The Hobby-Eberly Telescope (HET)(+), located in West Texas at the McDonald Observatory, operates with a fixed segmented primary (M1) and has a tracker, which moves the prime-focus corrector and instrument package to track the sidereal and non-sidereal motions of objects. We have completed a major multi-year upgrade of the HET that has substantially increased the pupil size to 10 meters and the field of view to 22 arcminutes by deploying the new Wide Field Corrector (WFC), new tracker system, and new Prime Focus Instrument Package (PFIP). The focus of this paper is on the delivery, installation, and on-sky verification of the WFC. We summarize the technical challenges encountered and resolutions to overcome such challenges during the construction of the system. We then detail the transportation from Tucson to the HET, on-site ground verification test results, post-installation static alignment among the WFC, PFIP, and M1, and on-sky verification of alignment and image quality via deploying multiple wavefront sensors across 22 arcminutes field of view. The new wide field HET will feed the revolutionary new integral field spectrograph called VIRUS, in support of the Hobby-Eberly Telescope Dark Energy Experiment (HETDEX), a new low resolution spectrograph (LRS2), an upgraded high resolution spectrograph (HRS2), and later the Habitable Zone Planet Finder (HPF).

Master of Science / Department of Chemistry / Daniel A. Higgins / Single molecule tracking (SMT) measurements have been applied to the study of molecular mobility in sol-gel-derived silica gradient films in this thesis. Such gradient films have broad potential applications in controlled adhesion and transport of cells, vesicles and polymers; separation of complex chemical mixtures and in the development of new catalysts. Silica films were prepared by “infusion-withdrawal dip-coating”. In this method, a suitable substrate is slowly withdrawn from a silica sol of time varying composition. The deposition reservoir is initially filled with a sol derived from one silica precursor (tetramethoxysilane). A second sol, prepared from a different precursor (methyltrimethoxysilane), is then infused into the deposition reservoir, as the mixed sol is withdrawn. Films thus prepared were initially characterized by bulk fluorescence spectroscopy, infrared (IR) microscopy, contact angle goniometry, spectroscopic ellipsometry and surface profilometry. The fluorescence, IR and contact angle data all demonstrate the presence of a gradient in the methyl content of the silica film. The primary objective of the work performed under this thesis was to investigate the diffusion of Nile Red molecules in and on these films, as a function of position along the gradient, by SMT methods. Histograms of the mean-square displacement of the molecules depict the presence of at least two distinct populations: one incorporating fixed (entrapped or adsorbed) molecules and the other clearly reflecting the presence of mobile molecules. The latter population was observed to vary along the gradient dimension and also changed as the films aged over the course of five days. Molecular mobility is attributed to the presence of liquid-like silica oligomers in the films. Spatial variations in the observed mobility are tentatively assigned to variations in oligomer viscosity along the gradient. Film viscosity also changes as the polymerization of the oligomers continues during film aging.

Despite being the most preventable cancer, cervical cancer remains the third leading cause of cancer death worldwide. Over 85% of cervical cancer incidence and mortality occurs in low-resource countries where screening programs for early detection are either inadequate or unavailable. In the developed world, where screening programs are well organized, incidence and mortality rates are greatly reduced. Recent advances in optical imaging have the potential to enable cervical cancer screening at the point-of-care, even in the hands of less experienced providers. High performance optical imaging systems can be constructed at relatively low cost, and image analysis can be automated; thus, these technologies may provide a way to bridge the gap to cervical cancer screening for developing countries. This work focuses on the design, construction, and clinical testing of a novel multimodal optical imaging (combination of wide-field imaging and high-resolution) for early detection of cervical neoplasia. The Multimodal Digital Imager (MDI) acquires in vivo images of cervical tissue in fluorescence, narrow band reflectance, and orthogonal polarized reflectance modes using multiple illumination wavelengths. The High Resolution Microendoscope (HRME) was used to interrogate clinically suspicious areas with subcellular spatial resolution, revealing changes in nuclear to cytoplasmic area ratio. In vivo image data from the wide-field system was combined with image data from a high- resolution microendoscope (HRME) in order to test the effectiveness of the multimodal optical imaging in discriminating between cervical neoplasia and non-neoplastic. Multimodal optical imaging coupled with computer aided diagnostic achieved a sensitivity of 82% and specificity of 85% for discriminating cervical neoplastic from non-neoplastic This work has demonstrated that multimodal optical imaging; combination of wide-field and high-resolution optical imaging of the cervix can assist in the detection of cervical neoplasia and can be implemented effectively in a low-resource setting.

abstract: Recent new experiments showed that wide-field imaging at millimeter scale is capable of recording hundreds of neurons in behaving mice brain. Monitoring hundreds of individual neurons at a high frame rate provides a promising tool for discovering spatiotemporal features of large neural networks. However, processing the massive data sets is impossible without automated procedures. Thus, this thesis aims at developing a new tool to automatically segment and track individual neuron cells. The new method used in this study employs two major ideas including feature extraction based on power spectral density of single neuron temporal activity and clustering tree to separate overlapping cells. To address issues associated with high-resolution imaging of a large recording area, focused areas and out-of-focus areas were analyzed separately. A static segmentation with a fixed PSD thresholding method is applied to within focus visual field. A dynamic segmentation by comparing maximum PSD with surrounding pixels is applied to out-of-focus area. Both approaches helped remove irrelevant pixels in the background. After detection of potential single cells, some of which appeared in groups due to overlapping cells in the image, a hierarchical clustering algorithm is applied to separate them. The hierarchical clustering uses correlation coefficient as a distance measurement to group similar pixels into single cells. As such, overlapping cells can be separated. We tested the entire algorithm using two real recordings with the respective truth carefully determined by manual inspections. The results show high accuracy on tested datasets while false positive error is controlled within an acceptable range. Furthermore, results indicate robustness of the algorithm when applied to different image sequences. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2016

The field of X-ray astronomy is only forty (43) years old, and grazing incidence X-ray telescopes have only been conceived and designed for a little over fifty (50) years. The Wolter Type I design is particularly well suited for stellar astronomical telescopes (very small field-of-view). The first orbiting X-ray observatory, HEAO-1 was launched in 1977, a mere twenty-eight (28) years ago. Since that time large nested Wolter Type I X-ray telescopes have been designed, build, and launched by the European Space Agency (ROSAT) and NASA (the Chandra Observatory). Several smaller grazing incidence telescopes have been launched for making solar observations (SOHO, HESP, SXI). These grazing incidence designs tend to suffer from severe aberrations and at these very short wavelengths scattering effects from residual optical fabrication errors are another major source of image degradation. The fabrication of precision optical surfaces for grazing incidence X-ray telescopes thus poses a great technological challenge. Both the residual "figure" errors and the residual microroughness or "finish" of the manufactured mirrors must be precisely measured, and the image degradation due to these fabrication errors must be accurately modeled in order to predict the final optical performance of the as manufactured telescope. The fabrication process thus consists of a series of polishing and testing cycles with the predictions from the metrology data of each cycle indicating the strategy for the next polishing cycle. Most commercially available optical design and analysis software analyzes the image degradation effects of diffraction and aberrations, but does not adequately model the image degradation effects of surface scatter or the effects of state-of-the-art mosaic detectors. The work presented in this dissertation is in support of the Solar X-ray Imager (SXI) program. We have developed a rigorous procedure by which to analyze detector effects in systems which exhibit severe field-dependent aberrations (conventional transfer function analysis is not applicable). Furthermore, we developed a technique to balance detector effects with geometrical aberrations, during the design process, for wide-field applications. We then included these detector effects in a complete systems engineering analysis (including the effects of diffraction, geometrical aberrations, surface scatter effects, the mirror manufacturer error budget tree, and detector effects) of image quality for the five SXI telescopes being fabricated for NOAA's next generation GOES weather satellites. In addition we have re-optimized the remaining optical design parameters after the grazing incidence SXI mirrors have been imperfectly fabricated. This ability depends critically upon the adoption of an image quality criterion, or merit function, appropriate for the specific application. In particular, we discuss in detail how the focal plane position can be adjusted to optimize the optical performance of the telescope to best compensate for optical figure and/or finish errors resulting from the optical fabrication process. Our systems engineering analysis was then used to predict the increase in performance achieved by the re-optimization procedure. The image quality predictions are also compared with real X-ray test data from the SXI program to experimentally validate our system engineering analysis capability.

Wide-field photometry is prone to various degradations, such as atmospheric ex- tinction, varying point spread functions, and aliasing in addition to classical noise sources such as photon, sky background, readout, and thermal noise. While space- borne observations do not suer from atmospheric eects, varying star images over a large sensor and aliasing may seriously impede good results. A measure of the achievable precision of ground-based dierential photometry with the prototype photometer for the BRITE satellite mission is reported, using real sky observa- tions. The data were obtained with the photometer attached to a paramount tracking platform, using the Image Reduction and Analysis Facility Software (IRAF) image reduction and analysis methods as well as the author's own Matlab Code. Special emphasis is placed on the analysis of varying apertures for vary- ing point spread functions, which shows that the accuracy can be improved by taking into account the statistics for each star instead of using a xed aperture. In addition a function is dened, which describes the expected error in terms of instrumental magnitudes, taking into account Poisson distributed noise and mag- nitude independent noise, mainly aliasing. This function is then t to observed data in a two-dimensional least squares sense, providing a calculated aliasing error of 7 millimagnitudes. This function is furthermore rewritten in terms of the stan- dard magnitude B. A maximum magnitude can then be determined for a certain precision, which shows that the Bright Target Explorer (BRITE) can reach a pho- tometric error of 1 millimagnitude for stars with magnitude B &lt; 3:5, assuming the worst case duty cycle of 15 minutes. / <p>Validerat; 20110211 (anonymous)</p>

Optical imaging techniques have improved much over the last fifty years since the invention of the laser. With a high brightness source many imaging applications which were once inaccessible to researchers have now become a reality. Among these techniques, the most beneficial one is the use of lasers for both wide-field and confocal imaging systems. The aim of this study was to design a laser imaging system based on the concept of laser scanning confocal microscopy. Specifically the optical system was based on optical fibers allowing the user to image remote areas such as the inner surface of rifled gun barrels and/or pipes with a high degree of precision (+/- 0.01 mm). In order to build such a system, initially the theoretical foundation for a confocal as well as a wide-field imaging system was analyzed. Using this basis a free-space optical confocal system was built and analyzed. The measurements support the fact that both the objective numerical aperture and pinhole size play an important role in the radial and axial resolution of the system as well as the quality of the images obtained. To begin construction of a confocal, optical-fiber based imaging system first an all fiber wide-field imaging system was designed and tested at a working wavelength of 1550 nm. Then an all fiber confocal system was designed at a working wavelength of 808 nm. In both cases results showed that while lateral resolution was adequate, axial resolution suffered since it was found that the design of the optical system needs to take into account under-filling of the objective lens, a result common with the use of laser beams whose divergence is not at all like that of a point source. The work done here will aid technology that will be used in the elimination process of faulty rifling fabrication in defense industry. The reason why the confocal technique is preferred to the conventional wide-field one is the need for better resolution in all directions. Theoretical concepts and mathematical background are discussed as well as the experimental results and the practical advantages of such a system.

Use of imaging systems for performing various situational awareness tasks in militaryand commercial settings has a long history. There is increasing recognition,however, that a much better job can be done by developing non-traditional opticalsystems that exploit the task-specific system aspects within the imager itself. Insome cases, a direct consequence of this approach can be real-time data compressionalong with increased measurement fidelity of the task-specific features. In others,compression can potentially allow us to perform high-level tasks such as direct trackingusing the compressed measurements without reconstructing the scene of interest.In this dissertation we present novel advancements in feature-specific (FS) imagersfor large field-of-view surveillence, and estimation of temporal object-scene changesutilizing the compressive imaging paradigm. We develop these two ideas in parallel.In the first case we show a feature-specific (FS) imager that optically multiplexesmultiple, encoded sub-fields of view onto a common focal plane. Sub-field encodingenables target tracking by creating a unique connection between target characteristicsin superposition space and the target's true position in real space. This isaccomplished without reconstructing a conventional image of the large field of view.System performance is evaluated in terms of two criteria: average decoding time andprobability of decoding error. We study these performance criteria as a functionof resolution in the encoding scheme and signal-to-noise ratio. We also includesimulation and experimental results demonstrating our novel tracking method. Inthe second case we present a FS imager for estimating temporal changes in the objectscene over time by quantifying these changes through a sequence of differenceimages. The difference images are estimated by taking compressive measurementsof the scene. Our goals are twofold. First, to design the optimal sensing matrixfor taking compressive measurements. In scenarios where such sensing matrices arenot tractable, we consider plausible candidate sensing matrices that either use theavailable <italic>a priori</italic> information or are non-adaptive. Second, we develop closed-form and iterative techniques for estimating the difference images. We present results to show the efficacy of these techniques and discuss the advantages of each.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes the application of wide-field single-molecule fluorescence microscopy techniques to investigations of DNA-surface interactions on chemically graded organosilane surfaces. The adsorption and desorption behaviors of double-stranded (ds) plasmid DNA along the amino-trimethoxysilane and octyl-trichlorosilane gradients were explored as a function of solution pH, solution ionic strength and surface properties. The results provide an improved fundamental understanding of DNA interactions with different surfaces and are certain to aid in the development and advancement of DNA-based biological and biomedical devices. Three distinct experiments were performed in completion of the work for this dissertation. In the first study, total internal reflection fluorescence (TIRF) microscopy was employed to study DNA interactions with aminosilane gradient surfaces under relatively acidic and basic environments. Electrical potentials were applied to assist DNA adsorption and desorption. The single-molecule data clearly showed that DNA capture and release was achieved on the monolayer and submonolayer coated regions of the aminosilane gradient surface under relatively basic pH conditions, with the help of an electrical potential. Meanwhile, DNA adsorption was found to be quasi-reversible on the multilayers at the high aminosilane end of the gradient in the relatively acidic solution. The results of these studies demonstrate the importance of manipulating the electrostatic interactions of DNA with charged surfaces in order to achieve DNA capture and release. The fundamental knowledge of the DNA-surface interactions gained in these studies will be helpful in diverse fields ranging from the layer-by-layer assembly of polyelectrolyte-based thin films to the selective electronic sensing of charged biomolecules. In the second study, the local dielectric properties of the least polar environments in dsDNA were assessed by using the solvatochromic dye, nile red, as a polarity-sensitive probe. TIRF spectroscopic imaging methods were employed in these studies. Although the dielectric constant within the least polar regions of dsDNA was previously predicted by theoretical and computational methods, no experimental measurements of its value had been reported to date. The results provide important knowledge of the factors governing the polarity of DNA microenvironments to which intercalators bind, and provide vital experimental support for the values determined in computational studies. In the third study, TIRF microscopy and single molecule tracking methods were employed to study DNA interactions with an opposed two-component C8-silane and aminosilane gradient surface as a function of solution pH. The mobility of surface-adsorbed DNA molecules was explored and quantified in these studies. The preliminary results further demonstrated the importance of electrostatic interactions over hydrophobic interactions in governing the adsorption of DNA to surfaces. The mobility of surface-adsorbed DNA was found to be largely independent of position along the two-component gradient. These studies were originally undertaken as a route to observation of cooperative effects that are believed to govern DNA-surface binding. Unfortunately, no clear evidence of cooperative effects was observed at the mixed regions of the two-component gradient surface.

The Great Observatories Origins Deep Survey North (GOODS-N) field, first surveyed by the HST, has been observed across numerous wavebands revealing populations of both Star Forming Galaxies (SFG) and Active Galactic Nuclei (AGN) over wide ranges of luminosities. It has been surmised that the evolution in the star forming population appears to diverge from that in the AGN population leading to a domination of SFGs at low flux densities. The number of starbursts can only be disentangled from the entire population if each source can be classified individually, which usually requires high angular resolution imaging. This is the motivation behind the e-MERLIN Galaxy Evolution survey, e-MERGE, which expands the depth of high resolution radio imaging in the GOODS-N field to increase the number of potentially classifiable sources. By use of wide-field imaging techniques, including a new high-speed mapping tool, together with a new semi-empirical primary beam-shape model for the e-MERLIN array, a deep wide-field high-resolution map is derived. This is the widest and deepest contiguous imaging yet obtained from e-MERLIN and JVLA observations, and yet contains less than 25% of the e-MERLIN data so far observed. The majority of the objects are shown to exhibit extended structure, and the angular size distribution place the median size around 1.2 arcsec, peaking between 0.5 and 0.7 arcsec. Automated algorithms are utilised to facilitate a new probabilistic classification tool based on multi-parameter correlations. 248 sources could be classified using the tool, each deriving a probability of AGN or SFG rather than forcing a binary category. Linear sizes of star-formation dominated sources are determined to lie in a range of 4 - 11 kpc, within the optical extent of galaxies. Differential source counting based on probabilistic classifications reveals that an increase in the luminosity evolution of SFGs is likely, although an apparent upturn in AGN may also exist to some lesser degree at low flux densities. The thesis establishes a clear roadmap for the remainder of the e-MERGE survey and a path to determine the star formation rate history of the Universe.