A Computed Tomographic Imaging Spectrometer (CTIS) is an imaging spectrometer which can acquire a hyper-spectral data set in a single snapshot (one focal plane array integration time) with no moving parts. A specially designed dispersing element, which separates light from the three-dimensional object cube into a grid of two-dimensional prismatic diffraction orders, is the key element in the instrument. The capabilities of the CTIS instrument can be improved by employing a more optimized grating design.There were two main goals to this research: (1) to design a novel CTIS disperser that will improve CTIS capabilities over the previous 5x5 disperser and (2) to integrate the new disperser into the CTIS and evaluate its performance compared to the 5x5 disperser. Six new disperser ideas were evaluated based on their performance in a number of computer simulations to determine the most optimal dispersion pattern. A new CTIS disperser incorporating a novel radial design pattern was developed and tested. Reconstruction results of various spatial and spectral targets are presented. Capabilities of the new CTIS instrument incorporating the radial grating are compared to the previous instrument employing a 5x5 disperser. While both dispersers perform similarly for point-source objects, the radial grating performs better than the previous disperser for extended sources.

Large optical systems fabrication is a demanding task due to the tight requirements and big scales. To make mirrors up to 8.4m in diameter necessitates technological development in materials, tooling, and metrology. These advancements are designed to not only produce optics on a near-unheard of scale, but to improve fabrication methods with each piece.For an optical surface to be properly polished, the amount of material removed during polishing must be greater than the volume of damage left behind by the grinding process. Mixed-mode grinding, which combines bound abrasives with a compliant binder material, is a valuable tool at this stage as it creates less damage while maintaining a fast and uniform cutting rate than traditional loose abrasive grinding.These materials are challenging for large optical surfaces due to the honeycomb structures used to lightweight the mirrors. Development is done to adapt the abrasive to handle the very low pressures and speeds required to avoid imprinting structure on the optical surface.We take a comprehensive approach in measuring mixed-mode behavior using 3M Trizact™. Prior works on bound abrasives have focused on specific properties: removal rates, subsurface damage, etc. None have yet to look at the entire scope of the material and its benefits. These properties will be analyzed along with different behaviors regarding surface scattering, Twyman effect bending moments, glazing, manufacturing expenses, and failure mechanisms. This comprehensive understanding of the abrasive allows manufacturers to create better grinding schedules and reduce overall expenses in fabrication.Trizact shows up to a three times faster removal rate while producing 30\% less subsurface damage than loose abrasives of similar size. Additionally, the surface has scatters less light which can be adapted through changes in processing to create a specular reflection for optical surface metrology.Based on our findings, this type of abrasive integrates into current optical fabrication processes as a pre-polishing material. Here, the transition to these abrasives becomes cost effective by rapidly eliminating damage created during the generating of the surface and reducing the amount of polishing required.

We present a new method for determining the complete set of patient-specific ocular parameters, including surface curvatures, asphericities, refractive indices, tilts, decentrations, thicknesses, and index gradients. The data consist of the raw detector outputs of one or more Shack-Hartmann wavefront sensors (WFSs); unlike conventional wavefront sensing, we do not perform centroid estimation, wavefront reconstruction, or wavefront correction. Parameters in the eye model are estimated by maximizing the likelihood. Since a purely Gaussian noise model is used to emulate electronic noise, maximum-likelihood (ML) estimation reduces to nonlinear least-squares fitting between the data and the output of our optical design program. Bounds on the estimate variances are computed with the Fisher information matrix (FIM) for different configurations of the data-acquisition system, thus enabling system optimization. A global search algorithm called simulated annealing (SA) is used for the estimation step, due to multiple local extrema in the likelihood surface. The ML approach to parameter estimation is very time-consuming, so rapid processing techniques are implemented with the graphics processing unit (GPU).We are leveraging our general method of reverse-engineering optical systems in optical shop testing for various applications. For surface profilometry of aspheres, which involves the estimation of high-order aspheric coefficients, we generated a rapid ray-tracing algorithm that is well-suited to the GPU architecture. Additionally, reconstruction of the index distribution of GRIN lenses is performed using analytic solutions to the eikonal equation. Another application is parameterized wavefront estimation, in which the pupil phase distribution of an optical system is estimated from multiple irradiance patterns near focus. The speed and accuracy of the forward computations are emphasized, and our approach has been refined to handle large wavefront aberrations and nuisance parameters in the imaging system.

A fiber filter spectrometer (FFS) is a novel imaging spectrometer design concept which uses the proximity filter method to create small, lightweight, and cost effective instruments with no detectable spectral crosstalk. An FFS sensor is created by coating the ends of a fiber optic image guide (FIG) with a spectral filter, the FIG is then coupled to a detector array. Using the FIG as the spectral filter substrate reduces the optical crosstalk to the point that it is inconsequential. This work describes the modeling, fabrication, and calibration of a hyperspectral FFS sensor. The image and spectral quality performance metrics are successfully predicted by the FFS model. The laboratory calibration of the instrument validates that the FIG has no substantial impact on the instrument image quality and spectral performance. The FFS concept eliminates the potential for spectral crosstalk and provides the advantages of a less complex imaging spectrometer instrument design with low mass and volume.

In this work, image processing algorithms are presented for an advanced sensor classification known collectively as imaging modulated polarimetry. The image processing algorithms presented are novel in that they use frequency domain based approaches, in comparison to the data domain based approaches that all previous algorithms have employed. Under the conditions on the data and imaging device derived in this work, the frequency domain based demodulation algorithms will optimally reduced reconstruction artifacts in a least squared sense. This work provides a framework for objectively comparing polarimeters that modulate in different domains (i.e. time vs. space), referred to as the spectral density response function. The spectral density response function is created as an analog to the modulation transfer function (or the more general transfer function for temporal devices) employed in the design of conventional imaging devices. The framework considers the total bandwidth of the object to be measured, and then can consider estimation artifacts that arise in both time and space due to the measurement modality that has been chosen. Using the framework for objectively comparing different modulated polarimeters (known as the spectral density response function), a method of developing a Wiener filter for multi-signal demodulation is developed, referred to as the polarimetric Wiener filter. This filter is then shown to be optimal for one extensive test case. This document provides one extensive example of implementing the algorithms and spectral density response calculations on a real system, known as the MSPI polarimeter. The MSPI polarimeter has been published extensively elsewhere, so only a basic system description here is used as necessary to describe how the methods presented here can be implemented on this system.

Signal formation in a photon-counting x-ray/gamma-ray imaging detector is a complex process resulting in detector signals governed by multiple random effects. Recovering maximum possible information about event attributes of interest requires a systematic collection of calibration data and analysis provided by estimation theory. In this context, a likelihood model provides a description of the connection between the observed signals and the event attributes. A quantitative measure of how well the measured signals can be used to produce an estimate of the parameters is given by Fisher Information analysis. In this work, we demonstrate several applications of the Fisher Information Matrix (FIM) as a powerful and practical tool for investigating and optimizing potential next-generation x-ray/gamma-ray detector designs, with an emphasis on medical-imaging applications. Using FIM as a design tool means to explore the physical detector design choices that have a relationship with the FIM through the likelihood function, how are they interrelated, and determining whether it is possible to modify any of these choices to yield or retain higher values for Fisher Information. We begin by testing these ideas by investigating a new type of a semiconductor detector, a Cadmium Telluride (CdTe) detector with double-sided-strip geometry developed by our collaborators at the Japan Aerospace Exploration Agency (JAXA). The statistical properties of the detector signals as a function of interaction positions in 3D (x, y, z) are presented with mathematical expressions as well as experimental data from measurements using synchrotron radiation at the Advanced Photon Source at Argonne National Laboratory. We show the computation of FIM for evaluating positioning performance and discuss how various detector parameters, that are identified to affect FIM, can be used in detector optimization. Next, we show the application of FIM analysis in a detector system based on multi-anode photomultiplier tubes coupled to a monolithic scintillator in the design of smart electronic read-out strategies. We conclude by arguing that a detector system is expected to perform the best when the hardware is optimized jointly with the estimation algorithm (simply referred to as the "software" in this context) that will be used with it. The results of this work lead to the idea of a detector development approach where the detector hardware platform is developed concurrently with the software and firmware in order to achieve optimal performance.

A compact multi-photon microscope (MPM) was designed and developed with the use of low-cost mode-locked fiber lasers operating at 1040nm and 1560nm. The MPM was assembled in-house and the system aberration was investigated using the optical design software: Zemax. A novel characterization methodology based on 'nonlinear knife-edge' technique was also introduced to measure the axial, lateral resolution, and the field curvature of the multi-photon microscope's image plane. The field curvature was then post-corrected using data processing in MATLAB. A customized laser scanning software based on LabVIEW was developed for data acquisition, image display and controlling peripheral electronics. Finally, different modalities of multi-photon excitation such as second- and third harmonic generation, two- and three-photon fluorescence were utilized to study a wide variety of samples from cancerous cells to 2D-layered materials.

The growing field of high-order aspheric and freeform optical fabrication has inspired the creation of optical surfaces and systems which are difficult to align. Advances in optical alignment technology are critical to fabricating and integrating aspheric components in advanced optical systems. This dissertation explores the field of optical alignment with a computer-generated hologram (CGH) used as a reference. A CGH is a diffractive optic which may be used to create a desired phase profile across a beam of light, project irradiance patterns, or serve as a mask for an incident beam. The alignment methods presented in this dissertation are concerned with the use of a CGH to create reference phase profiles, or "wavefronts" , in a beam. In one application a set of axisymmetric CGH references are co-aligned. Each CGH has also been aligned to an aspheric mirror so the co-alignment of the CGH references is also a co-alignment of the aspheric mirrors. Another application is concerned with aligning an interferometer to test an aspheric mirror surface. The interferometer measures a "null" interference pattern when its wavefront accommodates a known surface profile. In this alignment application the CGH creates wavefronts which accommodate a known set of small spherical reference features at the test surface. An interference null from all the "phase fiducial" reference features indicates an aligned projection of the CGH. The CGH co-alignment method is implemented on a 4-mirror prime focus corrector known as the Hobby-Eberly Telescope Wide Field Corrector (HET WFC). It is shown that this method was very successful for centration alignment of some mirrors, whereas mechanical stability was the hardware limitation for other degrees of freedom. The additional alignment methods used in this project are described in detail and the expected alignment of the HET WFC is reported.The fabrication, characterization and application of spherical phase fiducials is demonstrated in a CGH-corrected Fizeau test prototype. It is shown that these reference features achieve <±1.5µm transverse alignment precision. A pair of phase fiducials is also applied to constrain the clocking and magnification of a projected wavefront. Fabrication and coordinate measurement of the features present the dominant challenges in these demonstrations.

In this dissertation I present experimental results obtained on the mercury optical clock project in the research group of Jason Jones at the University of Arizona. The project began in 2008 with the purpose of investigating the feasibility of neutral mercury as an optical clock species. The first series of investigations involved building the essential apparatus and scanning the doppler-broadened 6¹S₀ - 6³P₀ clock transition in ¹⁹⁹Hg. Here I present significant modifications to the cooling and trapping laser, improvements to the spectroscopy laser linewidth, and attempts to measure the 2-photon transition in ¹⁹⁹Hg. After previously demonstrating spectroscopy of the mercury clock transition using an optically-pumped semiconductor laser for the cooling and trapping source (OPSL), we replaced the OPSL with a a fiber-amplified ECLD system. We custom built a fiber amplifier to provide gain at 1015 nm, demonstrating the system can yield up to 5 W of signal power with excellent suppression of the ASE power. We find that the ASE is well suppressed by using a two-stage configuration and short sections of gain fiber. The linewidth of our original spectroscopy laser was over 10 kHz, which is unsuitable to resolve of sub-Doppler features. To enhance the performance of our spectroscopy system, we integrated faster feedback bandwidth using AOMs, and incorporated derivative gain into the system. This resulted in a feedback bandwidth for our spectroscopy laser of over 200 kHz. With this system, we demonstrate anactively stabilized linewidth of 525 Hz for our spectroscopy system. Using the upgraded cooling and spectroscopy laser systems, we demonstrate spectroscopy of the clock system and confirm temperature measurements derived from the transition linewidth. We also describe attempts to detect the recoil shift and 2-photon transition in neutral mercury.

The search for life on other worlds is an exciting scientific endeavor that could change the way we perceive our place in the universe. Thousands of extrasolar planets have been discovered using indirect detection techniques. One of the most promising methods for discovering new exoplanets and searching for life is direct imaging with a coronagraph. Exoplanet coronagraphy of Earth-like planets is a challenging task, but we have developed many of the tools necessary to make it feasible. The Phase-Induced Amplitude Apodization (PIAA) Coronagraph is one of the highest-performing architectures for direct exoplanet imaging. With a complex phase-shifting focal plane mask, the PIAA Complex Mask Coronagraph (PIAACMC) can approach the theoretical performance limit for any direct detection technique. The architecture design is flexible enough to be applied to any arbitrary aperture shape, including segmented and obscured apertures. This is an important feature for compatibility with next-generation ground and space-based telescopes. PIAA and PIAACMC focal plane masks have been demonstrated in monochromatic light. An important next step for high-performance coronagraphy is the development of broadband phase-shifting focal plane masks. In this dissertation, we present an algorithm for designing the PIAA and PIAACMC focal plane masks to operate in broadband. We also demonstrate manufacturing of the focal plane masks, and show laboratory results. We use simulations to show the potential performance of the coronagraph system, and the use of wavefront control to correct for mask manufacturing errors. Given the laboratory results and simulations, we show new areas of exoplanet science that can potentially be explored using coronagraph technology. The main conclusion of this dissertation is that we now have the tools required to design and manufacture PIAA and PIAACMC achromatic focal plane masks. These tools can be applied to current and future telescope systems to enable new discoveries in exoplanet science.