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.

Positron Emission Tomography (PET) is an imaging modality that has become increasingly beneficial in Radiotherapy by improving treatment planning (1). PET reveals tumor volumes that are not well visualized on computed tomography CT or MRI, recognizes metastatic disease, and assesses radiotherapy treatment (1). It also reveals areas of the tumor that are more radiosensitive allowing for dose painting - a non-homogenous dose treatment across the tumor (1). However, PET is not without limitations. The quantitative unit of PET images, the Standardized Uptake Value (SUV), is affected by many factors such as reconstruction algorithm, patient weight, and tracer uptake time (2). In fact, PET is so sensitive that a patient imaged twice in a single day on the same machine and same protocol will produce different SUV values. The objective of this research was to increase the capabilities of PET by exploring other quantitative PET/CT measures for Radiotherapy treatment applications. The technique of quantitative image feature analysis, nowadays known as radiomics, was applied to PET and CT images. Image features were then extracted from PET/CT images and how the features differed between conventional and respiratory-gated PET/CT images in lung cancer was analyzed. The influence of noise on image features was analyzed by applying uncorrelated, Gaussian noise to PET/CT images and measuring how significantly noise affected features. Quantitative PET/CT measures outside of image feature analysis were also investigated. The correlation of esophageal metabolic tumor volumes (tumor volume demonstrating high metabolic uptake) and endoscopically implanted fiducial markers was studied. It was found that certain image features differed greatly between conventional and respiratory-gated PET/CT. The differences were mainly due to the effect of respiratory motion including affine motion, rotational motion and tumor deformation. Also, certain feature groups were more affected by noise than others. For instance, contour-dependent shape features exhibited the least change with noise. Comparatively, GLSZM features exhibited the greatest change with added noise. Discordance was discovered between the inferior and superior tumor fiducial markers and metabolic tumor volume (MTV). This demonstrated a need for both fiducial markers and MTV to provide a comprehensive view of a tumor. These studies called attention to the differences in features caused by factors such as motion, acquisition parameters, and noise, etc. Investigators should be aware of these effects. PET/CT radiomic features are indeed highly affected by noise and motion. For accurate clinical use, these effects must be account by investigators and future clinical users. Further investigation is warranted towards the standardization of PET/CT radiomic feature acquisition and clinical application.