This thesis describes work on a novel 3D imaging system that successfully implements optical feedback and noise rejection mechanisms. The system is a combination of three relatively new technologies, namely, holographic projection, Time of Flight (ToF) ranging and Single Photon Avalanche Diode (SPAD) sensors. Holographic projection is used to provide structured illumination with optical feedback instead of more commonly used uniform illumination in similar imaging systems. It is obtained using a Ferro-electric Liquid Crystal on Silicon Spatial Light Modulator (FLCoS SLM). The structured illumination with optical feedback can be operated at up to 60 Hz with the current device, and has been shown to provide an average gain of about 1.56 in useful light levels. Alternatively, a gain over a limited area of up to a factor of 9 is possible with the current system. Time of Flight ranging is a method of choice for the system when depth estimation is concerned. It works even at very low light levels and allows for sub-centimetre depth resolution. ToF method was implemented using 20 MHz laser diode with 50 ps pulse duration and 200 mW peak power, as well as a SPAD sensor. The SPAD sensor consisted of a 32 32 array of 50 μm pixels, each with 10 bit Time to Digital Converter (TDC) with 50 ps timing resolution. Sensor pixels feature 100 Hz mean Dark Count Rate (DCR). The use of SPAD sensors with an adaptive sensing algorithm presented in this work has been demonstrated to reduce effective noise levels as seen by the sensor by a factor of 16. As a result, a significant gain in depth resolution can be achieved. The quantification of this gain is explained in more detail within this work. Furthermore, the work describes in detail system design, methodology of experimental procedure as well as different algorithms essential to the correct operation of the system. Significant amount of time is dedicated to diffraction pattern generation for the use in holographic projection, as well as modelling of photon detection in SPAD sensors and associated peak detection necessary to extract depth information from histograms of timed of photons. Moreover, the thesis discusses potential applications for the system based on the results of system characterisation presented in this work. The current state of the system suggests best suitability for gaming and machine vision applications. Finally, the work offers potential solutions to the practical issues that remain unresolved in the current system, alternatives for components used and paths for potential future development of the system proposed.

archives@tulane.edu / Photoacoustic imaging functions via two foundations: light delivery and acoustic signal reception. In order for acoustic signal to be received and processed into an image, photons must first penetrate the tissue. However, biological media highly attenuates light, and the maximum imaging depth for photoacoustic images lies between 2-3 centimeters. Thus, models and simulations are integral to approach this problem, and they can be used to easily change imaging parameters and simulate various conditions. This study used a MATLAB Monte Carlo simulation algorithm to model and simulate a homogeneous placental tissue sample. The simulated data was compared to experimental ex vivo placental images taken under identical conditions of the simulation. These two data sets were used to gauge the simulation’s accuracy to predicting fluence trends in tissue, and the results were then applied to a heterogeneous tissue model simulating in vivo placental imaging. It was found that to maximize fluence in the placenta during in vivo imaging, 808 nm and 950 nm both offer different benefits to maximize fluence in the placenta. This simulation toolbox can be used to determine which experimental setup can maximize fluence in photoacoustic images, resulting in high-quality, high-contrast images. / 1 / Adam Kolkin

Dans cette thèse, on étudie l’interaction optomécanique dans les cavités des cristaux phoxoniques définis comme des cristaux à la fois photonique et phononique. Ces structures périodiques peuvent présenter simultanément des bandes interdites absolues pour les ondes électromagnétiques et pour les ondes acoustiques. L’introduction de défauts tels qu’une cavité dans le cristal permet d’obtenir à la fois des photons et des phonons localisés. Ce confinement simultané des deux excitations à l’intérieur d’une même cavité permet d’exalter leur interaction et d’envisager de nouveaux dispositifs acousto-optiques à l’échelle submicronique. Nous avons étudié théoriquement cette interaction optomécanique dans différentes structures de cristaux phoxoniques (2D, plaques et nanoguide structuré). Nous avons mis en évidence l’effet du changement du matériau et de la longueur d’onde incidente sur le couplage optomécanique. Les résultats pour le nanoguide structuré ont été comparés à des résultats expérimentaux réalisés par nos partenaires. Enfin, le couplage phonon-plasmon est abordé à la fois en terme de premiers résultats et de perspective. / In this thesis, we study optomechanic interactions in phoxonic crystals which are defined as dual phononic/photonic crystals that can exhibit simultaneously phononic and photonic band gaps. The existence of absolute band gaps allows the simultaneous confinement of both waves that, in turn, can produce the enhancement of their interaction for the purpose of novel and high-performance optomechanical and acousto-optic devices and applications. A main objective is the modulation of light by acoustic waves when both excitations are confined inside the same cavity or propagate with a slow group velocity inside a waveguide. We have studied theoretically the optomechanic interactions in different (2D, slabs and strip) phoxonic crystals cavities. We have demonstrated the dependence of these optomechanic interactions as a function of both the nature of the material and the incoming optical wavelength. The results for strip waveguides have been compared with experimental results performed by our partners. Finally, as a perspective, we began to study the phonon-plasmon coupling.

A new molecular imaging modality has been developed to detect and locate positive axillary and sentinel lymph nodes non-invasively in breast cancer patients undergoing lymphoscintigraphy. The modality is based on fluorescent photon detection to locate the presence of indocyanine green (ICG) in the lymph subsequent to peritumoral injection of ICG into the breast. The imaging system consists of a gain-modulated intensified charge-coupled device (ICCD) camera, which captures low-intensity, near-infrared, and frequency-modulated photons. A four-fold ‘optical lymphography’ study was conducted to (1) examine fluorescence depth penetration and ICCD system accuracy at clinically relevant depths, (2) compare image quality of the ICCD system vs. conventional gamma imaging, (3) measure ICG pharmacokinetics in vivo, and (4) develop a clinical protocol while examining pre-clinical factors such as the outcome of combining ICG with sulfur colloids used in lymphoscintigraphy. The frequency-domain ICCD system was found to precisely detect modulation amplitude, IAC, and phase, θ, at depths up to 9 cm and with IAC accuracy less than 20% and θ less than 2º using an 80-mW laser incident on phantoms having ranging tissue optical properties. Significant differences in the mean depth of penetration owing to 0.62-ns lifetime and 100-MHz frequency increases were detected. An in vivo optical vs. nuclear image quality comparison demonstrated statistically similar (α=0.05) target-to-background ratios for optical (1.4+/-0.3) and nuclear (1.5+/-0.2). Alternatively, resulting image signal-to-noise ratios (SNR) from the ICCD system were greater than that achieved with a conventional gamma camera (pvalue<<0.01). Analysis of SNR versus contrast showed greater sensitivity of optical over nuclear imaging for subcutaneous tumors. In vivo and rapid detection of ICG in the blood-stream of nude mice was accomplished with a home-built avalanche photodiode dynamic fluorescence measurement system. Intensity data upon i.v. injection were regressed with a pharmacokinetic model describing the partitioning of ICG from the blood to the surrounding tissues. ICG blood-clearance was detected approximately 15 min after injection. Lastly, a human subject protocol was written, practiced, and federally approved for the application of optical lymphography. Furthermore, ICG was unaffected when mixed with sulfur colloids thus supporting the feasibility for combining fluorescence imaging with lymphoscintigraphy in breast cancer patients.

This thesis represents a quantum chemical treatise ofvarious types of interactions between radiation and molecularsystems, with special emphasis on the nonlinear opticalprocesses of Multi-Photon Absorption and Excited StateAbsorption. Excitation energies, transition dipole moments,two-photon and three-photon tensor elements have beencalculated from different approaches; density functional theoryandab-initiotheory, employing different orders ofcorrelation treatment with the purpose to provide accuratevalues as well as evaluate the quality of the lower ordermethods. A combined study of the Multi-Photon Absorption andExcited State Absorption processes is motivated partly becausethey both contribute to the total optical response of a systemsubjected to intense radiation, but also because of theirconnection through so-called sum-over-states expressions. Thelatter feature is exploited in a generalized few-states model,which incorporates the polarization of the light and thedirections of the transition dipole moments constructing anexcitation channel, which thereby enables a more comprehensivecomparison of the attained transition dipole moments withexperimental data. Moreover, by decomposing a complex nonlinearresponse process such as Two-Photon Absorption into moreintuitive quantities, generalized few-states models may alsoenable a more elaborate interpretation of computed orexperimental results from which guidelines can be extracted inorder to control or optimize the property of interest. Ageneral conclusion originating from these models is that thetransition dipole moments in an excitation channel should bealigned in order to maximize the Two-Photon Absorptionprobability. The computational framework employed is responsetheory which through the response functions (linear, quadratic,cubic) offers alternative routes for evaluating the propertiesin focus; either directly and untruncated through the singleresidue of the quadratic or cubic response func- tions orthrough various schemes of truncated sum-over-statesexpressions where the key ingredients, transition dipolemoments, can be identified from the single residue of thelinear response function and double residue of the quadraticresponse function. The range of systems treated in the thesisstretches from diatomics, such as carbon monoxide and lithiumhydride, via small to large fundamental organic molecules, suchas formaldehyde, tetrazine and the trans-polyenes, to largechro- mophores, such astrans-stilbene, cumulenes, dithienothiophene,paracyclophane and organo-metallic systems, such as theplatinum(II)ethynyl compounds. / QC 20120320

Astrocytes, the major type of non-neuronal cells in the brain, play an important functional role in the brains extracellular potassium (K+) and pH homeostasis. Pathological brain states have been shown to cause astrocyte swelling. However, these volume changes have never before been verified to occur in response to physiological activity. In the present thesis, two-photon laser scanning microscopy was used to visualize real-time astrocyte volume changes in the stratum radiatum of the CA1 region of the hippocampus. Astrocyte somas and primary processes were observed to swell by 19.0±0.9% in response to a physiological (3 mM) increase in the concentration of extracellular K+. Astrocyte swelling was partially mediated by K+ influx through inwardly rectifying K+ channels (Kir), as their inhibition resulted in a significant decrease of the increased K+ induced astrocyte swelling (13.9±0.9%). In addition, the bicarbonate ion (HCO3-) was found to play a significant role in the increased K+ induced astrocyte swelling. The astrocyte swelling was significantly decreased when the influx of HCO3- was decreased in 1) a HCO3- free extracellular solution (5.4±0.7%), 2) in the presence of an extracellular carbonic anhydrase inhibitor (11.4±0.6% ), and 3) when the activity of the sodium-bicarbonate cotransporter (NBC) was blocked (8.3±0.7%) . Conversely, astrocytes were found to shrink by 7.7±0.5% in response to ã-Amino-butyric Acid (GABA) receptor activation. GABAA receptor mediated astrocyte shrinkage was significantly decreased to 5.0±0.6% when HCO3- efflux was reduced. Furthermore, in this thesis it was shown for the first time that astrocytes swell in response to neuronal stimulation (4.0±0.4%). This activity induced astrocyte swelling was significantly decreased to 1.5±0.2% in a HCO3- free extracellular solution. These astrocyte volume changes may have important implications for the regulation of brain activity under both physiological and pathological brain states.

Esta tesis presenta la medida de la sección eficaz de producción de fotones inmediatos con |η|<1.0, pT > 30 GeV y asilamiento < 2 GeV usando 2.5 fb-1 de datos tomados por el detector CDF entre febrero de 2002 y agosto de 2007. La medida incluye 6 veces más datos que el último resultado publicado al momento de su realización, extendiendo el rango de pT cubierto por la misma en 100 GeV. La sección eficaz se mide para fotones de hasta 400 GeV, y testea las predicciones teóricas sobre 6 órdenes de magnitud, un orden de magnitud más que en resultados previos. La medida de la sección eficaz de fotones inmediatos ofrece una oportunidad única para poner a prueba las técnicas de indentificación de fotones en Física de Altas Energías. En esta tesis, presentamos una nueva técnica para suprimir el ruido de fondo irreducible que viene de los fotones producidos por la desintegracion de mesones. El método consiste en ajustar la variable de aislamiento energetico del fotón en el calorímetro a la suma de las formas esperadas (templates) para esta variable para la señal y para el ruido de fondo, en diferentes rangos en el momento transverso del fotón. El método de las templates es simple y está basado únicamente en información del calorímetro. Además, reduce significativamente el error sistemático asociado con la pureza de los fotones. En medidas previas durante el Run I de CDF se emplearon técnicas basadas en la información de los detectores CES y CPR, resultando en errores sistemáticos y estadísticos de considerable magnitud. Con el método introducido en esta tesis, el error sistemático en la pureza de los fotones se reduce desde el 30% de las medidas previas durante el Run I, a un 5% a alto pT de los fotones. Con la mejora de las simulaciones de Monte Carlo, el método de las templates tiene el potencial de convertirse en una poderosa herramienta para futuras búsquedas de nueva física usando estados finales con fotones. En esta medida, los datos se comparan con predicciones teóricas dadas por JETPHOX, con CTEQ6.1M PDF, funciones de fragmentación BFGII, y las escalas de renormalización, fragmentación y factorización fijadas para igualar el momento transverso del fotón. Los datos se corrigen por efectos de acceptancia y de resolución del detector, así como por ineficiencias en el proceso de identificación de los fotones, usando muestras simuladas de fotones inclusivos con PYTHIA. Este procedimento se denomina unfolding. Los factores derivados del unfolding no presentan una dependencia fuerte con el pT del fotón, y varían entre un 64% y un 69% en todo el rango de pT considerado. Las predicciones teóricas están corregidas para tener en cuenta los efectos no perturbativos, no considerados inicialmente en los cálculos teóricos. Los errores sistemáticos en la medida son el orden del 13% a bajo pT, dominados por las incertidumbres en la determinación de la fracción de fotones reales, mientras a alto pT son del orden de un 15%, mayormente debidos a la incertidumbre en la escala de energías del fotón. Las incertidumbres en la teoría son debidas a la incertidumbre en las PDF, de un 5% bajo pT, pero que se incrementa hasta llegar a un 15% a alto pT. La dependencia en las predicciones debido a la particular elección en las escalas es de un 15% a bajo pT, decreciendo hasta un 8% a alto pT. Los resultados muestran que la teoría describe bien los datos para fotones por encima de 40 GeV. En el rango hasta 150 GeV, la producción de fotones inmediatos está dominada por el proceso Compton de QCD, mientras que para pT más altos los gluones contribuyen substancialmente a la sección eficaz, y la medida es útil para imponer límites en las PDF de los gluones. Para pT < 40 GeV los datos están por encima de las predicciones, reproduciendo las tendencias ya observadas anteriormente en otras medidas, tanto en colisionadores como en experimentos de blanco fijo. Ésta es por tanto, probablemente debida no sólo a los efectos sistemáticos en la técnica experimental empleada, sino que encierran efectos físicos que no han sido tenidos en cuenta en los cálculos teóricos. La comparación de los datos con predicciones obtenidas usando la parametrización MRST04 para las PDF resulta en resultados similares, tanto en forma como en magnitud, a los obtenidos con CTEQ6.1M. El cuociente data sobre teoría tiene un comportamiento similar en ambos para fotones de bajo pT, aunque en la totalidad del rango considerado ambas tienen una pendiente ligeramente distinta. La medida está aprobada por la Colaboración de CDF y se ha mostrado en numerosas conferencias internacionales. Los resultados han sido publicados en Physics Review D. / This thesis presents the measurement of the inclusive photon cross section for photons with |!|<1.0, pT > 30 GeV and isolation < 2 GeV using 2.5 fb-1 of data taken by the CDF detector between February 2002 and August 2007. This measurement includes 6 times more data than the last published result, extending its pT coverage by 100 GeV. The cross section is measured up to 400 GeV, and tests the theoretical predictions over 6 orders of magnitude, one order of magnitude more than in previous results. The prompt photon cross section measurement offers a unique opportunity to test the photon identification variables over a large energy range. In this thesis we present a new technique to suppress the irreducible isolated photons from meson decays. The method consists of fitting the calorimeter isolation distribution in the data to pure signal and background templates for every bin in the photon pT. The template method is simple and is based only on the information from the calorimeter. Moreover, it significantly reduces the systematic uncertainty associated to the photon purity. Previous CDF Run I measurements used techniques based on the information collected by the CES and the CPR detectors, which have considerable statistical dilution and systematics. With the method introduced in this thesis, the systematic uncertainty in the photon purity is reduced from 30% in the previous CDF Run I measurements to 5% at high pT. With the improvement of the Monte Carlo simulations, the template method has the potential to become a powerful tool for future searches using photon signatures. In this measurement, the data are compared to theoretical predictions given by JETPHOX using CTEQ6.1M PDF, BFGII fragmentation functions, and renormalization, fragmentation and factorization scales set to equal the transverse momentum of the photon. Data are unfolded back to hadron level to correct for efficiencies and detector acceptance and resolution using a bib-by-bin unfolding procedure implemented in a PYTHIA inclusive photon Monte Carlo sample. The unfolding factors do not present a strong dependence on the photon pT, and vary between 64% and 69% in the range considered. The theoretical predictions are corrected for non-perturbative QCD effects. The systematic uncertainties in the measurement are of 13% at low pT, dominated by the signal fractions, while at high pT they are of about 15%, mainly coming from the photon energy scale. The uncertainties in the theory are due to the PDF, of around 5% at low pT and increasing to 15% at high pT. The dependence left in the prediction due to the choice of the scales is of 15% ay low pT and decreases to around 8% at high pT. We find agreement between data and theory above 40 GeV. In the pT range until 150 GeV, the prompt photon production is dominated by the QCD Compton process, while for higher pT gluons substantially contribute to the prompt photon production, though they are not the dominant source, and the measurement is useful to constrain the gluon PDF. For pT < 40 GeV the data falls above the theory, reproducing a trend already seen in previous measurements, both in colliders and fixed-target experiments, and it is probably not only due to systematic effects in the experimental method but more likely to other physics effects that are not accounted for in the theoretical calculations. The comparison to the predictions obtained using the MRST04 parameterization for the PDF is in agreement with the results obtained with CTEQ6.1M for the whole measured range. The ratio data over theory has a similar shape for both for low pT photons, though in the whole pT range the ratio presents a slightly different slope. The measurement is approved by the CDF Collaboration and has been shown in a large number of international conferences. The results have been also published as a rapid communication in Physics Review D.

Astrocytes, the major type of non-neuronal cells in the brain, play an important functional role in the brains extracellular potassium (K+) and pH homeostasis. Pathological brain states have been shown to cause astrocyte swelling. However, these volume changes have never before been verified to occur in response to physiological activity. In the present thesis, two-photon laser scanning microscopy was used to visualize real-time astrocyte volume changes in the stratum radiatum of the CA1 region of the hippocampus. Astrocyte somas and primary processes were observed to swell by 19.0±0.9% in response to a physiological (3 mM) increase in the concentration of extracellular K+. Astrocyte swelling was partially mediated by K+ influx through inwardly rectifying K+ channels (Kir), as their inhibition resulted in a significant decrease of the increased K+ induced astrocyte swelling (13.9±0.9%). In addition, the bicarbonate ion (HCO3-) was found to play a significant role in the increased K+ induced astrocyte swelling. The astrocyte swelling was significantly decreased when the influx of HCO3- was decreased in 1) a HCO3- free extracellular solution (5.4±0.7%), 2) in the presence of an extracellular carbonic anhydrase inhibitor (11.4±0.6% ), and 3) when the activity of the sodium-bicarbonate cotransporter (NBC) was blocked (8.3±0.7%) . Conversely, astrocytes were found to shrink by 7.7±0.5% in response to ã-Amino-butyric Acid (GABA) receptor activation. GABAA receptor mediated astrocyte shrinkage was significantly decreased to 5.0±0.6% when HCO3- efflux was reduced. Furthermore, in this thesis it was shown for the first time that astrocytes swell in response to neuronal stimulation (4.0±0.4%). This activity induced astrocyte swelling was significantly decreased to 1.5±0.2% in a HCO3- free extracellular solution. These astrocyte volume changes may have important implications for the regulation of brain activity under both physiological and pathological brain states.

Coherent control of laser induced processes is based on the quantum interference among multiple excitation pathways. Progress in the field has been fueled by advances in pulse shaping techniques, allowing modulation of phase and amplitude across the bandwidth of ultra short pulses. This dissertation makes use of coherent control technique for the optimization of two-photon fluorescence (TPF) and its applications in selective excitation for biomedical imaging. Different physical processes, e.g. TPF, second harmonic generation (SHG) and their ratios (e.g. TPF/SHG) were optimized by using feedback control pulse shaping technique with an evolutionary algorithm. Various nonlinear effects, e.g. filamentation, intensity clamping and white light generation were studied using two-photon fluorescence and Z-scan technique with different dyes and biomarkers. Simultaneous measurements of different nonlinear effects were performed. Novel methods were proposed and implemented to obtain two-photon excitation characteristics in intensity-resolved manner. Understanding of these nonlinear effects can give new solution to the issues of spatial resolution and molecular contrast for cellular and tissue imaging.

The techniques of optical beam induced current (OBIC) have found wide-spread applications in characterizing many semiconductor and optoelectronic devices. A two-photon confocal microscope is adapted for investigating the dynamics of light emitting devices through the contrast mechanisms of two-photon DC and radio frequency (RF) optical beam induced current (OBIC). For comparison, the 2p-OBIC technique detects the photocurrent signal by exciting the semiconductor sample with a pulsed laser that has a wavelength below the bandgap of the semiconductor. It has high accuracy and spatial resolution. We demonstrate that the bias on the devices (forward and reverse) strongly modifies the DC and RF OBIC signals. Finally we will discuss how to explain this result, and we will provide a program to show the phase distribution of GaP LED.