. Images constructed from auto-contrasted input images were of significantly higher quality than images reconstructed from original images. Of the 2 other images assessed (modified degree of polarization (DOPM) and the first element of the Stokes vector (S0)), DOPM and S0 yielded significant average image quality improvements quantified by entropy except for the DOPM image of the RNFL. SNR was not improved significantly when either SVR image was compared to the best CSLO images. Compared to the best auto-contrasted CSLO images, neither DOPM nor S0 improved average image quality significantly. This result might change with a larger number of participants. When MMR were applied to images of malaria infected retinal slides, image quality was improved by 19.7% and 15.3% in terms of entropy and SNR, respectively, when compared to the best CSLO image. The DOPM image yielded image quality improvements of 8.6% and -24.3% and the S0 image gave improvements of 9.5% and 9.4% in entropy and SNR, respectively. Although percent increase in image quality was reduced when images were compared to initial auto-contrasted CSLO images, the final image quality was improved when auto-contrasting occurred prior to polarimetry calculations for max SNR and max entropy images. Quantitative values of retardance could not be found due to physical constraints in the CSLM that did not allow for characterization of its polarization properties and vibrational noise. Mueller matrix polarimetry used to find the retardance image of a malaria infected retina sample did yield visualization of hemozoin within the vessel but only qualitatively. In conclusion, improvements in the acquisition and registration of CSLO images were successful in leading to considerably shorter experimentation and processing times. In terms of polarimetric image quality improvement techniques, when compared to the best CSLO image. A large proportion of the improvement was in fact due to partially or completely stretching the pixel values across the dynamic range of the images within the algorithm of each technique. However, in general the image quality was still improved by the Mueller matrix reconstruction techniques using both entropy and SNR to generate the CSLO retinal images and the CSLM imaged malaria infected sample. In the malaria sample, retinal blood vessel visualization was also qualitatively improved. The images yielded from Mueller matrix polarimetry applied to a malaria infected retinal sample localized hemozoin within the blood vessel, but a quantitative image of the phase retardance could not be achieved.

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