abstract: The development of new Ultra-Violet/Visible/IR range (UV/Vis/IR) astronomical instrumentation that use novel approaches for imaging and increase the accessibility of observing time for more research groups is essential for rapid innovation within the community. Unique focal planes that are rapid-prototyped, low cost, and provide high resolution are key. In this dissertation the emergent designs of three unique focal planes are discussed. These focal planes were each designed for a different astronomical platform: suborbital balloon, suborbital rocket, and ground-based observatory. The balloon-based payload is a hexapod-actuated focal plane that uses tip-tilt motion to increase angular resolution through the removal of jitter – known as the HExapod Resolution-Enhancement SYstem (HERESY), the suborbital rocket imaging payload is a Jet Propulsion Laboratory (JPL) delta-doped charge-coupled device (CCD) packaged to survive the rigors of launch and image far-ultra-violet (FUV) spectra, and the ground-based observatory payload is a star centroid tracking modification to the balloon version of HERESY for the tip-tilt correction of atmospheric turbulence. The design, construction, verification, and validation of each focal plane payload is discussed in detail. For HERESY’s balloon implementation, pointing error data from the Stratospheric Terahertz Observatory (STO) Antarctic balloon mission was used to form an experimental lab test setup to demonstrate the hexapod can eliminate jitter in flight-like conditions. For the suborbital rocket focal plane, a harsh set of unit-level tests to ensure the payload could survive launch and space conditions, as well as the characterization and optimization of the JPL detector, are detailed. Finally, a modification of co-mounting a fast-read detector to the HERESY focal plane, for use on ground-based observatories, intended to reduce atmospherically induced tip-tilt error through the centroid tracking of bright natural guidestars, is described. / Dissertation/Thesis / Doctoral Dissertation Exploration Systems Design 2019

This thesis works through the design of a radar-based system for imaging snowpacks remotely and over large areas to assist in avalanche prediction. The key to such a system is the ability to image volumes of snow at shallow, spatially-varying angles of incidence. To achieve this prerequisite, the design calls for a ground-based Synthetic Aperture Radar (SAR) capable of generating three-dimensional, ultra-high-resolution images of a snowpack. To arrive at design parameters for this SAR, the thesis works through relevant principles in avalanche mechanics, alpine-snowpack geophysics, and electromagnetic scattering theory. The thesis also works through principles of radar, SAR, antenna, and image processing theory to this end. A preliminary system is implemented to test the feasibility of the overall design. The preliminary system demonstrates ultra-high-resolution, three-dimensional imaging capabilities and the ability to image the volume of multiple alpine snowpacks. Images of these snowpacks display the structural patterns indicative of different layers in the snowpacks. Possible attributions of the patterns to physical properties in the snowpack are explored, but conclusions are not arrived at. Finally, lessons from the implementation of this preliminary system are discussed in terms of opportunities to be capitalized upon and problems to be overcome in future systems that more faithfully realize the complete design set forth in the thesis.

Reconstructed tomographic image resolution of small animal PET imaging systems is improving with advances in radiation detector development. However the trend towards higher resolution systems has come with an increase in price and system complexity. Recent developments in the area of solid-state photomultiplication devices like silicon photomultiplier arrays (SPMA) are creating opportunities for new high performance tools for PET scanner design. Imaging of excised small animal organs and tissues has been used as part of post-mortem studies in order to gain detailed, high-resolution anatomical information on sacrificed animals. However, this kind of ex-vivo specimen imaging has largely been limited to ultra-high resolution μCT. The inherent limitations to PET resolution have, to date, excluded PET imaging from these ex-vivo imaging studies. In this work, we leverage the diminishing physical size of current generation SPMA designs to create a very small, simple, and high-resolution prototype detector system targeting ex-vivo tomographic imaging of small animal organs and tissues. We investigate sensitivity, spatial resolution, and the reconstructed image quality of a prototype small animal PET scanner designed specifically for imaging of excised murine tissue and organs. We aim to demonstrate that a cost-effective silicon photomultiplier (SiPM) array based design with thin crystals (2 mm) to minimize depth of interaction errors might be able to achieve sub-millimeter resolution. We hypothesize that the substantial decrease in sensitivity associated with the thin crystals can be compensated for with increased solid angle detection, longer acquisitions, higher activity and wider acceptance energy windows (due to minimal scatter from excised organs). The constructed system has a functional field of view (FoV) of 40 mm diameter, which is adequate for most small animal specimen studies. We perform both analytical (3D-FBP) and iterative (ML-EM) methods in order to reconstruct tomographic images. Results demonstrate good agreement between the simulation and the prototype. Our detector system with pixelated crystals is able to separate small objects as close as 1.25 mm apart, whereas spatial resolution converges to the theoretical limit of 1.6 mm (half the size of the smallest detecting element), which is to comparable to the spatial resolution of the existing commercial small animal PET systems. Better system spatial resolution is achievable with new generation SiPM detector boards with 1 mm x 1 mm cell dimensions. We demonstrate through Monte Carlo simulations that it is possible to achieve sub-millimeter spatial image resolution (0.7 mm for our scanner) in complex objects using monolithic crystals and exploiting the light-sharing mechanism among the neighboring detector cells. Results also suggest that scanner (or object) rotation minimizes artifacts arising from poor angular sampling, which is even more significant in smaller PET designs as the gaps between the sensitive regions of the detector have a more exaggerated effect on the overall reconstructed image quality when the design is more compact. Sensitivity of the system, on the other hand, can be doubled by adding two additional detector heads resulting in a, fully closed, 4π geometry.

The goal of this Master’s thesis is to develop a more realistic simulation of Synthetic Aperture Radar (SAR) that has the ability to image detailed targets, and that can be used for Automatic Target Recognition (ATR). This thesis project is part of ongoing SAR ATR research at California Polytechnic State University (Cal Poly) sponsored by Raytheon Space & Airborne Systems and supervised by Dr. John Saghri. SAR is a form of radar that takes advantage of the forward motion of an antenna mounted on a moving platform (such as an airplane or spacecraft) to synthetically produce the effect of a longer antenna. Since most SAR images used for military ATR are classified and not available to the general public, all academic research to date on ATR has been limited to a small data set of Moving and Stationary Target Acquisition and Recognition Radar (MSTAR) images. Due to the unavailability of radar equipment or a greater range of SAR data, it has been necessary to create a SAR image generation scheme in which the parameters of the radar platform can be directly modified and controlled to be used for ATR applications. This thesis project focuses on making several improvements to Matthew Schlutz’s ‘Synthetic Aperture Radar Imaging Simulated in Matlab’ thesis. First, the simulation is optimized by porting the antenna pattern and echo generator from Matlab to C++, and the efficiency of the code is improved to reduced processing time. A three-dimensional (3-D) graphics application called Blender is used to create and position the target models in the scene imaged by the radar platform and to give altitude, target range (range of closest approach from the platform to the center area of the target) and elevation angle information to the radar platform. Blender allows the user to take pictures of the target as seen from the radar platform, and outputs range information from the radar platform plane to each point in the image. One of the major advantages of using Blender is that it also outputs range and reflectivity information about each pixel in the image. This is a significant characteristic that was hardcoded in the previous theses, making those simulations less realistic. For this thesis project, once the target scene is created in Blender, an image is rendered and saved as an OpenEXR file. The image is rendered in orthographic mode, which is a form of projection whereby the target plane is parallel with the projection plane. This parameter means that the simulation cannot image point targets that appear and disappear during the platform motion. The echo generation program then uses the range and reflectivity obtained from the OpenEXR file, the optimized antenna pattern, and several other user defined parameters to create the echo (received signal). Once the echo is created in the echo generation program, it is then read into Matlab in order for it to go through the Range Doppler Algorithm (RDA) and then output the final SAR image.

Thin film arrays of molecules or supramolecules are active subjects of investigation because of their potential value in electronics, chemical sensing, catalysis, and other areas. Scanning probe microscopes (SPMs), including scanning tunneling microscopes (STMs) and atomic force microscopes (AFMs) are commonly used for the characterization and metrology of thin film arrays. As opposed to transmission electron microscopy (TEM), SPMs have the advantage that they can often make observations of thin films in air or liquid, while TEM requires highly specialized techniques if the sample is to be in anything but vacuum. SPM is a surface imaging technique, while TEM typically images a 2D projection of a thin 3D sample. Additionally, variants of SPM can make observations of more than just topography; for instance, magnetic force microscopy measures nanoscale magnetic properties. Thin film arrays are typically two-dimensionally periodic. A perfect, infinite two-dimensionally periodic array is mathematically constrained to belong to one of only 17 possible 2D plane symmetry groups. Any real image is both finite and imperfect. Crystallographic Image Processing (CIP) is an algorithm that Fourier transforms a real image into a 2D array of complex numbers, the Fourier coefficients of the image intensity, and then uses the relationship between those coefficients to first ascertain the 2D plane symmetry group that the imperfect, finite image is most likely to possess, and then adjust those coefficients that are symmetry-related so as to perfect the symmetry. A Fourier synthesis of the symmetrized coefficients leads to a perfectly symmetric image in direct space (when accumulated rounding and calculation errors are ignored). The technique is, thus, an averaging technique over the direct space experimental data that were selected from the thin film array. The image must have periodicity in two dimensions in order for this technique to be applicable. CIP has been developed over the past 40 years by the electron crystallography community, which works with 2D projections from 3D samples. Any periodic sample, whether it is 2D or 3D has an "ideal structure" which is the structure absent any crystal defects. The ideal structure can be considered one average unit cell, propagated by translation into the whole sample. The "real structure" is an actual sample containing vacancies, dislocations, and other defects. Typically the goal of electron and other types of microscopy is examination of the real structure, as the ideal structure of a crystal is already known from X-ray crystallography. High resolution transmission electron microscope image based electron crystallography, on the other hand, reveals the ideal crystal structure by crystallographic averaging. The ideal structure of a 2D thin film cannot be easily in a spatially selective fashion examined by grazing incidence X-ray or low energy electron diffraction based crystallography. SPMs straightforwardly observe thin films in direct space, but SPM accuracy is hampered by blunt or multiple tips and other unavoidable instrument errors. Especially since the film is often of a supramolecular system whose molecules are weakly bonded (via pi bonds, hydrogen bonds, etc.) both to the substrate and to each other, it is relatively easy for a molecule from the film to adhere to the scanning tip during the scan and become part of the tip during subsequent observation. If the thin film array has two-dimensional periodicity, CIP is a unique and effective tool both for image enhancement (determination of ideal structure) and for the quantification of overall instrument error. In addition, if a sample of known 2D periodicity is scanned, CIP can return information about the contribution of the instrument itself to the image. In this thesis we show how the technique is applied to images of two dimensionally periodic samples taken by SPMs. To the best of our knowledge, this has never been done before. Since 2D periodic thin film arrays have an ideal structure that is mathematically constrained to belong to one of the 17 plane symmetry groups, we can use CIP to determine that group and use it for a particularly effective averaging algorithm. We demonstrate that the use of this averaging algorithm removes noise and random error from images more effectively than translational averaging, also known as "lattice averaging" or "Fourier filtering". We also demonstrate the ability to correct systematic errors caused by hysteresis in the scanning process. These results have the effect of obtaining the ideal structure of the sample, averaging out the defects crystallographically, by providing an average unit cell which, when translated, represents the ideal structure. In addition, if one has recorded a scanning probe image of a 2D periodic sample of known symmetry, we demonstrate that it is possible to use the Fourier coefficients of the image transform to solve the inverse problem and calculate the point spread function (PSF) of the instrument. Any real scanning probe instrument departs from the ideal PSF of a Dirac delta function, and CIP allows us to quantify this departure as far as point symmetries are concerned. The result is a deconvolution of the "effective tip", which includes any blunt or multiple tip effects, as well as the effects caused by adhesion of a sample molecule to the scanning tip, or scanning irregularities unrelated to the physical tip. We also demonstrate that the PSF, once known, can be used on a second image taken by the same instrument under approximately the same experimental conditions to remove errors introduced during that second imaging process. The preponderance of two-dimensionally periodic samples as subjects of SPM observation makes the application of CIP to SPM images a valuable technique to extract a maximum amount of information from these images. The improved resolution of current SPMs creates images with more higher-order Fourier coefficients than earlier, "softer" images; these higher-order coefficients are especially amenable to CIP, which can then effectively magnify the resolution improvement created by better hardware. The improved resolution combined with the current interest in supramolecular structures (which although 3D usually start building on a 2D periodic surface) appears to provide an opportunity for CIP to significantly contribute to SPM image processing.

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Doctor of Philosophy / Precision Agriculture (PA) strives towards holistic production and environmental management. A fundamental research challenge is the continuous expansion of ideas about how PA can contribute to sustainable agriculture. Some associated pragmatic research challenges include quantification of spatio-temporal variation of crop yield; crop growth simulation modelling within a PA context and; evaluating long-term financial and environmental outcomes from site-specific crop management (SSCM). In Chapter 1 literature about managing whole farms with a mind towards sustainability was reviewed. Alternative agricultural systems and concepts including systems thinking, agro-ecology, mosaic farming and PA were investigated. With respect to environmental outcomes it was found that PA research is relatively immature. There is scope to thoroughly evaluate PA from a long-term, whole-farm environmental and financial perspective. Comparatively, the emphasis of PA research on managing spatial variability offers promising and innovative ways forward, particularly in terms of designing new farming systems. It was found that using crop growth simulation modelling in a PA context is potentially very useful. Modelling high-resolution spatial and temporal variability with current simulation models poses a number of immediate research issues. This research focused on three whole farms located in Australia that grow predominantly grains without irrigation. These study sites represent three important grain growing regions within Australia. These are northern NSW, north-east Victoria and South Australia. Note-worthy environmental and climatic differences between these regions such as rainfall timing, soil type and topographic features were outlined in Chapter 2. When considering adoption of SSCM, it is essential to understand the impact of temporal variation on the potential value of managing spatial variation. Quantifying spatiotemporal variation of crop yield serves this purpose; however, this is a conceptually and practically challenging undertaking. A small number of previous studies have found that the magnitude of temporal variation far exceeds that of spatial variation. Chapter 3 of this thesis dealt with existing and new approaches quantifying the relationship between spatial and temporal variability in crop yield. It was found that using pseudo cross variography to obtain spatial and temporal variation ‘equivalents’ is a promising approach to quantitatively comparing spatial and temporal variation. The results from this research indicate that more data in the temporal dimension is required to enable thorough analysis using this approach. This is particularly relevant when questioning the suitability of SSCM. Crop growth simulation modelling offers PA a number of benefits such as the ability to simulate a considerable volume of data in the temporal dimension. A dominant challenge recognised within the PA/modelling literature is the mismatch between the spatial resolution of point-based model output (and therefore input) and the spatial resolution of information demanded by PA. This culminates into questions about the conceptual model underpinning the simulation model and the practicality of using point-based models to simulate spatial variability. iii The ability of point-based models to simulate appropriate spatial and temporal variability of crop yield and the importance of soil available water capacity (AWC) for these simulations were investigated in Chapter 4. The results indicated that simulated spatial variation is low compared to some previously reported spatial variability of real yield data for some climate years. It was found that the structure of spatial yield variation was directly related to the structure of the AWC and interactions between AWC and climate. It is apparent that varying AWC spatially is a reasonable starting point for modelling spatial variation of crop yield. A trade-off between capturing adequate spatio-temporal variation of crop yield and the inclusion of realistically obtainable model inputs is identified. A number of practical solutions to model parameterisation for PA purposes are identified in the literature. A popular approach is to minimise the number of simulations required. Another approach that enables modelling at every desired point across a study area involves taking advantage of high-resolution yield information from a number of years to estimate site-specific soil properties with the inverse use of a crop growth simulation model. Inverse meta-modelling was undertaken in Chapter 5 to estimate AWC on 10- metre grids across each of the study farms. This proved to be an efficient approach to obtaining high-resolution AWC information at the spatial extent of whole farms. The AWC estimates proved useful for yield prediction using simple linear regression as opposed to application within a complex crop growth simulation model. The ability of point-based models to simulate spatial variation was re-visited in Chapter 6 with respect to the exclusion of lateral water movement. The addition of a topographic component into the simple point-based yield prediction models substantially improved yield predictions. The value of these additions was interpreted using coefficients of determination and comparing variograms for each of the yield prediction components. A result consistent with the preceding chapter is the importance of further validating the yield prediction models with further yield data when it becomes available. Finally, some whole-farm management scenarios using SSCM were synthesised in Chapter 7. A framework that enables evaluation of the long-term (50 years) farm outcomes soil carbon sequestration, nitrogen leaching and crop yield was established. The suitability of SSCM across whole-farms over the long term was investigated and it was found that the suitability of SSCM is confined to certain fields. This analysis also enabled identification of parts of the farms that are the least financially and environmentally viable. SSCM in conjunction with other PA management strategies is identified as a promising approach to long-term and whole-farm integrated management.

Since twenty years wavelet transform was recognized as a privileged tool for analysis of the fractals objects. We exploited the self-similarity of the wavelet transform to detect singularity which is a fractal signal characterization .In a first part, we use the wavelet transform modulus maxima lines (WTMM) as a tool for analysis of synthetics fractals signals. In second part we applied this technique to the data of wells located in the Algerian Sahara, we proposed then an automatic algorithm of segmentation which is applied thereafter to a simple resolution well-logs data another with a high resolution. We demonstrate the potentialities of the method in the segmentation of different geological formations. We finalize this work by planning a multilayer perceptron neuronal machine. We used the precedents results as information able to detect the lithology and the nature of the pores fluid . Keywords: Wavelet transform, WTMM, Segmentation, simple resolution, High resolution.

<p>Reflection seismic and seismic tomography methods can be used to image the upper kilometer of hard bedrock and the loose unconsolidated sediments covering it. Developments of these two methods and their application, as well as identifying issues concerning their usage, are the main focus of the thesis. Data used for this development were acquired at three different sites in Sweden, in Forsmark 140 km north of Stockholm, in the Oskarshamn area in southern Sweden, and in the northern part of the Siljan Ring impact crater area.</p><p>The reflection seismic data were acquired with long source-receiver offsets relative to some of the targeted depths to be imaged. In the initial processing standard steps were applied, but the uppermost part of the sections were not always clear. The longer offsets imply that pre-stack migration is necessary in order to image the uppermost bedrock as clearly as possible. Careful choice of filters and velocity functions improve the pre-stack migrated image, allowing better correlation with near-surface geological information.</p><p>The seismic tomography method has been enhanced to calculate, simultaneously with the velocity inversion, optimal corrections to the picked first break travel times in order to compensate for the delays due to the seismic waves passing through the loose sediments covering the bedrock.</p><p>The reflection seismic processing used in this thesis has produced high-quality images of the upper kilometers, and in one example from the Forsmark site, the image of the uppermost 250 meters of the bedrock has been improved. The three-dimensional orientation of reflections has been determined at the Oskarshamn site. Correlation with borehole data shows that many of these reflections originate from fracture zones. </p><p>The developed seismic tomography method produces high-detail velocity models for the site in the Siljan impact area and for the Forsmark site. In Forsmark, detailed estimates of the bedrock topography were calculated with the use of the developed tomography method.</p>