Theses and Dissertations at Montana State University (MSU)

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Opto-mechanical design and analysis for coherent active imaging
(Montana State University - Bozeman, College of Engineering, 2022) Neeley, Jaime Branson; Co-chairs, Graduate Committee: Wm. Randall Babbitt and Joseph A. Shaw
The objective of this thesis project was to design a monostatic lidar transmit (Tx) and receive (Rx) opto-mechanical apparatus for remote sensing at a variable range of 50 m - 500 m. The scope of this project begins from the fiber output of a pre-designed Frequency-Modulated Continuous Wave (FMCW) lidar system. After design criteria for the lidar module are given, the optical and mechanical design is presented, opto-mechanical tolerancing is presented, and assembly, alignment, and testing procedures are covered as well. This thesis shows that the required design criteria of diffraction-limited optical performance was achieved while accounting for predictable manufacturing and assembly errors modeled using a Monte Carlo tolerance analysis. Furthermore, this thesis shows that the modeled and measured optical performance results were in good agreement and recommendations are given for improvements for the next-generation revision of the lidar Tx/Rx module.
Adapting archetypal analysis to scientific imaging applications
(Montana State University - Bozeman, College of Letters & Science, 2022) Potts, Catherine Gabriel; Chairperson, Graduate Committee: Dominique Zosso
Scientific imaging applications create large sets of high-dimensional data, which may be difficult to process using traditional supervised machine learning representative models. First, many representative models generate computational elements that are difficult to interpret in terms of the scientific application and second, the high embedding dimension of the images often makes generating the models computationally inefficient. We propose using archetypal analysis (AA) as the representative model for these scientific imaging problems, since the computational elements, so called archetypes, resemble members of the original dataset. Specifically, the archetypes are generated as extreme points to an approximation of the convex hull of the data cloud, which means they maintain the structure of individual data points. To improve the computational task of generating the AA model, we propose a sketch-based AA method which projects the data to a lower embedding dimension before calculating the computational elements, lowering computation time for these high-dimensional problems, while at the same time retaining the geometric structure enough so that the computational elements closely match the results of AA. We also applied a primal-dual hybrid gradient (PDHG) solver to the AA algorithm structure attempting to speed up computation. To verify the significance of the interpretation of AA, we applied AA to transient fluorescent calcium images, recorded in the Kunze Neuroengineering lab as videos, in order to determine whether or not adding different nanoparticles changed the way the neurons in culture communicate. We also applied our sketch-based AA method to other sorts of imaging data sets, exploring the differences between our method and the standard AA method. Our experimentation shows the different ways that AA can be adapted to scientific imaging applications, providing a machine learning representation model that is interpretable in the context of the imaging problem and verifies the benefits of the sketch-based method in terms of computation time.
Techniques for improving activity based biosensors: a Kuhl platform for engineering
(Montana State University - Bozeman, College of Agriculture, 2020) Thomas, Merrilee Anne; Chairperson, Graduate Committee: Thomas Hughes and Susy C. Kohout (co-chair); Thomas E. Hughes was a co-author of the article, 'Optically activated, customizable, excitable cells Kuhl platform for evolving next gen biosensors' submitted to the journal 'PLOS One' which is contained within this dissertation.
According to Kuhn, ''there are three classes of problems - determination of significant facts, matching of facts with theory, and articulation of that theory (Kuhn 2012).'' The current paradigm in molecular neuroscience is that there is a need for revolutionary tool development in neuroscience. Interestingly, the need for better tools in neuroscience is to answer neuroscience theories and provide the determination and articulation of those theories. Currently, the neuroscientist's toolbox is growing and the ways in which those tools are used is rapidly changing. Neuroscience underwent a revolution when we were able to take single-cell recording in vivo and then assign field properties to individual neurons based upon those responses (O'Keefe and Bouma 1969; O'Keefe and Dostrovsky 1971; Moser et al. 1995). Scientists became adept at imaging increasingly smaller regions of the functioning human brain (Price 2012). We have since been able to genetically encode and manipulate proteins and pathways while recording from them using fluorescence (Southern and Berg 1982; Chalfie 2009). In vitro and in vivo we have harnessed the use of light to stimulate or inhibit specific neurons or ligands (Boyden 2011; Adamantidis et al. 2007). These tools are just the beginning and by no means is this an exhaustive list. We introduce the Kuhl synthetic cell system that provides a customizable de-novo excitable cell. The Kuhl system is activated using a blue light photo activated cyclase bPAC. It can be used to create better tools to image the brain and can be used to screen multi-color fluorescent sensors. Interestingly, sensors that are within bPACs activation spectrum can be used in these synthetic cells. We show that both red and green Ca 2+ sensors can be imaged simultaneously, and both Ca 2+ and Voltage sensors can be screened in the Kuhl system. The Kuhl system has the potential to be used to screen for drug compounds and in theory, they could be used in studying pathways that are less understood, such as the mTOR pathway.
Characterization of a division-of-focal-plane polarization imager
(Montana State University - Bozeman, College of Engineering, 2020) Syed, Musaddeque Anwar Al Abedin; Chairperson, Graduate Committee: Joseph A. Shaw
Polarization is a fundamental property of light that can be detected with polarization-sensitive instruments. Imaging polarimetry has an immensely wide range of applications, and while much has been accomplished in recent years, there is still a need for sensor systems with improved accuracy, precision, and stability. This paper presents the optical characterization of a commercial division-of-focal plane (DoFP) polarization imager, in an effort to evaluate its performance as a promising instrument in the application of ground-based cloud thermodynamic phase detection. Radiometric characterization values were well within the acceptable region, but the polarimetric contrast was in the range of 20-30, much lower than expected, which may be a result of the broadband measurements being impaired by poor polarizer performance at the blue end of the spectrum. Later, a narrowband polarimetric measurement at 532 + or - 5 nm produced a much enhanced result, with polarimetric contrast in the higher 300s, making the imager a viable option for many remote sensing applications. Also, all-sky imaging of clear daytime sky and its analysis of degree of linear polarization (DoLP) showed encouraging result.
Validation of high strain rate, multiaxial loads using an in-plane loader, digital image correlation, and FEA
(Montana State University - Bozeman, College of Engineering, 2018) Stroili, Christopher; Chairperson, Graduate Committee: David A. Miller
Montana State University's In-Plane Loader (IPL) is a machine designed to test for mechanical properties at multi-axial states of stress and strain by in-plane translation and rotation. Historically the machine has been used to characterize composite lay-ups, where applying multi-axial loads can better describe anisotropic materials. The IPL testing machine uses Digital Image Correlation (DIC) software and a stereoscopic camera system to measure strains on the surface of the test coupon by tracking a stochastic pattern applied to the gage section. The focus of this work was to test the capabilities beyond quasi-static composites testing, specifically looking to explore the feasibility of testing plastics and metals at strain rates from 10 0 to 10 3 s -1. This work explored the speed and loading capabilities of the IPL and determined a suitable coupon geometry which balances gage section area with material strength. 304 Stainless Steel was tested both on the IPL and in uniaxial tension. Experimental tensile test data was fit to a Johnson Cook strain rate sensitive constitutive model. This constitutive equation was then used with an implicit dynamic finite element analysis (FEA) model. To study the validity of high rate testing of steel in the IPL, strain from the DIC experimental data was compared with the FEA results. While the strains predicted by the FEA model varied from experimental results, a better understanding of the IPL capabilities has been achieved. Moving forward, a series of recommendations have been made so that high strain rate multi-axial testing of metals can be implemented with more robust constitutive models.
Development of an active/adaptive laser scanning microscope
(Montana State University - Bozeman, College of Engineering, 2018) Archer-Zhang, Christian Chunzi; Chairperson, Graduate Committee: David L. Dickensheets
Laser scanning techniques such as confocal microscopy and two-photon excitation fluorescence microscopy (TPM) are powerful tools for imaging biological samples with high resolution, offering three-dimensional (3D) visualization of the behavior of cells in their natural environment. Traditionally, the 3D images are acquired from 2D image stacks with focusing depth controlled through mechanical movement of the specimen relative to the objective lens. The slow mechanical movement (~<20Hz) does not allow the spot of light to be scanned axially sufficiently fast to monitor cell:cell and cell:environment interactions in real time over hundreds of microns in all three dimensions. A fast focus control mirror supports agile scan patterns such as vertical or oblique planes or even arbitrary surfaces, minimizing the time and photo damage required to monitor features of interest within the 3D volume. Because aberrations cause image quality to decrease as the focal point of the beam penetrates deeper into the sample, adaptive optics can enhance resolution and contrast at depth for confocal microscopy and TPM. Combining a fast focus control mirror with a fast aberration correcting mirror leads to a flexible platform called the active/adaptive laser scanning microscope, capable of aberration-corrected beam scanning throughout a 3D volume of tissue. This opens up the possibility of fully corrected, variable-depth imaging along oblique sections or more complex user-defined surfaces within a single image frame.
Phase gradient averaging for holographic aperture LIDAR in the presence of turbulence
(Montana State University - Bozeman, College of Engineering, 2017) Blaszczyk, Christopher Ross; Chairperson, Graduate Committee: Joseph A. Shaw
The resolution of an image is dictated by the size and quality of the imaging system. The imaging system has a physical limit to the resolution dictated by the diffraction limited resolution. This limit can be improved by making the aperture larger on the imaging system. The increase in the physical aperture size can only be practical to a certain extent. However, to get beyond these physical constraints it is possible to use synthetic aperture methods to allow for the aperture to appear to be increased. Synthetic apertures are created by adding apertures coherently together to create a larger aperture that increases the diffraction limited resolution. To sum the aperture coherently the phase information needs to be available. One way to have access to the phase information is to capture the image as hologram. These holograms are captured by using a coherent light source with a reference beam to create an interference pattern that contains the phase information of the target. Holographic apertures can be used in a synthetic aperture method called Holographic Aperture Lidar (HAL). A problem that can arise while capturing images is turbulence in the atmosphere. Turbulence is a change in the index of refraction caused by a change in the temperature and pressure of the atmosphere. This causes the phase of the light to distort dynamically as it propagates making HAL imaging difficult. This thesis will cover a method to restore the original phase of the signal that has passed through turbulence so that it can be used in digital holography and HAL. This method uses averaging of the phase gradient to remove the dynamic turbulence and keep the phase information of the static target. The improvements observed in actual experiments were small, but the basics of the method worked, and the reason for only small improvement are discussed.
Imaging performance of elliptical-boundary varifocal mirrors in active optical systems
(Montana State University - Bozeman, College of Engineering, 2015) Lukes, Sarah Jane; Chairperson, Graduate Committee: David L. Dickensheets
Micro-electro-mechanical systems deformable-membrane mirrors provide a means of focus control and attendant spherical aberration correction for miniaturized imaging systems. The technology has greatly advanced in the last decade, thereby extending their focal range capabilities. This dissertation describes a novel SU-8 2002 silicon-on-insulator wafer deformable mirror. A 4.000 mm x 5.657 mm mirror for 45° incident light rays achieves 22 micron stroke or 65 diopters, limited by snapdown. The mirrors show excellent optical quality while flat. Most have peak-to-valley difference of less than 150 nm and root-mean-square less than 25 nm. The process proves simple, only requiring a silicon-on-insulator wafer, SU-8 2002, and a metal layer. Xenon difluoride etches the silicon to release the mirrors. Greater than 90% of the devices survive fabrication and release. While current literature includes several aberration analyses on static mirrors, analyses that incorporate the dynamic nature of these mirrors do not exist. Optical designers may have a choice between deformable mirrors and other types of varifocal mirrors or lenses. Furthermore, a dynamic mirror at an incidence angle other than normal may be desired due to space limitations or for higher throughput (normal incidence requires a beam splitter). This dissertation presents an analysis based on the characteristic function of the system. It provides 2nd and 3rd order aberration coefficients in terms of dynamic focus range and base ray incidence angle. These afford an understanding of the significance of different types of aberrations. Root-mean-square and Strehl calculations provide insight into overall imaging performance for various conditions. I present general guidelines for maximum incidence angle and field of fiew that provide near diffraction-limited performance. Experimental verification of the MEMS mirrors at 5° and 45° incidence angles validates the analytical results. A Blu-ray optical pick-up imaging demonstration shows the utility of these mirrors for focus control and spherical aberration correction. Imaging results of the first demonstration of a deformable mirror for dynamic agile focus control and spherical aberration correction in a commercial table-top confocal microscope are also shown.
Synthetic x-ray imager for solar plasma loops
(Montana State University - Bozeman, College of Engineering, 1998) Lundberg, Steven Kenneth
Extraction of data from digital images of microorganisms
(Montana State University - Bozeman, College of Engineering, 1993) Shope, Paul Andrew

Theses and Dissertations at Montana State University (MSU)

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