Little numerical analysis has been done on fluorescence lifetime imaging \emph{in-vivo}. Here, a 3D fluorescence Monte Carlo model is used to evaluate a microvasculature geometry obtained via two-photon microscopy. I found that a bulk-vascularization assumption does not provide an accurate picture of penetration depth of the collected fluorescence signal. Instead the degree of absorption difference between extravascular and intravascular space, as well as the absorption difference between excitation and emission wavelengths must be taken into account to determine the depth distribution. Additionally, I found that using targeted illumination can provide for superior surface vessel sensitivity over wide-field illumination, with small area detection offering an even greater amount of sensitivity to surface vasculature. Depth sensitivity can be enhanced by either increasing the detector area or increasing the illumination area. Finally, it is shown that the excitation wavelength and vessel size can affect intra-vessel sampling distribution, as well as the amount of signal that originates from inside the vessel under targeted illumination conditions. / text

Yes / Finding a path towards a more accurate prediction of light propagation in human skin remains an aspiration of biomedical scientists working on cutaneous applications both for diagnostic and therapeutic reasons. The objective of this study was to investigate variability of the optical properties of human skin compartments reported in literature, to explore the underlying rational of this variability and to propose a dataset of values, to better represent an in vivo case and recommend a solution towards a more accurate prediction of light propagation through cutaneous compartments. To achieve this, we undertook a novel, logical yet simple approach. We first reviewed scientific articles published between 1981 and 2013 that reported on skin optical properties, to reveal the spread in the reported quantitative values. We found variations of up to 100-fold. Then we extracted the most trust-worthy datasets guided by a rule that the spectral properties should reflect the specific biochemical composition of each of the skin layers. This resulted in the narrowing of the spread in the calculated photon densities to 6-fold. We conclude with a recommendation to use the identified most robust datasets when estimating light propagation in human skin using Monte Carlo simulations. Alternatively, otherwise follow our proposed strategy to screen any new datasets to determine their biological relevance. / European Marie-Curie Actions Programme, Grant agreement no. 607886

Materials with resonant features can have a rapidly changing refractive index spectrally or temporally that gives rise to a changing group index. Depending on the wavelength of the input light, this light can see regimes of normal or anomalous dispersion. Within these regions, the group index can become large, depending on the optical effect used, and give rise to slow or fast light effects. This thesis covers two platforms that exhibit the use of slow and fast light. Slow and fast light are used to manipulate and enhance other optical effects in question. As the focus of this thesis, we examine a rotating ruby rod and spaceplates based on multilayer stacks, both considered as slow- and fast-light media. Light propagation through each platform is modelled and simulated to compare to the experiment. The simulation results for both platforms match well with the measured experimental effects and show the feasibility and utility of slow or fast light to manipulate or enhance optical effects. We simulate light propagation in a rotating ruby rod as a rotating, anisotropic medium with thermal nonlinearity using generalized nonlinear Schrodinger equations, modelling the interplay of many optical effects, including nonlinear refraction, birefringence, and a nonlinear group index. The results are fit to experimentally measured results, revealing two key relationships: The photon drag effect can have a nonlinear component that is dependent on the motion of the medium, and the temporal dynamics of the moving birefringent nonlinear medium create distorted figure-eight-like transverse trajectories at the output. We observe light propagation through a rotating ruby rod where the light is subject to drag. Light drag is often negligible due to the linear refractive index but can be enhanced by slow or fast light, i.e., a large group index. We find that the nonlinear refractive index can also play a crucial role in the propagation of light in moving media and results in a beam deflection. An experiment is performed on the crystal that exhibits a very large negative group index and a positive nonlinear refractive index. The negative group index drags the light opposite to the motion of the medium. However, the positive nonlinear refractive index deflects the beam along with the motion of the medium and hinders the observation of the negative drag effect. Therefore, it is deemed necessary to measure not only the transverse shift of the beam but also its output angle to discriminate the light-drag effect from beam deflection. This work could be applied to dynamic control of light trajectories, for example, beam steering and velocimetry. For the following two chapters, we will focus on a different slow-light platform. This platform focuses on optics that we developed and tested that compress the amount of free-space propagation using multilayered stacks of thin films known as spaceplates. We design and characterize four multilayer stack-based spaceplates based on two design philosophies: coupled resonators and gradient descent. Using the transfer-matrix method, we simulate and extract the angular and wavelength dependence of the transmission phase and transmittance to extract and predict compression factors for each device. A brief theoretical investigation is developed to predict resonance positions, spacing, and bandwidth. We measure the transverse walk-off to extract the compression factor of four multilayer stack-based spaceplates as a function of angle and wavelength. One of the devices was found to have a compression factor of $R=176\pm14$, more than ten times larger than previous experimental records. We increased the numerical aperture of one of the devices by ten times, and we still observed a compression factor of $R=30\pm3$, two times larger than the most recent experimental measurements. We also measured focal shifts up to 800 microns, more than 40 times the device size, typically 10-12 microns thick. The multilayer stack-based spaceplates we studied here show great promise for ultrathin flat optical systems that can easily be integrated into a modern-day imaging system.

The IceCube Neutrino Telescope is designed to detect high energy neutrinos with a large array of photomultiplier tubes placed deep within the Antarctic ice. The way that light propagates through the ice needs to be modelled accurately to enable the paths of charged particles to be reconstructed from the distribution of their Cerenkov radiation. Light travelling through even the purest of ice will undergo scattering and absorption processes, however the ice in which IceCube is embedded has optical properties that vary significantly with depth which need to be accurately modelled. Currently, simulation of the muon background using the current ice model is unable to fully replicate experimental data. In this thesis we investigate a potential method of improving on the current generation of ice models. We introduce thin, highly absorbing layers into the current description of the detection medium and investigate the effect on the simulation of muon tracks in IceCube. We find that better agreement between simulation and data can be seen in the occupancy of optical modules, through the introduction of such absorptive layers into the existing ice layers.

The IceCube Neutrino Telescope is designed to detect high energy neutrinos with a large array of photomultiplier tubes placed deep within the Antarctic ice. The way that light propagates through the ice needs to be modelled accurately to enable the paths of charged particles to be reconstructed from the distribution of their Cerenkov radiation. Light travelling through even the purest of ice will undergo scattering and absorption processes, however the ice in which IceCube is embedded has optical properties that vary significantly with depth which need to be accurately modelled. Currently, simulation of the muon background using the current ice model is unable to fully replicate experimental data. In this thesis we investigate a potential method of improving on the current generation of ice models. We introduce thin, highly absorbing layers into the current description of the detection medium and investigate the effect on the simulation of muon tracks in IceCube. We find that better agreement between simulation and data can be seen in the occupancy of optical modules, through the introduction of such absorptive layers into the existing ice layers.

This thesis deals with problem of computation of global illumination in real-time. Two methods are described. Namely Reflective Shadow Maps and Light Propagation Volumes. The first of them deals with the problem by using extended Shadow Mapping algorithm. The second one uses scene embedded into a 3D grid together with Spherical harmonics to compute light propagation in the scene. Furthermore this thesis contains results of measurement of the rendering speed of the Light Propagation Volumes algorithm with various settings on several machines. Quality of the resulting output of the algorithm is also evaluated.

Non-invasive blood analysis devices that can measure characteristics less prominent than the oxygenation of hemoglobin are of interest in the medical community. An important step in creating these devices is to model the interaction of photons with human tissue in increasingly greater physiological detail. We have modeled, using a Monte Carlo technique, the interaction of photons through epidermis, blood and water arranged both in layers and in a homogeneous mixture. We confirm the expected linear relation between photon attenuation and material volumetric percentage in our two-layer models. We discovered that this relationship becomes non-linear in the homogeneously mixed models where volumetric percentage must be replaced with interaction volume percentage. These nonlinearities become significant when the values of the interaction coefficient, µt, differ by an order of magnitude or more and could prove crucial in accurately reading oxygenation or other constituents in the blood and also in modeling radiation delivered to a patient in photodynamic therapy.

L’évaluation visuelle de lésions cutanées est l’analyse la plus couramment réalisée par les dermatologues. Ce diagnostic s’effectue principalement à l’œil nu et se base sur des critères tels que la taille, la forme, la symétrie mais principalement la couleur. Cependant, cette analyse est subjective car dépendante de l’expérience du praticien et des conditions d’utilisation. Nous proposons dans ce manuscrit (1) le développement d’une caméra multispectrale spécialement conçue pour un usage en dermatologie. Cette caméra multispectrale se base sur la technologie de roue porte-filtres composée de filtres interférentiels et d’un algorithme basé sur les réseaux de neurones générant un cube hyperspectral de données cutanées. Cet ensemble combine l’avantage d’un spectrophotomètre (information spectrale), et celui d’une caméra (information spatiale). Son intérêt est également de délivrer une information reproductible et indépendante des conditions d’acquisition. La mise en place d’un protocole d’acquisition de données de peaux saines issues de cinq des six phototypes existants a permis la validation de notre système en comparant les spectres générés par notre système avec des spectres théoriques acquis par un spectrophotomètre professionnel. (2) La réflectance spectrale de données de peau fournit une information précieuse, car directement liée à sa composition en chromophores. La mesure quantitative des propriétés optiques du tissu cutané peut être basée sur la modélisation de la propagation de la lumière dans la peau. Pour cela, nous nous sommes appuyés sur le modèle de Kubelka-Munk, auquel nous avons associé une méthode d’optimisation basée sur les algorithmes évolutionnaires. Cette dernière apporte une réponse à l’inversion de ce modèle. A partir de cette approche, la quantification de divers paramètres de la peau peut être obtenue, tels que la mélanine et l’hémoglobine. (3) La validation de cette méthodologie est effectuée sur des données pathologiques (vitiligo et melasma) et permet de quantifier une différence de composition entre zone saine et zone affectée sur une même image. / Visual evaluation of cutaneous lesions is the analysis the most commonly performedby dermatologists. This diagnostic is mainly done by naked eye and is based on criterionsuch as the size, shape, symmetry but principally on colour of the lesions. However, thisanalysis is subjective because it depends on the practician experience and the acquisitionconditions. We propose in this dissertation (1) the development of a multispectralcamera specifically dedicated for dermatological use. This device is based on a filterwheel composed of interferential filters and a neural network-based algorithm, generatinga hyperspectral cube of cutaneous data. This setting combines advantage of both spectrophotometer(spectral information) and digital camera (spatial information). Its maininterest is also to provide reproducible information which is independent of the acquisitionconditions. The setting-up of an acquisition protocol of healthy skin data from five of thesix exisiting skin phototypes allows the validation of our system by comparing spectragenerated by our system and theoretical spectra acquired by professional spectrophotometer.(2) Skin spectral reflectance provides precious information because it is directly linkedto the skin chromophore composition. Quantitative measure of cutaneous tissue opticalproperties can be based on the modelisation of light propagation in skin. For this purpose,we based our method on Kubelka-Munk model with which we associated an optimizationmethod based on evolutionary algorithm. This method helps for the model inversion.Using this approach, quantification of diverse parameters of skin can be obtained such asmelanin and haemoglobin. (3) The validation of this model is performed on disease skindata (vitiligo and melasma) and allows to quantify difference between healthy and affectedskin area within a single image.

This work is about a realistic visualization technique called raytracing. It studies its original form, its extensions and optimizations. Raytracing casts rays through pixels and follows their propagation in the scene, according to the physical laws. It enables rendering of correct shadows, reflections and refractions. Distributed raytracing serves for better visualization and advanced effects. One ray is replaced with a beam of rays that allows soft shadows, fuzzy translucency, depth of field and antialiasing. With the increasing number of rays, the render time rises as well, so it is needed to use some optimization techniques and tools. A way of using this rendering method for visualization of alcoholic beverages is also described.

The aim of master thesis is to describe different calculation of global illumination methods including Light Propagation Volumes. All three steps of LPV calculation are widely described: injection, propagation and rendering. It is also proposed several custom extensions improving graphics quality of this method. Two parts of design and implementation are focused on scene description, rendering system, shadow rendering, implementation of LPV method and proposed extensions. As conclusion, measurement and several images of application are presented, followed by comparison in environment with diffenent parameters, thesis summary with evaluation of achieved results and suggestions of further improvements.