Radio-Frequency (RF) lesioning, or RF ablation, is a method that uses high frequency currents for thermal coagulation of pathological tissue or signal pathways. The current is delivered from an electrode, which also contains a temperature sensor permitting control of the current at a desired target temperature. In the brain, RF lesioning can e.g. be used for treatment of severe chronic pain and movement disorders such as Parkinson’s disease. This thesis focuses on modelling and simulation with the aim of gaining better understanding and predictability of the lesioning process in the central brain.   The finite element method (FEM), together with experimental comparisons, was used to study the effects of electric and thermal conductivity, blood perfusion (Paper I), and cerebrospinal fluid (CSF) filled cysts (Paper II) on resulting lesion volume and shape in brain tissue. The influence of blood perfusion was modelled as an increase in thermal conductivity in non-coagulated tissue. This model gave smaller simulated lesions with increasing blood perfusion as heat was more efficiently conducted from the rim of the lesion. If the coagulation was not taken into consideration, the lesion became larger with increasing thermal conductivity instead, as the increase in conducted heat was compensated for through an increased power output in order to maintain the target temperature. Simulated lesions corresponded well to experimental in-vivo lesions. The electric conductivity in a homogeneous surrounding had little impact but this was not true for a heterogeneous surrounding. CSF has a much higher electric conductivity than brain tissue, which focused the current to the cyst if the electrode tip was in contact with both a cyst and brain tissue. Heating of CSF could also cause considerable convective flow and as a result a very efficient heat transfer. This affected both simulated and experimental lesion sizes and shapes. As a result both very large and very small lesions could be obtained depending on whether sufficient power was supplied or if the heating was mitigated over a large volume.   Clinical (Paper IV) and experimental (Paper III) measurements were used for investigation of changes in reflected light intensity from undamaged and coagulating brain tissue respectively. Monte Carlo (MC) simulations for light transport were made for comparison (Paper V). For the optical measurements, an RF electrode with adjacent optical fibres was used and this electrode was also modelled for the optical simulations. According to the MC simulations, coagulation should make grey matter lighter and white matter darker, while thalamic light grey should remain approximately the same. Experiments in ex-vivo porcine tissue gave an increase in reflected light intensity from grey matter at approximately 50 °C but the signal was very variable and the isotherm 60 °C gave better agreement between simulated and experimental lesions. No consistent decrease in reflected light intensity could be seen during coagulation of white matter. Clinical measurements were performed during the creation of 21 trajectories for deep brain stimulation electrodes. In agreement with the simulations, reflected light intensity was found to differentiate well between undamaged grey, light grey and white matter.   In conclusion, blood perfusion and CSF in particular may greatly affect the lesioning process and can be important to consider when planning surgery. Reflected light intensity seems unreliable for the detection of coagulation in light grey brain matter such as the thalamus. However, it seems very promising for navigation in the brain and for detection of coagulation in other tissue types such as muscle.

Le phénotypage consiste à caractériser les plantes et leur comportement en vue de la sélection génétique. Cette étude a évalué le potentiel de l'imagerie hyperspectrale de proximité pour répondre à ces besoins. Elle s'appuie sur le lien existant entre la physiologie des plantes et leurs propriétés optiques. Cette étude a montré qu'il est possible de retrouver la réflectance des feuilles en dépit d'un éclairage naturel variable. La procédure de correction mise en place permet de retrouver la réflectance vraie de feuilles à plat et introduit un effet additif (dû à la réflexion spéculaire), un effet multiplicatif (dû au niveau d'éclairement) et un effet non linéaire (dû aux réflexions multiples) sur les feuilles inclinées des plantes au champ. Cependant, nous avons montré également que, grâce à des pré-traitements des spectres adéquats et à la PLS (Partial Least Square regression), la concentration en azote est accessible à partir de la réflectance (400-1000~nm) de feuilles fraîches sur pied. L'étude de spectres simulés a montré que la non prise en compte des réflexions multiples dans l'étalonnage d'un modèle conduisait à une surestimation de la concentration en azote des feuilles subissant des réflexions multiples. Enfin, cette étude a illustré l'intérêt de l'imagerie hyperspectrale de proximité par rapport à la spectrométrie ponctuelle. Le fait d'avoir une image, combiné à la haute résolution spatiale permet d'obtenir des données plus représentatives de la parcelle et de calculer une vitesse de fermeture de couvert. La réalisation de cartographies d'azote permet de suivre la concentration en azote dans différents étages foliaires ou parties d'une même feuille. / Henotyping consists in characterising plants and their behavior with the aim of the genetic selection. This study estimated the potential of the close-range hyperspectral imaging to meet these needs. It leans on the link existing between plant physiology and their optical properties. This study showed that it is possible to find leaf reflectance in spite of a variable natural lighting. The developed correction procedure allows finding the true reflectance of flat leaves and introduces an additive effect (due to specular reflection), a multiplicative effect (due to illumination level) and a not linear effect (due to the multiple reflections) on inclinated leaves of plants in the field. However, we also showed that, thanks to adequate preprocessing of the spectra and to PLS (Partial Least Square regression), the nitrogen concentration is accessible from the reflectance (400-1000~nm) of fresh leaves on standing plants. The study of simulated spectra showed that the not consideration of the multiple reflections in the calibration of a model lead to an overestimation of the nitrogen concentration leaves undergoing multiple reflections. Finally, this study illustrated the interest of close-range hyperspectral imaging with regard to the punctual spectrometry. The fact of having an image, combined with the high spatial resolution allows to obtain more representative data of the plot and to calculate a speed of cover closure. Nitrogen mappings allow following the nitrogen concentration in various leaf level or parts of the same leaf.

<p>Diffuse reflectance spectroscopy (DRS) is a simple, yet powerful technique that has the potential to offer practical, non-invasive, and cost effective information for op- tical diagnostics and therapeutics guidance. Any progress towards moving DRS systems from their current laboratory settings to clinical settings, field settings and ambitiously to home settings, is a significant contribution to society in terms of reducing ever growing healthcare expenditures of an aging society. Additionally, im- proving on the existing mathematical models used to analyze DRS signals; in terms of speed, robustness, accuracy, and capability in accounting for larger feature space dimensionality (i.e. extraction of more tissue-relevant information) is equally im- portant for real-time diagnosis in the desired settings and to enable use of DRS in as many biomedical applications (e.g. skin cancer diagnosis, diabetics care, tissue oxygenation monitoring) as possible. Improving the reflectance signal complexity and density through novel DRS instrumentation, would facilitate development of the desired models or put the existing ones built on simulations in practical use; which otherwise could not go beyond being a theoretical demonstration.</p><p>DRS studies tissue morphology and composition through quantification of one or more (ideally all of them) of the tissue- and wavelength-specific optical properties: absorption coefficient (μa), reduced scattering coefficient (μ1s), scattering anisotropy (g), tissue thickness, and scattering phase function details (e.g. higher order moments of the scattering phase function). DRS involves sampling of diffusely reflected photons which experience multiple scattering and absorption as they travel within the tissue, at the tissue surface. Spatially resolved diffuse reflectance spectroscopy (SRDRS) is a subset of general DRS technique, which involves sampling of diffuse reflectance signals at multiple distances to an illumination source. SRDRS provides additional spatial information about the photon path; yielding depth-resolved tissue information critical to layered tissue analysis and early cancer diagnostics. Exist- ing SRDRS systems use fiber optic probes, which are limited in accommodation of large number and high-density collection fibers (i.e. yielding more and dense spa- tially resolved diffuse reflectance (SRDR) measurement data) due to difficulty of fiber multiplexing. The circular shape of the fibers restricts the implementable probe ge- ometries and reduces the fill factor for a given source to detector (i.e. collection fiber) separation (SDS); resulting in reduced light collection efficiency. The finite fiber nu- merical aperture (NA) reduces the light collection efficiency well as; and prevents selective interrogation of superficial tissues where most cancers emerge. Addition- ally, SRDR systems using fiber optic probes for photon collection, require one or more photodetectors (i.e. a cooled CCD); which are often expensive components of the systems.</p><p>This thesis deals with development of an innovative silicon SRDRS probe, which partially addresses the challenge of realizing high measurement density, miniaturized, and inexpensive SRDRS systems. The probe is fabricated by conventional, flexible and inexpensive silicon fabrication technology, which demonstrates the feasibility of developing SRDRS probes in any desired geometry and complexity. Although this approach is simple and straightforward, it has been overlooked by the DRS community due to availability of the conventional fiber optic probe technology. This new probe accommodates large number and high density of detectors; and it is in the form of a concentric semi-annular photodiode (PD) array (CMPA) with a central illumination aperture. This is the first multiple source-detector spacing Si SRDRS probe reported to date, and the most densely packed SRDRS probe reported to date for all types of SRDRS systems. The closely spaced and densely packed detectors enable higher density SRDR measurements compared to fiber-based SRDR probes, and the higher PD NA compared to that of fibers results in a higher SNR increasing light collection efficiency. The higher NA of the PDs and the presence of PDs positioned at very short distances from the illumination aperture center enable superficial tissue analysis as well as depth analysis.</p> / Dissertation

<p>Worldwide, head and neck squamous cell cancers (HNSCC) account for over 375,000 deaths annually. The majority of these cancers arise in the outermost squamous cells which progress through a series of precancerous changes before developing into invasive HNSCC. It is widely accepted that prognosis is strongly correlated to the stage of diagnosis, with early detection more than doubling the patient’s chance of survival. Currently, however, 60% of HNSCCs are diagnosed when they have already progressed to stage 3 or stage 4 disease. The current diagnostic method of visual examination often fails to recognize early indicators of HNSCC, thereby missing an important prevention window.</p><p> </p><p>Determination of cancer from non-malignant tissues is dependent on pathological examination of lesion biopsies. Thus, all patients with any clinically suspicious lesions undergo surgical biopsies. Furthermore, these surgical biopsies carry risks. In addition to the risk of general anesthesia for patients undergoing panedoscopy, some patients have poor healing and develop ulcerations or infections as a result of surgical biopsy at any anatomical site. Additionally, studies have shown that approximately 50% of suspected biopsies are later pathologically confirmed normal. An enormous amount of labor, facility, and monetary resources are expended on non-malignant biopsies and patients who ultimately have no malignancy. It would be of immense overall benefit to clinicians and patients to have a non-invasive and portable technique that could rapidly identify those patients that would benefit from further surgical biopsy from those that only need follow-up clinical observations.</p><p> </p><p>Once carcinoma is confirmed in a patient, treatment currently involves modalities of surgery, radiation, and chemotherapy. Radiotherapy plays a significant role, particularly in the management of localized HNSCC, because it is a non-invasive and function-preserving modality. However, the effectiveness of radiotherapy is limited by hypoxia. Previous studies showed that tumors reoxygenated during radiotherapy treatment may have a better prognosis. Despite decades of work, there is still no reliable, cost-effective way for measuring tumor hypoxia over multiple time points to estimate the prognosis. </p><p>To address these unmet clinical needs, three aims were proposed. The first aim was to improve early detection by identifying biomarkers of early pre-cancer as well as developing an objective algorithm to detect early disease. Neovasculature is an important biomarker for early cancer diagnosis. Even before the development of a clinically detectable lesion, the tumor vasculature undergoes structural and morphological changes in response to oncogenic signaling pathways [8]. Without receiving a sufficient supply of oxygen and nutrients to proliferate, early tumor growth is limited to only 1-2 mm. High-resolution optical imaging is well suited to characterize the earliest neovascularization changes that accompany neoplasia owing to its sensitivity to hemoglobin absorption and resolution to visualize capillary level architecture. Dark field microscopy is a low-cost and robust method to image the neovasculature. We imaged neovascularization in vivo in a spontaneous hamster oral mucosa carcinogen model using a label-free, reflected-light spectral dark field microscope. Hamsters’ cheek pouches were painted with 7, 12-Dimethylbenz[a]anthracene (DMBA) to induce precancerous to cancerous changes, or mineral oil as control. Spectral dark field images were obtained during carcinogenesis and in control oral mucosa, and quantitative vascular features were computed. Vascular tortuosity increased significantly in oral mucosa diagnosed as hyperplasia, dysplasia and squamous cell carcinoma (SCC) compared to normal. Vascular diameter and area fraction decreased significantly in dysplasia and SCC compared to normal. The areas under the receiver operative characteristic (ROC) curves (AUC) computed using a Support Vector Machine (SVM) were 0.95 and 0.84 for identifying SCC or dysplasia, respectively, vs. normal and hyperplasia oral mucosa combined. To improve AUCs for identifying dysplasia, quantitative vascular features were computed again after the vessels were split into large and small vessels based on diameter. The large vessels preserved the same significant trends, while small vessels demonstrated the opposite trends. Significant increases in diameter and decreases in area fraction were observed in SCC and dysplasia. The AUCs were improved to 0.99 and 0.92 for identifying SCC and dysplasia. These results suggest that dark field vascular imaging is a promising tool for pre-cancer detection.</p><p>Optical imaging can also be applied to quantifying other important characteristics of solid tumors in head and neck cancer (HNC), such as hypoxia, abnormal vascularity and cell proliferation. Diffuse reflectance spectroscopy is a simple and robust method to measure tissue oxygenation, vascularity and cell density. It is particularly suitable for applications in the operation room because of its compact design and portability. In addition, a fiber probe-based system is ideal for obtaining measurements at suspicious lesions in the head and neck area during surgery. Thus, my second aim was to reduce the number of unnecessary HNSCC biopsies by developing a robust tool and rapid analysis method appropriate for clinical settings. We propose the use of morphological optical biomarkers for rapid detection of human HNSCC by leveraging the underlying tissue characteristics in the aerodigestive tracts Prior to biopsy, diffuse reflectance spectra were obtained from malignant and contra-lateral non-malignant tissues of 57 patients undergoing panendoscopy. Oxygen saturation (SO2), total hemoglobin concentration ([THb]), and the reduced scattering coefficient were extracted using an inverse Monte Carlo (MC) method previously developed by former student in our lab. Differences in malignant and non-malignant tissues were examined based on two different groupings: by anatomical site and by morphological tissue type. Measurements were acquired from 252 sites, 51 of which were pathologically classified as SCC. Optical biomarkers exhibited statistical differences between malignant and non-malignant samples. Contrast was enhanced when parsing tissues by morphological classification rather than by anatomical subtype for unpaired comparisons. Corresponding linear discriminant models using multiple optical biomarkers showed improved predictive ability when accounting for morphological classification, particularly in node-positive lesions. The false-positive rate was retrospectively found to decrease by 34.2% in morphologically- vs. anatomically-derived predictive models. In glottic tissue, the surgeon exhibited a false-positive rate of 45.7% while the device showed a lower false-positive rate of only 12.4%. Additionally, comparisons of optical parameters were made to further understand the physiology of tumor staging and potential causes of high surgeon false-positive rates. Optical spectroscopy is a user-friendly, non-invasive tool capable of providing quantitative information to discriminate malignant from non-malignant head and neck tissues. Predictive models demonstrated promising results for diagnostics. Furthermore, the strategy described appears to be well suited to reduce the clinical false-positive rate.</p><p>To further improve the speed for extracting the tissue oxygenation and [THb] to reduce the time when patients were under anesthesia, the third aim was to develop a rapid heuristic ratiometric analysis for estimating tissue [THb] and SO2 from measured tissue diffuse reflectance spectra. The analysis was validated in tissue-mimicking phantoms and applied to clinical measurements in head and neck, cervical and breast tissues. The analysis works in two steps. First, a linear equation that translates the ratio of the diffuse reflectance spectra at 584 nm to 545 nm to estimate the tissue [THb] using a Monte carlo (MC)-based lookup table was developed. This equation is independent of tissue scattering and oxygen saturation. Second, SO2 was estimated using non-linear logistic equations that translate the ratio of the diffuse reflectance spectra at 539 nm to 545 nm into the tissue SO2. Correlations coefficients of 0.89 (0.86), 0.77 (0.71) and 0.69 (0.43) were obtained for the tissue hemoglobin concentration (oxygen saturation) values extracted using the full spectral MC and the ratiometric analysis, for clinical measurements in head and neck, breast and cervical tissues, respectively. The ratiometric analysis was more than 4000 times faster than the inverse MC analysis for estimating tissue [THb] and SO2 in simulated phantom experiments. In addition, the discriminatory power of the two analyses was similar. These results show the potential of such empirical tools to rapidly estimate tissue hemoglobin and oxygenation for real-time applications.</p><p>In addition to its use as a diagnostic marker for various cancers, tissue oxygenation is believed to play a role in the success of cancer therapies, particularly radiotherapy. However, since little effort has been made to develop tools to exploit this relationship, the fourth aim was to estimate patient prognosis by measuring tumor hypoxia over multiple time points so physicians are able to develop more informed and effective clinical treatment plan. To test if oxygenation kinetics correlates with the likelihood for local tumor control following fractionated radiotherapy, we again used diffuse reflectance spectroscopy to noninvasively measure tumor vascular oxygenation and [THb] associated with radiotherapy of 5 daily fractions (7.5, 9 or 13.5 Gy/day) in FaDu xenografts. Spectroscopy measurements were obtained immediately before each daily radiation fraction and during the week after radiotherapy. SO2 and [THb] were computed using an inverse MC model. Oxygenation kinetics during and after radiotherapy, but before a change in tumor volume, was associated with local tumor control. Locally controlled tumors exhibited significantly faster increases in oxygenation after radiotherapy (days 12-15) compared with tumors that recurred locally. (2) Within the group of tumors that recurred, faster increases in oxygenation during radiotherapy (days 3-5) were correlated with earlier recurrence times. An AUC of 0.74 was achieved when classifying the local control tumors from all irradiated tumors using the oxygen kinetics with a logistic regression model. (3) The rate of increase in oxygenation was radiation dose dependent. Radiation doses ≤9.5 Gy/day did not initiate an increase in oxygenation whereas 13.5 Gy/day triggered significant increases in oxygenation during and after radiotherapy. Additional confirmation is required in other tumor models, but these results suggest that monitoring tumor oxygenation kinetics could aid in the prediction of local tumor control after radiotherapy.</p><p>Angiogenesis is a highly regulated process to support tissue growth. Neovasculature is designed by nature to grow toward areas lacking nutrition and oxygen. Cancer cells proliferate too quickly to have their nutritional and oxygen needs completely satisfied, which results in an imbalanced state of angiogenesis leading to tortuous blood vessels, hypoxic tissues and radioresistance. We characterized the tumor-induced vascular features with simple, robust and low-cost dark field microscopy and spectroscopy to enable early cancer diagnosis, improvement of surgical biopsy accuracy and better predict the prognosis of radiotherapy for HNC. Our results demonstrated that these noninvasively measured, label-free vascular features are able to detect pre-cancer, reduce unnecessary surgical biopsies and predict prognosis of radiotherapy.</p> / Dissertation

The Salish Sea is a ecologically important coastal region located on the southwest part of British Columbia. Optical measurements were taken using a set of hyperspectral radiometers, the SAS Solar Tracker developed by Satlantic. This sensor is installed on the Queen of Oak Bay ferry, that runs between Nanaimo and Vancouver, as part of the Ferry Ocean Colour Observation Systems (FOCOS) project. We developed a computer program to process the raw sensor data and generate remote sensing reflectance (Rrs) values. This performs similar functions to Prosoft, Satlantic’s own software to process the data. However, we added new features such as an additional preprocessing step to filter the data based on longitude, and new meteorological flag testing and wind speed calculations. The system was tested using Pearson correlation to compare our output with the output from Satlantic Prosoft. Testing helped us identify a few issues, such as adding longitude flags to remove data at the start and end of the trip where the sensor could produce inaccurate results if aiming at land instead of water. Another issue was where the SAS Solar Tracker does not update its pointing angle fast enough when the ferry makes sharp turns and could result in inaccurate data. / Graduate

The objective of this dissertation is to understand the structural and optoelectronic properties of group III-nitride materials grown by High-Pressure Metal Organic Chemical Vapor Deposition (HP-MOCVD) and Migration Enhanced Plasma Assisted MOCVD by FTIR reflectance spectroscopy, Raman spectroscopy, X-ray diffraction, and Atomic Force Microscopy. The influence of the substrates/templates (Sapphire, AlN, Ga-polar GaN, N-polar GaN, n-GaN, and p-GaN) on the free carrier concentration, carrier mobility, short-range crystalline ordering, and surface morphology of the InN layers grown on HP-MOCVD were investigated using those techniques. The lowest carrier concentration of 7.1×1018 cm-3 with mobility of 660 cm2V-1s-1 was found in the InN film on AlN template, by FTIR reflectance spectra analysis. Furthermore, in addition to the bulk layer, an intermediate InN layers with different optoelectronic properties were identified in these samples. The best local crystalline order was observed in the InN/AlN/Sapphire by the Raman E2 high analysis. The smoothest InN surface was observed on the InN film on p-GaN template. The influence of reactor pressures (2.5–18.5 bar) on the long-range crystalline order, in plane structural quality, local crystalline order, free carrier concentration, and carrier mobility of the InN epilayers deposited on GaN/sapphire by HP-MOCVD has also been studied using those methods. Within the studied process parameter space, the best material properties were achieved at a reactor pressure of 12.5 bar and a group-V/III ratio of 2500 with a free carrier concentration of 1.5x1018 cm-3, a mobility in the bulk InN layer of 270 cm2 V-1s-1 and the Raman (E2 high) FWHM of 10.3 cm-1. The crystalline properties, probed by XRD 2θ–ω scans have shown an improvement with the increasing reactor pressure. The effect of an AlN buffer layer on the free carrier concentration, carrier mobility, local crystalline order, and surface morphology of InN layers grown by Migration-Enhanced Plasma Assisted MOCVD were also investigated. Here, the AlN nucleation layer was varied to assess the physical properties of the InN layers. This study was focused on optimization of the AlN nucleation layer (e.g. temporal precursor exposure, nitrogen plasma exposure, and plasma power) and its effect on the InN layer properties.

The application of high temporal satellite image data for designation of the spectral characteristic of vegetation Abstract The objektive of this paper is to evaluate possibilities of high temporal satellite data assimilation for continuous monitoring of the spectral characteristic of vegetation. There is also given the suggestion of metodology for processing MERIS data and for continuous monitoring of spectral characteristic of landscape objects. Finally, vegetation cover database for the Czech Republic in the year 2009 is created from sectorial analysis. In the paper there is used the LSU classification and thresholding of vegetation indicies histograms. The universal decision algorithm for classification of vegetation landscape component are described and particular thresholding values for the year 2009 given. The finally product of this paper is Czech vegetation cover database for the year 2009 with overall accuracy of 63,35 %. Accuracy for forest is even over 80 %. Keywords: remote sensing, MERIS, vegetation, spectral reflectance, LSU, BEAM

Master of Science / Department of Biology / Loretta Johnson / Plant epicuticular wax (ECW) isolates internal tissues from harsh external conditions increasing drought tolerance. Beta-diketone-rich ECW reflect light and result in a glaucous phenotype that may ameliorate the thermal environment of the leaf. The overall goal is to characterize the form and function of ECW in two closely related, but phenotypically divergent grasses. [italicized]Andropogon gerardii ssp. [italicized]gerardii, big bluestem, is a non-glaucous, agronomically and ecologically dominant grass in the United States while [italicized]Andropogon gerardii ssp. [italicized]hallii, sand bluestem, is a glaucous subspecies restricted to dry, sandy soils. The objectives are to contrast sand and big bluestem ECW chemistry, morphology, and physiology to determine the distinctions in ECW resulting in the glaucous phenotype and determine the effect this has on leaf optical qualities and permeability. Gas chromatography mass spectrometry (GC-MS) and scanning electron microscopy (SEM) were used to examine ECW chemistry and micromorphology. It was hypothesized that beta-diketones and beta-diketone tubules where present only in leaves of sand bluestem and that the ECW was more reflective and abundant and the cuticle was less permeable. Beta-diketones and tubular ECW were absent in big bluestem and common on sand bluestem’s surface, although less than 20% of ECW was beta-diketones. Functional implications of ECW phenotypes were investigated by comparing minimum conductance (G[subscript]min), wax load, reflectance, and transmittance. Reflectance, with and without ECW, and G [subscript]min were measured with an infrared gas analyzer and a spectroradiometer, respectively. Sand bluestem had twice the ECW in mg cm[superscript]2 (P=.01) and three times lower G [subscript]min in ms[superscript]-1 10[superscript]-5 (P=.02). Partial least squares (PLS) models were trained to predict subspecies from reflectance spectra and were able to distinguish the subspecies. These experiments indicate that in comparison to big bluestem, increased reflectance is a property uniquely imparted to sand bluestem by ECW and the presence of beta-diketones determines the distinction. Glaucous crop species have shown higher yield under drought and extreme weather, including drought, is expected to become more common. Therefore, this study of glaucous waxes, may be applied in engineering drought tolerance.

Label free detection of biologically relevant binding pairs has provided critical insight into the characterization of reagents used in both therapeutic and diagnostic applications. The Interferometric Reflectance Imaging Sensor (IRIS) platform has been developed for the multiplexed, real-time detection of such binding interactions. Improvements to experimental methodology and analysis applied to the latest iteration of the IRIS provided heretofore unseen binding characterizations with this multiplexed platform. Here, we extend and demonstrate the utility of the IRIS system to (1) evaluate and compare kinetic parameters to those obtained with more traditional label free methods (2) characterize multiple, disease relevant antibodies in multiple disease systems (anthrax, Zika, dengue and plague) (3) determine appropriate binding pairs in multiplexed label free formats and (4) obtain 10-fold improvements to the limits of detection for analyte in solution over previous IRIS iterations. Applications to immunoassay development are discussed throughout with exemplary datasets provided. Observations regarding additional IRIS utilities are also discussed, including qualifications of genetically engineered ligands, evaluating subcloned antibodies and screening unpurified antibody supernatants.

Metasurfaces, introduced as a compact 2D alternative of metamaterials, have developed into a vast field in recent times for light manipulation at an ultra-compact scale. Metasurface applications have found a place in the literature for compact alternatives to lens, holograms, polarizers, color filters. Plasmonic metasurfaces consisting of noble metals such as gold and silver provide light confinement on an unprecedented scale. Gold and silver grown conventionally on transparent substrates are polycrystalline, and exhibit losses and limit performance of the device. Moreover, these materials have a lower damage threshold and melting point. To circumvent the lower melting point and damage thresholds, new materials, and material growing techniques need to be researched. <br>In the first part of this work, a metasurface for color holography with an epitaxially grown silver thin film on a transparent substrate is shown. The demonstrated metasurface has been the first ever epitaxial silver metasurface that operated in the transmission mode. This plasmonic hologram has also been the thinnest metasurface hologram operating in transmission mode at the time of its reporting. The holographic image of all three basic color components of red, green, and blue has been demonstrated in the transmission mode. The control of color has been achieved by resonant sub-wavelength slits and the phase can be manipulated through altering slit orientation. This amplitude and phase control pave the way to applications of ultra-compact polychromatic plasmonic metasurfaces for advanced light manipulation. In the second part, we explore temperature rise due to the optical absorption in plasmonic structures. Titanium Nitride based metasurfaces structures are fabricated, that work in harsh environmental conditions and high temperature. A time domain thermo reflectance technique for rapid measurement of temperature is explored. Finally, a practical design prototype for thermo-photovoltaic (TPV) emitters using plasmonic metasurfaces is fabricated and characterized.<br><br>