Browsing by Subject "imaging"
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Item Acquisition and reconstruction of brain tissue using knife-edge scanning microscopy(Texas A&M University, 2004-09-30) Mayerich, David MatthewA fast method for gathering large-scale data sets through the serial sectioning of brain tissue is described. These data sets are retrieved using knife-edge scanning microscopy, a new technique developed in the Brain Networks Laboratory at Texas A&M University. This technique allows the imaging of tissue as it is cut by an ultramicrotome. In this thesis the development of a knife-edge scanner is discussed as well as the scanning techniques used to retrieve high-resolution data sets. Problems in knife-edge scanning microscopy, such as illumination, knife chatter, and focusing are discussed. Techniques are also shown to reduce these problems so that serial sections of tissue can be sampled at resolutions that are high enough to allow reconstruction of neurons at the cellular level.Item Determining Nighttime Atmospheric Optical Depth Using Mars Exploration Rover Images(2013-07-22) Bean, Keri MarieMartian clouds and dust play an important part of the radiative transfer and energy balance budget. To assist in fully understanding the impact of clouds and dust, the complete diurnal cycle needs to be characterized. One of the best methods to track diurnal variations on Mars is by measuring optical depth. The spatial and temporal trends of optical depth give insight into the dust and water cycles of the Martian atmosphere. Until now, spacecraft could only obtain optical depth during the day. In this thesis, nighttime images from the Mars Exploration Rover Spirit are used to calculate nighttime optical depth using photometric methods to capture star flux. Bright stars in well-known constellations are used in this analysis. The observed flux was compared to the expected flux to give nighttime optical depth values. The observed nighttime optical depth was consistently similar to the daytime optical depth values on both an individual image and sol-averaged basis. Recommendations are made going forward to use the Mars Science Laboratory Curiosity for conducting an optimal nighttime optical depth campaign to fully characterize the diurnal dust and water cycles of Mars. The Curiosity rover is well suited for nighttime imaging and can potentially provide valuable insight into the nighttime dust and cloud trends.Item Developing luminescent nanoprobes for labeling focal adhesion complex proteins and performing combined AFM-TIRF imaging of these conjugates(Texas A&M University, 2008-10-10) Nathwani, Bhavik BharatRecent progress in the field of semiconductor nanocrystals or Quantum Dots (QDs) has seen them find wider acceptance as a tool in biomedical research labs. As produced, high quality QDs synthesized by high temperature organometallic synthesis, are coated with a hydrophobic ligand. Therefore, they must be further processed to be soluble in water and made biocompatible. A process to coat the QDs with silk fibroin, a fibrous protein derived from the Bombyx mori silk worm, is described. Following the coating process, the characterization of size, optical properties and biocompatibility profile of these particle systems is described. In addition, conjugation of the silk fibroin coated QDs to different labeling proteins such as phalloidin and streptavidin is described. Proteins on the surface of ovarian cancer cells (HeyA8) and of cytoskeletal components participating in the formation of focal adhesion complex (FAC), such as F-actin in endothelial cells (HUVECS) were labeled using the bio-conjugated QDs. Various imaging techniques such as epi-fluorescence, TIRF and AFM were used to study the QD labeled cells. Overall the project has produced luminescent nanoprobes that enable the study of FAC formation dynamics and potentially a better in vivo fluorescent marker tool.Item Development of the Ultrashort Pulse Nonlinear Optical Microscopy Spectral Imaging System(2012-10-19) Lee, Anthony Chien-derNonlinear Optical Microscopy (NLOM) has been shown to be a valuable tool for noninvasive imaging of complex biological systems. An effective approach for multicolor molecular microscopy is simultaneous excitation of multiple fluorophores by broadband sub-10-fs pulses. This dissertation will discuss the development of two spectral imaging systems using the principles of nonlinear optical microscopy for pixel-by-pixel spectral segmentation of multiple fluorescent spectra. The first spectral system is reliant on a fiber-optic cable to transmit fluorescent signal to a spectrometer, while the second is based on a spectrometer with an aberration-corrected concave grating that is directly coupled to the microscope. A photon-counting, 16-channel multianode photomultiplier tube (PMT) is used for both systems. Custom software developed in LabVIEW controls multiple counter cards as well as a field-programmable gate array (FPGA) for 1 Hz acquisition of 256x256x16 spectral images. Biological specimen consisting of multicolor endothelial cells and zebrafish will be used for experimental verification. Results indicate successful spectral segmentation of multiple fluorophores with a decrease in signal-to-noise ratio in the FPGA-based imaging system.Item Exploring Tools for Improving Negative Capture(Texas Digital Library, 2022-05-23) Mazzei, ErinIn just the past few years, the technology for digitizing slides and negatives has been evolving rapidly. Boosted in part by individual photographers seeking better quality for their own negatives, the result is a wide variety of commercial products to improve image results from both flatbed scanners and camera capture stations. How do some these options compare to each other for use at institutions? This poster proposes to test and compare the results of several types of negative holder and introduce a framework for evaluating the quality and efficiency of others.Item I Am Not a Photographer: One Librarian’s Journey Toward Understanding FADGI, Image Quality, and Digitization Best Practices(2017-05-25) Willis, Shannon; University of North TexasIn digitization labs that have grown out of library departments, it has become common place for librarians to be tasked with overseeing the imaging and digitization of cultural heritage collections. While librarians are well trained in library and information science, there can frequently be a gap in their imaging and photography knowledge, making the task of establishing imaging workflows and judging image quality a challenge. While guidelines for imaging exist, they are not always clear and how best to apply them is not always apparent. In September of 2016, The Federal Agencies Digital Guidelines Initiative (FADGI), the organization who has historically established guidelines for imaging in the United States, issued a new version of their guidelines including a star-rating system for image quality. But questions still remain as to who is using these guidelines, and how do they apply them if they do. To attempt to bridge the imaging knowledge gap, and in light of the new FADGI guidelines, the Digital Projects Lab Manager at the University of North Texas (UNT) conducted site visits at over a dozen digitizing institutions across the country. Institutions included in the study were the Library of Congress, the Smithsonian, Crowley Company, Northwestern University, Metropolitan Museum of Art, the University of Maryland, New York Public Library, Yale University, Boston Public Library, MIT, Harvard University, Stanford University, San Francisco Public Library, and the University of California at Berkley. Funded by an internal grant, the Lab Manager was able to tour each institution’s digitization space and speak with its head of imaging. In viewing a range of digitization labs and observing a variety of approaches to digitization work, several common threads between institutions became apparent. From how to best apply FADGI guidelines, to common tools used, to how the best-of-the-best do imaging, many lessons were learned from this research. With the information gleaned from these institutions, the Digital Lab Manager was able to better outline for her institution the ways imaging at UNT could be improved and offer a number of options for potential future paths forward. This presentation will illuminate much of what was gleaned from an investigation of various top digitization labs and how it can be applied.Item Image resolution analysis: a new, robust approach to seismic survey design(Texas A&M University, 2005-08-29) Tzimeas, ConstantinosSeismic survey design methods often rely on qualitative measures to provide an optimal image of their objective target. Fold, ray tracing techniques counting ray hits on binned interfaces, and even advanced 3-D survey design methods that try to optimize o?set and azimuth coverage are prone to fail (especially in complex geological or structural settings) in their imaging predictions. The reason for the potential failure of these commonly used approaches derives from the fact that they do not take into account the ray geometry at the target points. Inverse theory results can provide quantitative and objective constraints on acquisition design. Beylkin??s contribution to this ?eld is an elegant and simple equation describing a reconstructed point scatterer given the source/receiver distribution used in the imaging experiment. Quantitative measures of spatial image resolution were developed to assess the e?cacy of competing acquisition geometries. Apart from the source/receiver con?guration, parameters such as the structure and seismic velocity also in?uence image resolution. Understanding their e?ect on image quality, allows us to better interpret the resolution results for the surveys under examination. A salt model was used to simulate imaging of target points located underneath and near the ?anks of the diapir. Three di?erent survey designs were examined. Results from these simulations show that contrary to simple models, near-o?sets do not always produce better resolved images than far-o?sets. However, consideration of decreasing signal-to-noise ratio revealed that images obtained from the far-o?set experiment are degrading faster than the near-o?set ones. The image analysis was performed on VSP ?eld data as well as synthetics generated by ?nite di?erence forward modeling. The predicted image resolution results were compared to measured resolution from the migrated sections of both the ?eld data and the synthetics. This comparison con?rms that image resolution analysis provides as good a resolution prediction as the prestack Kirchho? depth migrated section of the synthetic gathers. Even in the case of the migrated ?eld data, despite the presence of error introducing factors (di?erent signal-to-noise ratios, shape and frequency content of source wavelets, etc.), image resolution performed well exhibiting the same trends of resolution changes at di?erent test points.Item Improving Fluorescence Lifetime Imaging Microscopy Deconvolution Using Constrained Laguerre Basis Functions(2014-04-25) Khatkhatay, Mohammed MFluorescence lifetime imaging microscopy (FLIM) is a noninvasive invasive optical imaging modality which is finding new applications in medical imaging. In FLIM, the fluorescence time decay is measured at a pixel. The fluorescence impulse response function (IRF) is then estimated using a deconvolution of the instrument response and the measured fluorescence time decay. Two of the challenges facing FLIM are speed of the deconvolution and the accuracy of the IRFs. The linear expansion of the fluorescence decays based on the orthonormal Laguerre basis functions (LBFs) is among the fastest methods for estimating the IRFs. The automated implementation to optimize the Laguerre parameter improves the speed of the deconvolution using the LBFs but uses a global optimization. Therefore, the IRFs do not necessarily mimic exponential time decays, or monotonically decreasing functions. On the other hand, applying a constraint to the LBFs using the Active Set Nonnegative Least Squares (NNLS) method improves the IRF estimation. The estimation of the Laguerre parameter using the NNLS method, however, is about 10-15x slower. By combining these two deconvolution techniques, we found that the deconvolution time is similar to the automated global Laguerre parameter deconvolution while the IRF estimation always results in a monotonically decreasing function.Item Nanoscale Light Focusing and Imaging with Nano-Optical Devices(2014-09-23) Meenashi Sundaram, VijayEnergy transport analysis of micro/nano optics as well as their optimization to achieve high-throughput deep nanoscale patterning and microscopy is the goal of this study. To understand the energy transport in nano-optical devices, the transient heating behavior of a commercial available nano-optical probe, NSOM, under pulsed laser operation is examined first. Based on the thermal analysis, it is observed that the major limitation of the NSOM probe under higher energy operation arises from the joule heating of its thin metal coating and the resulting thermal/mechanical damage during operation. Based on the understanding, a diffraction-based micro-zone plate (MZP) optical probe suffers less from joule heating and with advantages of higher optical throughput as well as longer working distance is designed and constructed. The MZP is fabricated at the end face of an optical fiber with a micro-fabrication technique based on e-beam negative tone lift-off lithography on non-planar substrates. The fabricated MZP can achieve spot sizes ~ 0.7? at a focus distance of ~ 6? with an optical transport efficiency of 20 %, which is more than 3 orders higher than that of NSOM. To further reduce the size of the focus spot to deep sub-wavelength scales and to eliminate metallic structures which can cause joule heating during high energy operation, two all-dielectric optical probes are then designed/constructed, namely, (a) solid immersion probe, and (b) scattering dielectric probe. Both dielectric probes focus light by combining more than one of the diffraction mechanisms associated with dielectric material (e.g., refraction, solid immersion, Mie and near-field Rayleigh scattering) to achieve deep nanoscale light focusing with minimum energy loss. The solid immersion optical probe is constructed with a ball lens and microsphere for macro to micro scale focusing with far field refraction and micro to mesocale focusing with solid immersion. The ball lens and the microsphere are stacked on an optical fiber for achieving the cascade focusing configuration. The solid immersion probe can achieve a focus spot size of ~ 0.45?/n (~ 0.3? when n = 1.5) on a target in the near field of the surface of the microsphere when the light is radially polarized. To achieve an even smaller focal spot in the near field, the scattering dielectric optical probe combines the verified solid immersion probe with a nano-scatterer at its focal spot. Due to the near-field Rayleigh scattering, the nano scatterer can induce a deep nanoscale spot with a diameter comparable to the forward radius of curvature of the scatterer under radially polarized light. It is verified with full wave electrodynamics simulations that the resulting scattering optical probe can achieve a ~10 nm spot with an intensity enhancement of ~ 10^5, which can be valuable in all kinds of bio-detection as well as nano fabrications. At the end of the Ph.D study, mechanisms for deep sub-wavelength imaging resolutions with microspheres, which is recently demonstrated in different groups, are identified with full wave electrodynamics simulations. It is found that the high spatial imaging resolution of microlenses can be attributed to refractive index of the microsphere which is placed on the target plane (i.e. solid immersion effect), refractive index of the base material of the target and polarization of the emitters.Item Rethinking "But this is how we've always done it!"(2016-05-26) Willis, Shannon Nicole; University of North TexasIn the world of digital imaging, digital projects and labs can often get into a rut when it comes to digitizing procedures and workflows. Staff and workers alike can resist change or alterations to their processes, claiming “But this is how we’ve always done it.” Beyond the factuality of this statement being dubious in many cases (considering the relative youth of most digital projects), this is not the best reason to maintain any standard or workflow. This presentation looks at imaging and workflow testing as a way to define sound reasons for using given digitization procedures in the Digital Projects Lab at the University of North Texas. The presenter examined several possible imaging procedures (including scanner settings and post-scanning processing), both old and new to the lab, to identify the workflow that produced the most faithful representation of the items being digitized. Data collected using visual surveys by the digital lab staff better enabled the lab to identify the most efficient and accurate workflow for the digitization work.Item Root Morphological and Physiological Bases to Understand Genotypic Control of Mineral Acquisition in Rice Grains(2012-11-28) Chittoori, Ratnaprabha 1982-Rice (Oryza sativa L.) supports half of the human population. However, predominant rice consumption leads to malnutrition due to mineral deficiencies. The research goal was to support identification of genes responsible for the uptake/accumulation of potassium (K), iron (Fe), zinc (Zn) and molybdenum (Mo), thus promoting the breeding for rice with high grain concentrations of these elements. Prior studies identified rice genotypes with high grain-K, -Fe, -Zn or -Mo concentrations that were hypothesized to be due to differences in root traits. The research objective was to identify root traits associated with these elements. These traits could be bases for identifying genes. The first study determined if these genotypes showed similar accumulation patterns in leaves as in grains, which would hint at influences of the roots and enable identifying distinct root traits and possible genes in vegetative growth stages. The second study determined if root traits of high grain-Mo genotypes displayed an acid-tolerance mechanism as these genotypes originated from Malaysia where acidic soils strongly adsorb Mo making it unavailable for plants. The third study identified root trait differences of high grain-K, -Fe, -Zn and -Mo genotypes in hydroponics media, while the fourth determined root trait differences in these genotypes in sand-culture media including a 1-Naphthalene Acetic Acid (NAA) seed treatment for perturbation. The first study identified several high grain-Mo genotypes with similar Mo accumulation patterns in V4 to V6 stage-leaves as in grains, suggestive of a root influence. The second study established that gross morphological and physiological root traits of a high grain-Mo genotype were not part of an acid-tolerance mechanism. Neither the third nor fourth study identified root traits related to shoot K, Fe, Zn or Mo concentration, however positive associations of seedling vigor traits with several beneficial elements, including K, and negative associations with numerous toxic elements were established. Lack of correlation with root traits suggests other mechanisms (e.g. active uptake transporters) instead control the observed grain accumulation differences. Based on the fourth study, either direct effects of NAA on element uptake/transfer or indirect effects on soil pH and redox potential altered tissue Fe and Zn levels.Item Saving the Byrds: Reshaping Digitization Workflows for Photographic Materials(Texas Digital Library, 2023-05-18) Ekberg, SamanthaFrom 2019 to 2022 the University of North Texas Libraries was awarded a TexTreasures grant to digitize materials from the Byrd Williams Family Photography Collection. The Collection includes film and prints documenting more than 100 years of North Texas history through four generations of photographers in the Williams family. Due to the uniqueness, fragility, and historical value of some film, it was decided the materials selected for digitization would be digitized at a higher standard than other university collections to meet partner requests. Over the multi-year project, new equipment was acquired and workflows were adjusted and customized to properly address all the uniquely sized and degraded film. The presentation will detail the customized workflow established for this collection, as well as the unique problems and solutions that arose throughout the course of the project.Item Session 1C | TDL Imaging Group Birds-of-a-Feather(Texas Digital Library, 2021-05-24) Willis, Shannon; Mazzei, Erin; Jones, Jerrell; McIntosh, MarciaInterested in imaging projects, formats, standards, project management or anything else relating to digitization? Stop by the TDL Imaging Group’s Birds-of-a-Feather Meeting. This group was formed to hash out problems, cultivate interest, and trade regional imaging knowledge in an inviting and inclusive setting. Attendees of this birds-of-a-feather will be able to discuss among peers their imaging specific issues and triumphs, including, but not limited to, how the field has coped and adapted during the pandemic.Item Session 2E | How it’s Going: Creating and Modifying Camera Capture Stations at Texas State University(Texas Digital Library, 2021-05-25) Mazzei, ErinIn 2017, Texas State University received a TSLAC TexTreasures Grant, funded by the U.S. Institute of Museum and Library Services, to digitize at-risk photographic negatives in the University Archives. Since then, tens of thousands of negatives and documents have been captured through the two custom camera stations purchased through this grant and a number of additional changes to the original configuration were added to help improve function. This presentation will cover the on-going development of the stations themselves, including an overview of the benefits and risks of implementing a custom camera station, as well as lessons learned.Item The Texas Digital Library Digital Imaging Inventory Project(Texas Digital Library, 2020-05-15) Buchanan, Elizabeth