Multispectral imaging has been used for decades in remote sensing to enhance the classification, discrimination and characterization of materials. Only recently has this same technology been similarly applied to fixed biological samples in cytogenetics, pathology and medicine. A further extension to in vivo studies is often limited by the low levels of associated fluorescence as well as the increased temporal resolution required to analyze physiological changes. In addition, the cellular response to a specific agonist is often heterogeneous across the cellular field requiring a combination of sufficient spatial and temporal resolutions. A computed tomography imaging spectrometer (CTIS) has been developed which overcomes these limitations by simultaneously collecting extended range spectral information (470-740 nm, 5 nm sampling) across a 2-D field of view (200 μm x 200 μm, 0.96 μm sampling). The CTIS uses a computer generated hologram to produce a 5 x 5 array of images with differing amounts and directions of dispersion. This set of images allows the 3-D signal (x, y, λ) from a fluorescent sample to be mapped onto a 2-D detector array. In this way, the full spectral and spatial information is acquired for a 2-D cellular field during a single integration time (presently 2 sec for biological specimens). The CTIS's design, calibration, and underlying theory are described in detail. In addition, the capability of the CTIS to simultaneously collect the fluorescence emission of multiple fluorophores across a 2-D cellular field is demonstrated. Specifically, the combined spectral variations of seminapthorhodafluor-I and enhanced green fluorescent protein were followed in rat insulinoma cells in order to extend the linear range of intracellular pH detection.

Recent advances in model observers that predict human perceptual performance now make it possible to optimize medical imaging systems for human task performance. We illustrate the procedure by considering the design of a lens for use in an optically coupled digital mammography system. The channelized Hotelling observer is used to model human performance, and the channels chosen are differences of Gaussians (DOGs). The task performed by the model observer is detection of a lesion at a random but known location in a clustered lumpy background mimicking breast tissue. The entire system is simulated with a Monte Carlo application according to the physics principles, and the main system component under study is the imaging lens that couples a fluorescent screen to a CCD detector. The SNR of the channelized Hotelling observer is used to quantify the detectability of the simulated lesion (signal) upon the simulated mammographic background. In this work, plots of channelized Hotelling SNR vs. signal location for various lens apertures, various working distances, and various focusing places are shown. These plots thus illustrate the trade-off between coupling efficiency and blur in a task-based manner. In this way, the channelized Hotelling SNR is used as a merit function for lens design.

High sensitivity grating interferometry has become an important method in experimental mechanics to measure, with submicron sensitivity, the in-plane displacements of nearly flat objects under load. This study looks to extend the use of this interferometric setup through specific modifications to the interferometric setup, focusing specifically on developing the system's ability to register simultaneously both the in-plane and out-of-plane displacements so that dynamic events may be examined with great precision and speed. First presented is the author's approach for mapping in- and out-of-plane displacements through modifications to a conventional grating interferometer. Then, the author extends the method to the analysis of dynamic events, proposing a few workable solutions for registering two interferograms at the same time. Included in this discussion are suggestions for acquiring the orthogonal in-plane displacements u and v and the out-of-plane displacement w simultaneously. The second part of the work details the analysis of different phase measurement techniques, focusing on the error sources inherent in each approach. New, error-reducing algorithms are presented and the influence of the intensity sample weighting (window function) on phase errors is described. A spatial, phase measurement technique advanced by the author, the M-point technique, is chosen as the best choice for achieving fast analysis and high accuracy in displacement testing in the modified grating interferometric setup.

A broadband, multichannel, single mode, planar waveguide based ATR spectrometer was developed. A sensitivity enhancement of three orders of magnitude compared to the conventional transmission spectroscopic technique has been experimentally achieved. Applications to protein submonolayers adsorbed on glass surfaces provided the first results on the spectral characterization of those molecular films. The increased information content and the higher sensitivity response allowed us to experimentally determine the molecular orientation of organic films over a broad spectral range. The work developed here is a research tool that allows the investigation of some fundamental problems of molecular assemblies and a platform to develop new technological devices of high sensitivity and selectivity, such as biosensors.

A physical model developed from scattering theory by Hapke was applied to bidirectional reflectance factor (BRF) measurement data for several diffuse reflecting materials. All of the material samples were some form of polytetrafluoroethelyne (PTFE) powder. The solar illuminated diffuser for the Moderate Resolution Imaging Spectroradiometer (MODIS) was one of the samples. The BRF was characterized in seven wavelength bands, covering a spectral range of 400 nm to 2100 nm. The BRFs were determined, using the Santa Barbara Remote Sensing (SBRS) scattering goniopolarimeter, by measuring all four linear polarization components and using those measurements in the BRF equations of Clarke. The scattering goniopolarimeter was carefully characterized in a series of measurements. It was calibrated by comparing BRF measurements to the BRF calibration values of a reflectance standard. A detailed error analysis was done. The uncertainties for each of the four polarization components was considered individually, and then combined to obtain the total estimated uncertainty in the BRF values. The mean-square errors of the measured BRF sample averages were compared to the estimated uncertainties. Results of BRF evaluations and the measurement uncertainties for the different diffusers are presented. A study of several variations of the Hapke scattering model was made. The models were successfully applied to each of the four polarization components of BRF, in addition to the unpolarized BRF. The quality of the models was evaluated using the "root-mean-square of the fit" merit function, RMSf The simplest Hapke model gave RMSf values from two percent down to less than one percent, but the vegetation canopy form of the Hapke model gave higher RMSf values, from six to ten percent. The Henyey-Greenstein single scattering phase function, even when used in the simplest Hapke model, gave RMSf values between two and eight percent, whereas Legendre polynomial phase functions resulted in RMSf values of less than one percent. Equations with an additional forward scatter term usually made a slight improvement, on the order of one to two tenths of a percent. To obtain a representative model, at least two sets of BRF data at different incidence angles were needed.

This paper describes the development, characterization, and modeling of a Tunable Filter Camera (TFC). The TFC is a new multispectral instrument with electronically tuned spectral filtering and low-light-level sensitivity. It represents a hybrid between hyperspectral and multispectral imaging spectrometers that incorporates advantages from each, addressing issues such as complexity, cost, lack of sensitivity, and adaptability. These capabilities allow the TFC to be applied to low-altitude video surveillance for real-time spectral and spatial target detection and image exploitation. Described herein are the theory and principles of operation for the TFC, which includes a liquid crystal tunable filter, an intensified CCD, and a custom apochromatic lens. The results of proof-of-concept testing, and characterization of two prototype cameras are included, along with a summary of the design analyses for the development of a multiple-channel system. A significant result of this effort was the creation of a system-level model, which was used to facilitate development and predict performance. It includes models for the liquid crystal tunable filter and intensified CCD. Such modeling was necessary in the design of the system and is useful for evaluation of the system in remote-sensing applications. Also presented are characterization data from component testing, which included quantitative results for linearity, signal to noise ratio (SNR), linearity, and radiometric response. These data were used to help refine and validate the model. For a pre-defined source, the spatial and spectral response, and the noise of the camera, system can now be predicted. The innovation that sets this development apart is the fact that this instrument has been designed for integrated, multi-channel operation for the express purpose of real-time detection/identification in low-light-level conditions. Many of the requirements for the TFC were derived from this mission. In order to provide background for the design requirements for the TFC development, the mission and principles of operation behind the multi-channel system will be reviewed. Given the combination of the flexibility, simplicity, and sensitivity, the TFC and its multiple-channel extension can play a significant role in the next generation of remote-sensing instruments.

In this dissertation, we offer a novel phase-shifting interferometer/ellipsometer. The uniqueness arises from the fact that this study is the consolidation of four distinct ideas drawn from the field of optics and the field of statistics. A conventional four-step phase-shifting interferometer is modified to allow for both TE and TM polarized measurements. Maximum-likelihood estimation theory is then used to extract the three parameters of interest, namely the real and imaginary components of the complex index of refraction and the surface profile. Finally, Cramer-Rao lower bounds serve as a quantitative means of assessing the particular system design at the task of estimating the three parameters in question. As we will show, the unknown parameters n, k and h are related to the measured irradiance in a complicated, nonlinear way. As such, no analytical expressions to estimate the unknown parameters from the measured data have been found. Rather, the unknown parameters are found numerically through a minimization program, developed and optimized specifically for this task. The results from our Monte Carlo simulations will show that conventional designs such as the Twyman-Green interferometer perform poorly at reconstructing n, k and h. The estimates on n and k exhibit bias, where the mean is not equal to the true value, and are non-efficient, where the standard deviation is greater than the Cramer-Rao lower bound. While the estimate of h is unbiased and efficient, the performance is an order of magnitude worse than the case where only h is to be estimated. By incorporating tilt in the design, the performance on all three parameters improves considerably. The estimates on n and k are shown to be unbiased and efficient, and the performance of the h estimator is equivalent to the h-only case. The dissertation culminates with the development of a Mach-Zehnder prototype. We demonstrate the feasibility of the proposed technique, and show how three system parameters, namely the incident amplitude and the relationship between the TE and TM polarized light in terms of amplitude and phase, affect the performance. We also show how quantization of the measured irradiance affects the performance.

The goal of this dissertation is the derivation of a differential equation that describes the evolution of an electromagnetic field in a stable cavity that has no axial symmetry (a toroidal system). The approach uses concepts from the theory of Lie groups and Lie algebras. Since the mathematics may be unfamiliar to the general reader, before the derivation for toroidal systems is executed, the differential equation for an optical system with radial symmetry will be derived using the general mathematical approach. After some of the theorems and formalisms associated with toroidal systems are presented, a description of general toroidal systems and their actions on electromagnetic fields will be presented. The action of systems on electromagnetic fields will be shown to be a linear representation of a group (locally). Having established the preliminaries, the differential equation can be derived. The desired differential equation is derived in three steps. In the first step, a set of differential operators that appear in a simplified equation are derived by recognizing them as the basis of a Lie algebra representation associated with the local linear representation on electromagnetic fields. In the second step, coefficients for the reduced problem are derived. Finally, the complete differential equation is presented. Algorithms that allow one to implement the above results will be presented. These algorithms will be used to execute a computation in a numerical example. By way of verification, it will be shown that the results of this dissertation subsume previous work in several ways including the structure of modes in stable toroidal cavities and the prediction of angular momentum.

A novel line of integrated-optic-based chemical sensors was developed. The sensors are based on modification of the optical cavity of a single-mode semiconductor distributed Bragg reflector (DBR) laser. A sensitive layer changes its refractive index in presence of a specific chemical, thus changing the effective refractive index of the section and the optical length of the cavity. This results in laser frequency shift measured either directly or by heterodyne detection using a reference laser as the second source. It is shown that DBR-laser-based sensors can achieve in principle a much higher sensitivity than passive sensors, such as Mach-Zehnder interferometers, due to the narrow linewidth of DBR lasers. The theory of DBR-laser-based sensors is described. It allows optimizing the sensitive section length and field confinement in the sensitive layer for the lowest detection limit. The optimum parameters depend on cavity losses and absorption of the sensitive material. Numerical modeling shows a wide acceptable range of sensitive section parameters for low-loss materials, while for higher-loss materials this range becomes much narrower. Narrow-linewidth DBR lasers are required for high sensitivity. In this respect, sol-gel waveguides with and without Bragg grating were incorporated in the DBR laser scheme. Single-mode operation of DBR lasers with sol-gel waveguide gratings was demonstrated for the first time, with 34-dB side mode suppression and a short-term linewidth of 150 to 500 kHz. A 3-section configuration with sol-gel waveguides and fiber grating showed 28-dB side mode suppression and a short-term linewidth of 600 kHz. Chemical sensing was performed with fiber grating, sol-gel waveguide grating, and 3-section DBR lasers. The first two types showed frequency shift of over 130 MHz in the presence of acetone vapors, and reversibility within experimental errors. The 3-section scheme showed significant dispersion of response and lack of reversibility due to parasitic reflections and instability of the setup. The effect of reflections from facets on performance of this design was examined and found to reduce the maximum sensitivity.

Despite the many advances and achievements in the fields of atom optics and atom cooling, there remains a wealth of dynamical detail to be filled in. While the main features of the important phenomena of atomic cooling, trapping and manipulation by electromagnetic fields are well understood, there are interesting subsidiary effects that are worth our attention. An example, which we discuss in Ch. 5 is the discovery that atomic diffusion in optical lattices may not follow the normal diffusion equation. The work reported in this dissertation represents an investigation into possible few-body effects in some atom optical configurations of interest. The effects of indistinguishability, through the exchange force, on atomic diffraction by standing wave light fields is considered in Ch. 2. In Ch. 3, after a brief overview of atomic collisions in light fields, we look at the role that the dipole-dipole interaction might play, again in atomic diffraction. Chapters 4 and 5 are concerned with optical lattices, and lay the ground work for a study of the effect of the dipole-dipole interaction on the dynamics of atoms confined in such lattices.