Master of Science / Department of Statistics / Leigh Murray / Using remotely sensed reflectance data is an appealing tool for controlling invasive species of grasses by rangeland managers. Recent developments in functional data analysis include the functional boxplot (FBP) which is shown here to be a useful tool in the visualization of reflectance data. Functional boxplots are a novel method of visually inspecting functional data and determining the presence of outliers in the data. Implementation and interpretation of FBPs are both straightforward and intuitive. The goal of this study is to examine the use of FBPs for visualizing reflectance data, and to determine the efficacy of using the FBP to distinguish between native tall grasses and invasive Old World Bluestem (OWB, Bothriochloa spp.) monocultures in a Kansas prairie. Validation trials were conducted in order to determine the stability of the FBP when used to analyze spectral data. FBPs were shown to be highly stable for use with both native and OWB grasses at all times and subsets of wavelengths tested. Identification trials were conducted by introducing a single OWB observation to a test set of native tall grass observations and constructing a FBP. Results indicate that using observations recorded early in the growing season, the functional boxplot is able to successfully identify the OWB observation as an outlier in a test set of native tall grass observations with an estimated probability 100% and 95.45% when considering the visible and cellular spectrums, respectively. A 95% lower bound for the probability of successfully identifying the OWB observation using the cellular spectrum in May is found to be 89.67%.

Avhandlingen behandlar de teoretiska och praktiska aspekterna av att använda spektrala vinkelupplösta reflektansmätningar för optisk karakterisering av fiberbaserade material såsom papper och kartong. En spektral goniofotometer används för att mäta det reflekterade ljusets vinkelfördelning. En stor del av arbetet utgörs av att utvärdera instrumentets noggrannhet, samt utreda hur de vinkelupplösta mätningarna skall utföras på bästa sätt för att erhålla en så fullständig karakterisering som möjligt. Det reflekterade ljuset består av tre komponenter; ytreflektans, bulkreflektans samt fluorescens. En fullständig karakterisering förutsätter att dessa tre komponenter kan analyseras separat, vilket i detta arbete görs genom nyutvecklade metoder. En metod har utvecklats för separation av ytreflektans och bulkreflektans. Metoden bygger på att analysera hur den totala reflektansen förändras vid ökande absorption i det reflekterande materialet. Absorptionen kontrolleras genom inkjet-tryckning där tryckfärg appliceras på substratet i sådan mängd att bulkreflektansen helt släcks ut. Genom att kombinera mätningar på tryckt och otryckt substrat kan de båda komponenterna separeras. Trots att ytreflektansen från ett matt papper är liten i förhållande till bulkreflektansen, så visar resultaten att den ökar markant med ökande betraktningsvinkel och kan därmed ha stor inverkan på den totala reflektansen. Bidraget från fluorescens kan kvantitativt analyseras genom att kombinera mätningar utförda med respektive utan UV-filter. Vinkelupplösta mätningar och Monte Carlo-simuleringar av fluorescensens vinkelfördelning visar att dess anisotropi är relaterad till det medeldjup vid vilket fluorescensen emitteras. Resultaten förklarar observerade skillnader och motstridigheter i tidigare rapporterade studier kring huruvida fluorescens kan anses vara Lamberskt fördelad. Samtliga goniofotometriska mätningar är utförda med ett kompakt, kommersiellt tillgängligt, dubbelstråleinstrument. För att undersöka instrumentets lämplighet för absoluta reflektansmätningar utförs en analys av dess mätnoggrannhet. Resultaten visar att instrumentets kompakta storlek i kombination med den anisotropa reflektansen från papper introducerar systematiska fel av samma storleksordning som den totala mätnoggrannheten. Dessa fel uppstår på grund av den relativt stora detektorapertur som måste användas vid mätningar av diffus reflektans, vilket är karakteristiskt för papper och kartong. Resultaten visar även att felen är störst vid flacka mätvinklar och för prover med hög grad av anisotropisk reflektans, och en geometrisk korrektionsmetod för denna typ av systematiska fel föreslås. Spektrala och vinkelupplösta mätningar medför per automatik stora mängder mätdata. Genom att använda strålningstransportteori som en matematisk modell för hur ljus sprids i papper kan mätdatat reduceras till en uppsättning beskrivande materialparameterar. Att uppskatta dessa optiska parametrar utifrån vinkelupplösta reflektansmätningar är i sig ett komplicerat problem, vilket dessutom är känsligt för mätfel och val av mätvinklar. Detta inversa problem analyseras i detalj, och speciellt hur valet av mätvinklar kan reduceras utan att försämra förutsättningarna för estimeringen. Simuleringar visar att mätningarna kan begränsas till infallsplanet, eller till och med enbart framåtriktningen, så länge tillräckligt flacka mätvinklar är inkluderade i mätsekvensen. / This thesis is about measuring and modelling light reflected from paper by using goniophotometric measurements. Measuring bidirectional reflectance requires highly accurate instruments, and a large part of the work in this thesis is about establishing the requirements that must be fulfilled to ensure valid data. A spectral goniophotometer is used for measuring the light reflected from paper and methods are developed for analyzing the different components, i.e. the fluorescence, surface reflectance and bulk reflectance, separately. A separation of the surface and bulk reflectance is obtained by inkjet printing and analyzing the total reflectance in the absorption band of the ink. The main principle of the method is to add dye to the paper until the bulk scattered light is completely absorbed. The remaining reflectance is solely surface reflectance, which is subtracted from the total reflectance of the undyed sample to give the bulk reflectance. The results show that although the surface reflectance of a matte paper is small in comparison with the bulk reflectance, it grows rapidly with increasing viewing angle, and can have a large influence on the overall reflectance. A method for quantitative fluorescence measurements is developed, and used for analyzing the angular distribution of the fluoresced light. The long-standing issue whether fluorescence from turbid (or amorphous) media is Lambertian or not, is resolved by using both angle-resolved luminescence measurements and radiative transfer based Monte Carlo simulations. It is concluded that the degree of anisotropy of the fluoresced light is related to the average depth of emission, which in turn depends on factors such as concentration of fluorophores, angle of incident light and the absorption coefficient at the excitation wavelength. All measurements are conducted with a commercially available benchtop sized double-beam spectral goniophotometer designed for laboratory use. To obtain reliable results, its absolute measurement capability is evaluated in terms of measurement accuracy. The results show that the compact size of the instrument, combined with the anisotropic nature of reflectance from paper, can introduce significant systematic errors of the same order as the overall measurement uncertainty. The errors are related to the relatively large detection solid angle that is required when measuring diffusely reflecting materials. Situations where the errors are most severe, oblique viewing angles and samples with high degree of anisotropic scattering, are identified, and a geometrical correction is developed. Estimating optical properties of a material from bidirectional measurements has proved to be a challenging problem and the outcome is highly dependent on both the quality and quantity of the measurements. This problem is analyzed in detail for optically thick turbid media, and the study targets the case when a restricted set of detection angles are available. This is the case when e.g. an unobstructed view of the sample is not possible. Simulations show that the measurements can be restricted to the plane of incidence (in-plane), and even the forward direction only, without any significant reduction in the precision or stability of the estimation, as long as sufficiently oblique angles are included.

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Creating realistic-looking skin is one of the holy grails of computer graphics and is still an active area of research. The problem is challenging due to the inherent complexity of skin and its variations, not only across individuals but also spatially and temporally among one. Skin appearance and reflectance vary spatially in one individual depending on its location on the human body, but also vary temporally with the aging process and the body state. Emotions, health, physical activity, and cosmetics for example can all affect the appearance of skin. The spatially varying reflectance of skin is due to many parameters, such as skin micro- and meso-geometry, thickness, oiliness, and pigmentation. It is therefore a daunting task to derive a model that will include all these parameters to produce realistic-looking skin. The problem is also compounded by the fact that we are very well accustomed to the appearance of skin and especially sensitive to facial appearances and expressions. Skin modelling and rendering is crucial for many applications such as games, virtual reality, films, and the beauty industry, to name a few. Realistic-looking skin improves the believability and realism of applications. The complexity of skin makes the topic of skin modelling and rendering for computer graphics a very difficult, but highly stimulating one. Skin deformations and biomechanics is a vast topic that we will not address in this dissertation. We rather focus our attention on skin optics and present a simple model for the reflectance of human skin along with a system to support skin modelling and rendering.

The bidirectional reflectance distribution function has a four dimensional parameter space and such high dimensionality makes it impractical to use it directly in hardware rendering. When a BRDF has no analytical representation, common solutions to overcome this problem include expressing it as a sum of basis functions or factorizing it into several functions of smaller dimensions. This thesis describes factorization extensions that significantly improve factor computation speed and eliminate drawbacks of previous techniques that overemphasize low sample values. The improved algorithm is used to calculate factorizations and material maps from colored images. The technique presented in this thesis allows interactive definition of arbitrary materials, and although this method is based on physical parameters, it can be also used for achieving a variety of non-photorealistic effects.

<p>The optical properties of biological tissue provide quantitative information about the physiological structure and chemical composition of a tissue sample. The investigation of tissue optical properties through Diffuse Reflectance Spectroscopy (DRS) is a rapid, non-invasive technique with extensive applications in healthcare diagnostics and therapeutics. Breast conservation surgery, a clinical practice performed for nearly 15,000 patients annually, requires accurate diagnosis of the tissue margin, the healthy layer of tissue surrounding the excised tumor. This margin assessment has traditionally been performed via post-operative pathology through one of multiple time-intensive processes that are performed after the surgery is completed. However, the margin assessment can also be rapidly performed by DRS, leading towards pathological evaluations concurrent with the excision surgery. </p><p>Presently, DRS probe designs are limited to laboratory settings. They include illumination and collection optical fibers, spectrometers, and CCD detectors, which all add to the complexity, cost, and size of a diagnostic system. Recently, DRS probes have been designed with Silicon photodetectors (Si PDs), including detector arrays that enable simultaneous DRS imaging of multiple tissue sites. The Si PDs reduce probe system complexity by replacing the cumbersome fiber-based collection probes and CCD detectors. </p><p>However, these monolithic Si PD probes are rigid and flat. When imaging non-planar tissue samples, a rigid probe may experience reduced accuracy from uneven tissue pressure and loss of contact with the tissue surface. A physically flexible DRS probe can improve sensing accuracy by conforming to a tissue surface with arbitrary curvature.</p><p>This thesis presents the design, fabrication, and test of flexible DRS Si PD probes constructed with thin film single crystalline silicon heterogeneously bonded to a flexible polymer substrate. The PDs have dark currents and responsivities comparable to high performance standard thickness Si PDs. The responsivity and zero bias dark current of the flexible PDs were evaluated while flat and while curved up to a 10 mm radius of curvature, with measured variations in responsivity (±0.61%) and dark current (±3 pA).</p><p>The flexible DRS probe was evaluated on benign and malignant breast tissue representative liquid phantoms. DRS measurements were performed with the flexible DRS probe on both liquid phantoms over a wavelength range of 470 – 600 nm at five radii of curvature: flat, 50 mm, 25 mm, 15 mm, and 10 mm. The optical contrast between the benign and malignant phantom DRS measurements ranged from 4.0-13.6% across all measured wavelengths for the flat test case and 5.9-15.5% while curved. For both phantoms at all wavelengths, the DRS signal increased in response to increasing curvature. The increase in reflectance signal ranged from 4.8-12.3% when the liquid phantom curvature was brought from flat to a 10 mm radius of curvature. The experimental results were then compared to theoretical reflectance values generated through a forward Monte Carlo model. The mean error between experiment and theory was 2.33% for the benign phantom and 1.23% for the malignant phantom. </p><p>Pixel-to-pixel crosstalk, the portion of diffusely reflected light that enters the tissue near one PD but is detected at a different PD, was also evaluated using the same test setup as for the DRS signal. The crosstalk signal also increases due to curvature, with an increase of 33.2-40.0% across all measured wavelengths for the benign phantom. The experimental crosstalk signal for the benign phantom was compared to a forward Monte Carlo model with mean error of 4.85%. The crosstalk could not be measured on the malignant phantom due to lower reflected light levels that were below the noise floor of the PD. </p><p>The flexible Si PD probe presented herein shows promising results for optical tissue analysis and feature extraction on both flat and curved tissue surfaces. This flexible probe technology facilitates conformal tissue DRS imaging, potentially in a clinical diagnostic device.</p> / Dissertation

A study was conducted to optically determine the viability of the Gram +, endospore-forming bacterial genera Bacillus using a hyperspectral reflectance spectrometer. Endospores are a dormant, differentiated cellular capsule form taken by select bacteria to ensure survival when environmental conditions become unfavorable. Two species of Bacillus were used for this study, Bacillus megaterium and Bacillus subtilis. These endospores were killed using a chemical treatment of sodium hypochlorite or a physical treatment of heat and pressure in an autoclave. The treated samples along with viable samples were lyophilized to form a powder. A reflectance spectrometer measuring 350 nm to 2500 nm (UV to shortwave infrared) was used to collect optical data on bulk powders. The resulting spectra were analyzed using several different methods, including integration and a Support Vector Machine (SVM) to obtain optimal separability of viable and nonviable endospores. Results of this study demonstrated the significant spectral separability of live and dead endospores with a level of confidence <0.05 in both species.

This paper describes approaches to retrieve important aerosol results from the strong lidar return signals that are received by the space-borne CALIPSO lidar system after reflecting off-ocean surfaces. Relations, from which the theoretically expected values of area under ocean surface returns can be computed, are presented. A detailed description of the lidar system response to the ocean surface returns and the processes of sampling and averaging of lidar return signals are provided. An effective technique that reconstructs the lidar response to surface returnsstarting from down-linked samplesand calculates the area under it, has been developed and described. The calculated area values are validated after comparing them to their theoretically predicted counterpart values. Methods to retrieve aerosol optical depths (AODs) from these calculated areas are described and retrieval results are presented, including retrieval comparison with independent AOD measurements made by an airborne High Spectral Resolution Lidar (HSRL) that yielded quite good agreement. Techniques and results are also presented on using the spectral ratios of the surface response areas to determine spectral ratios of aerosol round-trip transmission and AOD spectral difference, without need of a specific/accurate ocean-surface reflectance model.

Reproduire efficacement l'apparence réaliste des matériaux est un problème crucial pour la synthèse d'images réalistes dans les productions cinématographiques et les jeux vidéo. Outre le transport global de la lumière, le réalisme d'une image de synthèse passe avant tout par une modélisation correcte du transport local, c'est-à-dire les interactions entre lumière et matière. La modélisation de ces interactions donne lieu à une grande variété de modèles de réflectance. Nous proposons une classification de ces modèles en s'appuyant sur l'échelle des détails géométriques abstraits. À partir de cette classification, nous étudions des modèles de réflectance particuliers : * un modèle de transmission pour les surfaces transparentes et rugueuses, tels que le verre dépoli. Son efficacité permet une utilisation au sein applications temps-réel * une analyse et une modélisation du transport de la lumière dans les matériaux composés d'agrégats de particules * une base alternative aux harmoniques sphériques pour représenter et illuminer efficacement les matériaux mesurés ayant une réflectance à basses fréquences. Ces modèles permettent une abstraction efficace des interactions locales tout en conservant la reproduction de leurs effets réalistes. / Reproducing efficiently the appearance of complex materials is a crucial problem in the synthesis of realistic images widely involved in the production of video games and movies. Apart from global light transport, the realism of a synthetic image is in large part due to the adequate modeling of local light transport, i.e. the interactions between light and matter. Modeling these interactions gives rise to a large variety of reflectance models. We therefore propose a classification of these models based on the scales of their abstract geometric details. From this classification, we can study particular reflectance models: a transmitting reflectance model for transparent rough surfaces such a frosted glass. The efficiency of our model allows real-time performances, a study and a model of energy propagation in material composed of dense packed discrete particles, an alternative basis for representing and lighting efficiently measured materials having a low frequency reflectance. These models permit the abstraction of local interactions while keeping the realism of fully simulated local light transport models.