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Girirajan, Thanu Prabha Kalambur. "Development of Spectral Imaging Microscope for Single Molecule Studies in Complex Biological Systems." Fogler Library, University of Maine, 2007. http://www.library.umaine.edu/theses/pdf/GirirajanTPK2007.pdf.
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Bilyeu, Taylor Thomas. "Crystallographic Image Processing with Unambiguous 2D Bravais Lattice Identification on the Basis of a Geometric Akaike Information Criterion." Thesis, Portland State University, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=1541427.
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Crystallographic image processing (CIP) is a technique first used to aid in the structure determination of periodic organic complexes imaged with a high-resolution transmission electron microscope (TEM). The technique has subsequently been utilized for TEM images of inorganic crystals, scanning TEM images, and even scanning probe microscope (SPM) images of two-dimensional periodic arrays. We have written software specialized for use on such SPM images. A key step in the CIP process requires that an experimental image be classified as one of only 17 possible mathematical plane symmetry groups. The current methods used for making this symmetry determination are not entirely objective, and there is no generally accepted method for measuring or quantifying deviations from ideal symmetry. Here, we discuss the crystallographic symmetries present in real images and the general techniques of CIP, with emphasis on the current methods for symmetry determination in an experimental 2D periodic image. The geometric Akaike information criterion (AIC) is introduced as a viable statistical criterion for both quantifying deviations from ideal symmetry and determining which 2D Bravais lattice best fits the experimental data from an image being processed with CIP. By objectively determining the statistically favored 2D Bravais lattice, the determination of plane symmetry in the CIP procedure can be greatly improved. As examples, we examine scanning tunneling microscope images of 2D molecular arrays of the following compounds: cobalt phthalocyanine on Au (111) substrate; nominal cobalt phthalocyanine on Ag (111); tetraphenoxyphthalocyanine on highly oriented pyrolitic graphite; hexaazatriphenylene-hexacarbonitrile on Ag (111). We show that the geometric AIC procedure can unambiguously determine which 2D Bravais lattice fits the experimental data for a variety of different lattice types. In some cases, the geometric AIC procedure can be used to determine which plane symmetry group best fits the experimental data, when traditional CIP methods fail to do so.
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Cuevas, Assunta Mariela. "Microstructure characterization of friction-stir processed nickel-aluminum bronze through orientation imaging microscopy." Thesis, Monterey, Calif. : Springfield, Va. : Naval Postgraduate School ; Available from National Technical Information Service, 2002. http://library.nps.navy.mil/uhtbin/hyperion-image/02sep%5FCuevas.
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Nellist, Peter David. "Image resolution improvement in scanning transmission electron microscopy." Thesis, University of Cambridge, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361613.
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Simmonds, Richard. "Adaptive optics for microscopy and photonic engineering." Thesis, University of Oxford, 2012. https://ora.ox.ac.uk/objects/uuid:0f1ed5cc-4e21-4ff5-9444-c9be0e3646e4.
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Aberrations affect the operation of optical systems, particularly those designed to work at the diffraction limit. These systems include high-resolution microscopes, widely used for imaging in biology and other areas. Similar problems are encountered in photonic engineering, specifically in laser fabrication systems used for the manufacture of fine structures. The work presented in this thesis covers various aspects of adaptive optics developed for applications in microscopes and laser fabrication. By mathematically modelling a range of idealised fluorescent structures, the effect of different aberrations on their intensity in various microscopes is presented. The effect of random aberrations on the contrast of these different structures is then calculated and the results displayed on idealised images. Images from a two-photon microscope demonstrate the predicted results. The contrast of two structures is compared when imaged first by a conventional microscope and then by the two-photon or confocal sectioning microscopes. The different specimen structures were seen to be affected to varying extents by each aberration mode. In order to correct for aberrations in microscopy and other photonic applications, adaptive elements such as deformable mirrors are incorporated into the optical setups. An important step is to train the deformable mirror so that it produces appropriate mode shapes to apply a phase to optical wavefronts. One such mirror is modelled using the membrane equation to predict the surface shape when an actuator is applied. Each of these influence functions is combined to produce a set of orthogonal mirror modes, which are used to experimentally produce a set of empirical modes in a two-photon microscope. An alternative method of training a deformable mirror from a spatial light modulator is employed. The focal spot of an optical system is imaged to provide a feedback metric for the mirror to replicate the phase pattern on the spatial light modulator. A two-photon microscope with adaptive optics is demonstrated by imaging the brains of Drosophila deep within the bulk, correcting for both system and specimen induced aberrations using the deformable mirror with empirical mirror modes applied. A harmonic generation microscope is also used to image both biological and non-biological specimens whilst performing aberration correction with a deformable mirror. Adaptive optical methods are also applied to a laser fabrication system, by constructing a dual adaptive optics setup to correct for aberrations induced when fabricating deep in the bulk of a substrate. The efficiency and fidelity of fabrication in diamond substrate is shown to be significantly increased as a result of the dual aberration correction. An outstanding problem in microscopy is the effect of spatially variant aberrations. Using measurements from the adaptive microscopes, the extent to which they are present in a range of specimens is quantified. One potential technique to be used to correct for these aberrations is multi-conjugate adaptive optics. Different configurations of a multi-conjugate adaptive optics system are modelled and the improvement on the Strehl ratio of aberrated images quantified for both simulated images and real data. The application of this technique in experimental microscopes is considered.
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Elad, Nadav. "GroEL mediated protein folding studied by electron microscopy and image processing." Thesis, Birkbeck (University of London), 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.498330.
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Kola, B. O. "Development of an image processing workstation for scanning Auger electron microscopy." Thesis, University of York, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.374183.
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Dyson, Mark Adam. "Advances in computational methods for transmission electron microscopy simulation and image processing." Thesis, University of Warwick, 2014. http://wrap.warwick.ac.uk/72953/.
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Modern electron microscopes are fitted with ever larger charge-coupled device (CCD) cameras capable of faster acquisition rates which in turn drives a concomitant increase in the bandwidth of data that is being collected and the amount of information in our datasets. At the same time, current increases in computational performance are largely being delivered through the addition of parallel execution units rather than explicit increases in the speed of single processors, this means techniques that cannot exploit their inherent parallelism are seeing little performance benefit from the generational improvements in computer processors. Many techniques used in electron microscopy to process these large datasets have not been adapted to utilise the modern methods available for parallel data processing which can lead to lengthy offline data processing techniques which could otherwise be performed in near real-time. Reimagining these methods to suit highly parallel computational architectures such as graphics processing units (GPUs) can offer improved performance orders of magnitude higher than their central processing unit (CPU) counterparts. In this thesis I have looked specifically at the case of transmission electron microscopy (TEM) image simulation via the multislice procedure, and exit wave reconstruction (EWR), which can both potentially see huge benefits by adapting these algorithms to exploit their parallelism. Software has been developed for performing multislice simulations using GPU computation where the increase in computational power also allows for modifications to be made which can increase the accuracy of the simulations at the expense of simulation time. The multislice software developed here has no minimum slice thickness limitations and the slice thickness no longer has to be coupled to the structure being simulated to ensure accuracy. The CCD detector characteristics and electron dose have also been incorporated within the simulation process. The use of GPUs has allowed these simulations to be performed in vastly less time than CPUs based equivalent simulations. Software has also been developed for performing EWR on either multicore CPUs or GPUs which lowers the time required to perform EWR sufficiently that real-time reconstruction at typical CCD frame-rates is a distinct possibility. This EWR software additionally features mutual information (MI) based image alignment which can handle accurate image alignment in cases where other methods are prone to failure. These software are used to aid in the investigation of fluorinated graphene conformation via multislice simulation and EWR, and in the study of self-assembled block co-polymer assemblies also by EWR.
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Roseman, Alan Michael. "Three dimensional structures of chaperonin complexes by electron microscopy and image processing." Thesis, Birkbeck (University of London), 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.267764.
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Cannone, Giuseppe. "Structural investigation of the archaeal replicative machinery by electron microscopy and digital image processing." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/17070.
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Previous studies suggest a degree of homology between eukaryotic replication, transcription and translation proteins and archaeal ones. Hence, Archaea are considered a simplified model for understanding the complex molecular machinery involved in eukaryotic DNA metabolism. DNA replication in eukaryotic cells is widely studied. In recent years, DNA replication studies expanded on the archaeal DNA replication machinery. P. abyssi was the first archaeon whose genome was fully sequenced. Genome sequencing and comparative genomics have highlighted an MCM-like protein in P. abyssi. In this study, I report the biochemical and structural characterisation of PabMCM. PabMCM is explored as model for understanding more complex eukaryotic MCM proteins and unravelling the biochemical mechanism by which MCM proteins release their helicase activity. The crenarchaeon Sulfolobus solfataricus possesses a simplified toolset for DNA replication compared to Eukaryotes. In particular, S. solfataricus has a subset of the eukaryotic Okazaki fragment maturation factors, among which there are a heterotrimeric DNA sliding clamp, (the proliferating cell nuclear antigen, PCNA), the DNA polymerase B1 (PolB1), the flap endonuclease (Fen1) and the ATP-dependent DNA ligase I (LigI). PCNA functions as a scaffold with each subunit having a specific binding affinity for each of the factors involved in Okazaki fragment maturation. Here, the 3D reconstruction of PCNA in complex with the Okazaki fragment maturation proteins PolB1, LigI and Fen1 is reported.
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Xinyu, Chang. "Neuron Segmentation and Inner Structure Analysis of 3D Electron Microscopy Data." Kent State University / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=kent1369834525.
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Dias, Philipe Ambrozio. "In situ microscopy for analysis of filamentous bacteria: optics end image evalaution." Universidade Tecnológica Federal do Paraná, 2016. http://repositorio.utfpr.edu.br/jspui/handle/1/1999.
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CAPES; CNPqIn the activated sludge process, problems of foaming and filamentous bulking can occur due to overgrowth of certain filamentous bacteria. Nowadays, these microorganisms are typically monitored by means of light microscopy combined with staining techniques. As drawbacks, these methods are susceptible to human errors, subjectivity and limited by the use of discontinuous microscopy. The present project aims the application of an in situ microscope (ISM) for continuous monitoring of filamentous bacteria, providing real-time examination, automated analysis and elimination of sampling, preparation and transport of samples. The ISM previously developed at the Hochschule Mannheim required adaptations for use within wastewater environment, specially in terms of impermeability and development of a cleaning mechanism. With a new objective lens design, the system was simplified to a single tubus and an externally activated cleaning system based on magnetism was created. A proper image processing algorithm was designed for automated recognition and measurement of filamentous objects, allowing real-time evaluation of images without any staining, phase-contrast or dilution techniques. Three main operations are performed: preprocessing and binarization; recognition of filaments using distance-maps and shape descriptors; measurement and display of total extended filament length. A 3D-printed prototype was used for experiments with respect to the new ISM’s design, providing images with resolution very close to the ones acquired with the previous microscope. The designed cleaning system has shown to be effective, removing dirt settled above the lens during tests. For evaluation of the image processing algorithm, samples from an industrial activated sludge plant were collected weekly for a period of twelve months and imaged without any prior conditioning, replicating real environment conditions. Experiments have shown that the developed algorithm correctly identifies trends of filament growth rate, which is the most important parameter for decision making. For reference images whose filaments were marked by specialists, the algorithm correctly recognized 72% of the filaments pixels, with a false positive rate of at most 14%. An average execution time of 0.7 second per image was achieved, demonstrating the algorithm suitability for real-time monitoring.
Em processos de lodo ativado, problemas de foaming e filamentous bulking podem ocorrer devido ao crescimento exagerado de bactérias filamentosas. Atualmente, o monitoramento de tais micro-organismos é feito por meio de métodos baseados em microscopia ótica combinada com técnicas de marcadores, os quais apresentam limitações intrínsecas da microscopia descontínua, são subjetivos e suscetíveis a erro humano. O presente projeto visa a aplicação de um microscópio in situ (ISM) para monitoramento contínuo de bactérias filamentosas, de forma a possibilitar análise instantânea, computadorizada, sem necessidades de recolher, preparar e transportar amostras. O ISM previamente desenvolvido na Hochschule Mannheim teve que ser adaptado para análise de águas residuais, especialmente em termos de impermeabilidade e a criação de um mecanismo de limpeza. Com a utilização de uma nova objetiva, o novo ISM foi simplificado para um tubo único e um sistema de limpeza ativado externamente baseado em magnetismo foi criado. Um algoritmo de processamento de imagens foi elaborado para reconhecimento e medição de comprimento de estruturas filamentosas, permitindo avaliação em tempo real de imagens sem qualquer técnica de marcadores, contraste de fase ou diluição. O mesmo consiste em três operações principais: pré-processamento e binarização; reconhecimento de filamentos por meio de mapeamento de dis- tâncias e descritores de forma; e, finalmente, medição e visualização do comprimento de cada filamento. Um protótipo construído via impressão 3D foi utilizado para avaliação o novo design do microscópio, fornecendo imagens com resolução bastante próxima das adquiridas com a versão anterior do sistema. O mecanismo de limpeza desenvolvido mostrou-se efetivo, capaz de remover partículas sedimentadas acima das lentes durante os testes. Para avaliação do algoritmo de processamento de imagens, amostras de uma planta industrial de lodo ativado foram coletadas semanalmente por um período de doze meses e imageadas sem qualquer condicionamento prévio, replicando condições reais de ambiente. Experimentos demonstraram que o algoritmo desenvolvido identifica corretamente tendências de aumento/decréscimo da concentração de filamentos, o que constitui o principal parâmetro para tomadas de decisão. Para imagens de referência cujos filamentos foram marcados por especialistas, o algoritmo reconheceu corretamente 80% dos pixels atribuídos a filamentos, com uma taxa de falso positivos de até 24%. Um tempo de execução médio de 0,7 segundo por imagem foi obtido, provando sua aptidão para formar uma ferramenta de monitoramento em tempo real.
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Hennessy, Richard Joseph. "STUDYING MILK COAGULATION KINETICS WITH LASER SCANNING CONFOCAL MICROSCOPY, IMAGE PROCESSING, AND COMPUTATIONAL MODELING." DigitalCommons@CalPoly, 2011. https://digitalcommons.calpoly.edu/theses/587.
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The kinetics of milk coagulation are complex and still not well understood. A deeper understanding of coagulation and the impact of the relevant factors would aid in both cheese manufacturing and also in determining the nutritional benefits of dairy products. A method using confocal microscopy was developed to follow the movement of milk fat globules and the formation of a milk protein network during the enzyme-induced coagulation of milk. Image processing methods were then used to quantify the rate of coagulation. It was found that the texture of the protein network is an indicator of the current status of the milk gelation, and hence can be used to monitor the coagulation process. The imaging experiment was performed on milk gels with different concentrations of the coagulation enzyme, chymosin. Rheological measurements were taken using free oscillation rheometry to validate the imaging results. Both methods showed an inverse relationship between rennet concentration and the coagulation time.
The results from the imaging study were used to create a computational model, which created simulated images of coagulating milk. The simulated images were then analyzed using the same image analysis algorithm. The temporal protein network texture behavior in the simulated images followed the same pattern as the protein texture in the confocal imaging data. The model was developed with temperature and rennet concentration as user inputs so that it could be implemented as a predictive tool for milk coagulation.
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Lee, Dong Gun. "Strain measurement of flip-chip solder bumps using digital image correlation with optical microscopy." Diss., Online access via UMI:, 2009.
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Thesis (M.S.)--State University of New York at Binghamton, Thomas J. Watson School of Engineering and Applied Science, Department of Mechanical Engineering, 2009.Includes bibliographical references.
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Moon, Bill. "Employment of Crystallographic Image Processing Techniques to Scanning Probe Microscopy Images of Two-Dimensional Periodic Objects." PDXScholar, 2011. https://pdxscholar.library.pdx.edu/open_access_etds/699.
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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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Kylberg, Gustaf. "Automatic Virus Identification using TEM : Image Segmentation and Texture Analysis." Doctoral thesis, Uppsala universitet, Avdelningen för visuell information och interaktion, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-217328.
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Viruses and their morphology have been detected and studied with electron microscopy (EM) since the end of the 1930s. The technique has been vital for the discovery of new viruses and in establishing the virus taxonomy. Today, electron microscopy is an important technique in clinical diagnostics. It both serves as a routine diagnostic technique as well as an essential tool for detecting infectious agents in new and unusual disease outbreaks. The technique does not depend on virus specific targets and can therefore detect any virus present in the sample. New or reemerging viruses can be detected in EM images while being unrecognizable by molecular methods. One problem with diagnostic EM is its high dependency on experts performing the analysis. Another problematic circumstance is that the EM facilities capable of handling the most dangerous pathogens are few, and decreasing in number. This thesis addresses these shortcomings with diagnostic EM by proposing image analysis methods mimicking the actions of an expert operating the microscope. The methods cover strategies for automatic image acquisition, segmentation of possible virus particles, as well as methods for extracting characteristic properties from the particles enabling virus identification. One discriminative property of viruses is their surface morphology or texture in the EM images. Describing texture in digital images is an important part of this thesis. Viruses show up in an arbitrary orientation in the TEM images, making rotation invariant texture description important. Rotation invariance and noise robustness are evaluated for several texture descriptors in the thesis. Three new texture datasets are introduced to facilitate these evaluations. Invariant features and generalization performance in texture recognition are also addressed in a more general context. The work presented in this thesis has been part of the project Panvirshield, aiming for an automatic diagnostic system for viral pathogens using EM. The work is also part of the miniTEM project where a new desktop low-voltage electron microscope is developed with the aspiration to become an easy to use system reaching high levels of automation for clinical tissue sections, viruses and other nano-sized particles.
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Philipp, Katrin, André Smolarski, Nektarios Koukourakis, Andreas Fischer, Moritz Stürmer, Ulrike Wallrabe, and Jürgen W. Czarske. "Volumetric HiLo microscopy employing an electrically tunable lens." Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-219727.
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Electrically tunable lenses exhibit strong potential for fast motion-free axial scanning in a variety of microscopes. However, they also lead to a degradation of the achievable resolution because of aberrations and misalignment between illumination and detection optics that are induced by the scan itself. Additionally, the typically nonlinear relation between actuation voltage and axial displacement leads to over- or under-sampled frame acquisition in most microscopic techniques because of their static depth-of-field. To overcome these limitations, we present an Adaptive-Lens-High-and-Low-frequency (AL-HiLo) microscope that enables volumetric measurements employing an electrically tunable lens. By using speckle-patterned illumination, we ensure stability against aberrations of the electrically tunable lens. Its depth-of-field can be adjusted a-posteriori and hence enables to create flexible scans, which compensates for irregular axial measurement positions. The adaptive HiLo microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 μm and sub-micron lateral resolution over the full scanning range. Proof of concept measurements at home-built specimens as well as zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are shown.
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Philipp, Katrin, André Smolarski, Nektarios Koukourakis, Andreas Fischer, Moritz Stürmer, Ulrike Wallrabe, and Jürgen W. Czarske. "Volumetric HiLo microscopy employing an electrically tunable lens." Optical Society of America, 2016. https://tud.qucosa.de/id/qucosa%3A30185.
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Electrically tunable lenses exhibit strong potential for fast motion-free axial scanning in a variety of microscopes. However, they also lead to a degradation of the achievable resolution because of aberrations and misalignment between illumination and detection optics that are induced by the scan itself. Additionally, the typically nonlinear relation between actuation voltage and axial displacement leads to over- or under-sampled frame acquisition in most microscopic techniques because of their static depth-of-field. To overcome these limitations, we present an Adaptive-Lens-High-and-Low-frequency (AL-HiLo) microscope that enables volumetric measurements employing an electrically tunable lens. By using speckle-patterned illumination, we ensure stability against aberrations of the electrically tunable lens. Its depth-of-field can be adjusted a-posteriori and hence enables to create flexible scans, which compensates for irregular axial measurement positions. The adaptive HiLo microscope provides an axial scanning range of 1 mm with an axial resolution of about 4 μm and sub-micron lateral resolution over the full scanning range. Proof of concept measurements at home-built specimens as well as zebrafish embryos with reporter gene-driven fluorescence in the thyroid gland are shown.
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Walker, Alasdair Michael. "Extrusion processing of chocolate crumb paste." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:1c54a2e6-a767-4fd3-8bf0-e2d250b7ac4a.
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This project considers the co-rotating twin screw extrusion of a confectionery paste comprising powdered proteins, sugars, water and fats. As is the case with many food industry products, this process has been developed experimentally with little quantitative understanding of how variations in processing conditions influence the formation of the extrudate. A variety of techniques have therefore been developed to characterise and quantify the dispersive mixing, distributive mixing and rheological flow properties of this complex, multiphase, viscoelastic, unstable material. These techniques have then been utilised in a pilot plant extruder study of the mechanics of mixing and paste formation during extrusion, considering the influence of both processing conditions and screw profile. The internal evolution of paste microstructure has been successfully tracked along the length of screw profile using dead-stop extractions of the screws. A rigorous off-line assessment of shear yield strength behaviour using cone penetrometry has shown the use of conventional off-line rheometers to be unviable due to rapid post extrusion hardening. This highlighted the need for an in-line rheological measurement technique for continuous extrusion analysis where the extruded material is severely time dependent and not extractable. In pursuit of this, a novel arrangement of bender elements is proposed and trialled, to rapidly characterise material parameters of viscoelastic pastes. A second technique looking to extend the application of shear wave interface reflection to multiphase pastes is also trialled. A novel analysis of thermogravimetric data (TGA) has generated a viable index of distributive mixing, suitable for use on complex multi-component materials where thermal decomposition temperatures of the components are not well defined. Quantitative image analysis of pastes using scanning electron microscopy (SEM), optical microscopy protein staining and a novel application of multiphoton microscopy (MPM) have been used to visualise paste microstructure and quantify dispersive mixing. From the pilot plant extruder study, the application of these techniques was successful in mapping the evolution of paste mixing and the resulting microstructure, as well as identifying key differences between pastes mixed by twin screw extrusion and batch mixing.
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Calíope, Priscila Braga. "Caracterização de nanofibras através de técnicas de processamento de imagens." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/3/3142/tde-28102009-172405/.
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O electrospinning (deposição eletrostática) representa um método simples e conveniente para preparar bras poliméricas e bras cerâmicas com interiores sólidos ou ocos, excepcionalmente longos em comprimento, uniformes no diâmetro, variando no intervalo de dezenas de nanômetros a vários micrômetros, com diversicadas composições. Apesar da potencialidade e versatilidade da Microscopia Eletrônica de Varredura existe um grande problema de caracterizar nanobras, já que este processo não é feito automaticamente. Este trabalho apresenta uma nova metodologia para extração automática de medidas em imagens SEM, como uma alternativa eciente em relação aos softwares semi-automáticos propostos na literatura. A metodologia proposta envolve o processamento das imagens SEM usando Morfologia Matemática e os resultados obtidos são discutidos e comparados àqueles processados por Redes Neurais Celulares e pelo método de Otsu. Imagens coletadas do microscópio foram analisadas por técnicas de processamento de imagens para determinação do diâmetro das nanobras. Os resultados mostraram boa concordância entre as metodologias estudadas e o método padrão-ouro indicando que os mesmos podem substituí-lo para constituir uma alternativa automática na caracterização de nanobras.The electrospinning technique represents a simple and convenient process to provide polymers and ceramics bers with both solid and hollow interiors that are exceptionally long in length, uniform in diameter, varying within the interval of few nanometers to several microns, and diversied in composition. Despite the versatility and potencially the scanning electron microscopy (SEM) there is a serious problem to characterize nanobers, as it is not made automatically. This work presents novel methodology software for automatic measurement in SEM images, as an eficient alternative in comparison with semi-automatic softwares proposed in literature. The proposed methodology involves the image processing SEM using Mathematical Morphology and the obtained results are argued and compared with those processing for Celullar Neural Network and Otsu method. The microscope images were assessed and analysed by imagery processing techniques to determinate diameters of nanobers. The results has shown good agreement between the investigated and gold standard methods suggesting that the same ones can substitute it to constitute an automatic alternative in the nanobers characterization.
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Moebel, Emmanuel. "New strategies for the identification and enumeration of macromolecules in 3D images of cryo electron tomography." Thesis, Rennes 1, 2019. http://www.theses.fr/2019REN1S007/document.
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La cryo-tomographie électronique (cryo-ET) est une technique d'imagerie capable de produire des vues 3D de spécimens biologiques. Cette technologie permet d’imager de larges portions de cellules vitrifiées à une résolution nanométrique. Elle permet de combiner plusieurs échelles de compréhension de la machinerie cellulaire, allant des interactions entre les groupes de protéines à leur structure atomique. La cryo-ET a donc le potentiel d'agir comme un lien entre l'imagerie cellulaire in vivo et les techniques atteignant la résolution atomique. Cependant, ces images sont corrompues par un niveau de bruit élevé et d'artefacts d'imagerie. Leur interprétabilité dépend fortement des méthodes de traitement d'image. Les méthodes computationelles existantes permettent actuellement d'identifier de larges macromolécules telles que les ribosomes, mais il est avéré que ces détections sont incomplètes. De plus, ces méthodes sont limitées lorsque les objets recherchés sont de très petite taille ou présentent une plus grande variabilité structurelle. L'objectif de cette thèse est de proposer de nouvelles méthodes d'analyse d'images, afin de permettre une identification plus robuste des macromolécules d'intérêt. Nous proposons deux méthodes computationelles pour atteindre cet objectif. La première vise à réduire le bruit et les artefacts d'imagerie, et fonctionne en ajoutant et en supprimant de façon itérative un bruit artificiel à l'image. Nous fournissons des preuves mathématiques et expérimentales de ce concept qui permet d'améliorer le signal dans les images de cryo-ET. La deuxième méthode s'appuie sur les progrès récents de l'apprentissage automatique et les méthodes convolutionelles pour améliorer la localisation des macromolécules. La méthode est basée sur un réseau neuronal convolutif et nous montrons comment l'adapter pour obtenir des taux de détection supérieur à l'état de l'artCryo electron tomography (cryo-ET) is an imaging technique capable of producing 3D views of biological specimens. This technology enables to capture large field of views of vitrified cells at nanometer resolution. These features allow to combine several scales of understanding of the cellular machinery, from the interactions between groups of proteins to their atomic structure. Cryo-ET therefore has the potential to act as a link between in vivo cell imaging and atomic resolution techniques. However, cryo-ET images suffer from a high amount of noise and imaging artifacts, and the interpretability of these images heavily depends on computational image analysis methods. Existing methods allow to identify large macromolecules such as ribosomes, but there is evidence that the detections are incomplete. In addition, these methods are limited when searched objects are smaller and have more structural variability. The purpose of this thesis is to propose new image analysis methods, in order to enable a more robust identification of macromolecules of interest. We propose two computational methods to achieve this goal. The first aims at reducing the noise and imaging artifacts, and operates by iteratively adding and removing artificial noise to the image. We provide both mathematical and experimental evidence that this concept allows to enhance signal in cryo-ET images. The second method builds on recent advances in machine learning to improve macromolecule localization. The method is based on a convolutional neural network, and we show how it can be adapted to achieve better detection rates than the current state-of- the-art
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Matějka, Milan. "Pozorování izolantů v ESEM." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2008. http://www.nusl.cz/ntk/nusl-217628.
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This graduation theses in introduction deals with principle and problems of electron signal detection in scanning electron microscopy and charging of insulating specimens in SEM. The experimental part of the thesis describe the methods of qualification and quantification of insulating specimen charging effect observed in environmental scanning electron microscope through the use of ionisation and scintillation detector in dependence on water vapour pressure in specimen chamber. The goal of the thesis is formation of the methodics useful to evaluate charging effect at insulating specimens observing and on the basis of measuring, determine optimal conditions for insulating specimen observation with ionisation and scintillation detector.
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Le, Floch Hervé. "Acquisition des images en microscopie electronique a balayage in situ." Toulouse 3, 1986. http://www.theses.fr/1986TOU30026.
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Chaine d'acquisition du signal image du mebis. Etude des sources de bruit associees aux detecteurs a semiconducteur et mise au point d'un processus de realisation de diodes de detection a barriere de surface. Conception d'une carte electronique compatible avec un microordinateur. Cette carte permet la numerisation, le stockage sur disquette et la visualisation des images fournies par le mebis
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Gorley, Michael. "Powder processing of oxide dispersion strengthened steels for nuclear applications." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6a3f2843-d87d-45b8-8c41-676220412813.
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Ferritic ODS steels show improved high temperature strength and irradiation tolerance compared with conventional ferritic steels, and are one of the key potential materials for fusion blanket structural applications. The processing of ODS steels is critical to their subsequent performance; however knowledge of the optimum processing approaches for these alloys is not complete. The microstructural evolution of ODS steels containing Y2O3 and other additions during manufacture has been investigated and the processing conditions optimised based on microstructural and mechanical investigations. Ferritic powders with Y2O3 and other additions were investigated, primarily using analysis on the micro- and nano-scale, with an emphasis on identifying the requirements for homogenization of the Y within the steel matrix. The Y2O3 dispersion and subsequent development of the nano-precipitates during thermal treatment was investigated using in-situ neutron diffraction. The nano-precipitates were resolved at approximately 900◦C after 1hr, with coarsening and/or re-precipitation progressively increasing at higher temperatures. A significantly increased number density of nano-precipitates (∼2x1023m−3 to ∼7x1023m−3) was established by hot isostatically pressing an Fe-14Cr-3W-0.2Ti0.25Y2O3 alloy at 950◦C compared with more traditional temperatures at 1150◦C, attributed to the increased coarsening and/or re-precipitation of the nano-precipitates at the higher temperatures. The influence of the mechanical alloy (MA)ing conditions on bulk mechanical properties was investigated using four point bend. The highest fracture toughness of ∼55MN/m3/2 and ultimate strength of ∼1450MPa was achieved under conditions that minimised the mechanical alloying time and increased the average final size of the powders. An Fe-14Cr-3W-0.2Ti-0.25Y2O3 (wt%) ODS alloy manufactured under optimised conditions showed a bi-modal grain structure size distribution and had a comparatively high yield strength of >1200MPa at 20◦C and >330MPa at 700◦C. The grain structure and high yield strength were attributed to the random distribution of 25nm radius of gyration (Rg) Y, Ti and O rich nano-precipitates randomly dispersed throughout the alloy. Long term thermal ageing (750hr at 1000◦C) reduced the room temperature yield strength and increased the proportion of larger grains in the bi-modal distribution, but high temperature yield strength was remarkably stable.
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Baimpas, Nikolaos. "'Hybrid' non-destructive imaging techniques for engineering materials applications." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:1aa00fed-34e6-4a5e-951b-c710e21ac23c.
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The combination of X-ray imaging and diffraction techniques provides a unique tool for structural and mechanical analysis of engineering components. A variety of modes can be employed in terms of the spatial resolution (length-scale), time resolution (frequency), and the nature of the physical quantity being interrogated. This thesis describes my contributions towards the development of novel X-ray “rich” imaging experimental techniques and data interpretation. The experimental findings have been validated via comparison with other experimental methods and numerical modelling. The combination of fast acquisition rate and high penetration properties of X-ray beams allows the collection of high-resolution 3-D tomographic data sets at submicron resolution during in situ deformation experiments. Digital Volume Correlation analysis tools developed in this study help understand crack propagation mechanisms in quasi-brittle materials and elasto-plastic deformation in co-sprayed composites. For the cases of crystalline specimens where the knowledge of “live” or residual elastic strain distributions is required, diffraction techniques have been advanced. Diffraction Strain Tomography (DST) allows non-destructive reconstruction of the 2-D (in-plane) variation of the out-of-plane strain component. Another diffraction modality dubbed Laue Orientation Tomography (LOT), a grain mapping approach has been proposed and developed based on the translate-rotate tomographic acquisition strategy. It allows the reconstruction of grain shape and orientation within polycrystalline samples, and provides information about intragranular lattice strain and distortion. The implications of this method have been thoroughly investigated. State-of-the-art engineering characterisation techniques evolve towards scrutinising submicron scale structural features and strain variation using the complementarity of X-ray imaging and diffraction. The first successful feasibility study is reported of in operando stress analysis in an internal combustion engine. Finally, further advancement of ‘rich’ imaging techniques is illustrated via the first successful application of Time-of-Flight Neutron Diffraction Strain (TOF-NDST) tomography for non-destructive reconstruction of the complete strain tensor using an inverse eigenstrain formulation.
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Kaspar, Pavel. "Zpracování signálů z moderních mikroskopů pro lokální charakterizaci materiálů." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2013. http://www.nusl.cz/ntk/nusl-220056.
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Signal processing from modern microscopes for local characteristics of materials Image processing is more and more important for the advancement of image evaluation taken from microscopes. This thesis engages the problem of artefact detection and removal from images taken by electron microscope, more accurately by low energy electron microscopy (LEEM). It then offers a possible course of processing such images by edge detection and its theoretical use. These operations are all made in MatLAB language.
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LOBO, RAQUEL de M. "Reconstrucao tridimensional de superficies de fratura de materiais compositos do tipo CFRP." reponame:Repositório Institucional do IPEN, 2009. http://repositorio.ipen.br:8080/xmlui/handle/123456789/9414.
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Made available in DSpace on 2014-10-09T12:26:37Z (GMT). No. of bitstreams: 0Made available in DSpace on 2014-10-09T14:06:22Z (GMT). No. of bitstreams: 0
Tese (Doutoramento)
IPEN/T
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP
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Luengo, Lydie. "Développement de méthodes d’analyse d’images dédiées à la caractérisation morphologique et nano structurale des noirs de carbone dans les matrices polymères." Thesis, Orléans, 2017. http://www.theses.fr/2017ORLE2038.
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Pour la confection des matériaux polymères à base de caoutchouc, le noir de carbone (NC) reste la charge renforçante la plus utilisée. Sa caractérisation morphologique et nano structurale est essentielle dans la maitrise des propriétés physico-chimiques qu’il confère aux matériaux auxquels il est mélangé. Les analyses classiques ne permettent d’accéder que de façon indirecte et incomplète à ces propriétés. Cette thèse propose une méthode de caractérisation innovante par le couplage d’un détecteur STEM (Scanning Transmission Electron Microscopy) et d’une chaine d’analyse d’images complètement automatique pour identifier les types de NC. Une étude statistique approfondie d’une centaine de caractéristiques morphologiques et structurales des NC a été réalisée sur les 6000 images STEM acquises. Cette étude a permis d’introduire 7 nouveaux descripteurs et de sélectionner les 37 descripteurs les plus discriminants pour la création du modèle d’identification. Pour rendre le processus le plus automatique possible, un algorithme de segmentation non supervisé a été développé et évalué. Cinq classifieurs ont ensuite été entraînés et comparés sur une base de près de 65000 agrégats. Le modèle le plus adapté s’avère les réseaux de neurones avec une identification des NC avoisinant les 100%. L’identification étant réalisée à partir de projections 2D des agrégats via les images STEM, une confrontation statistique valide la capacité des descripteurs 2D à caractériser la structure tridimensionnelle des NC observée par tomographies électroniques. L'approche complète proposée, depuis le protocole de préparation des échantillons et l'acquisition d'images STEM jusqu'à leur classification en passant par les étapes d'analyse d'images, offre une nouvelle méthode de caractérisation fiable des NC (à l’état natif ou au sein de mélanges élastomères) exploitable en routineIn the field of rubber material development, CB is the most commonly used reinforcing filler. The characterization of CB morphology and nanostructure is therefore crucial to understand the physicochemical properties induced by the introduction of CB in rubber materials. Classical analytical methods only allow indirect and incomplete access to these properties. This PhD offers an innovative method that allows the automatic identification of CB grades by coupling Scanning Transmission Electron Microscopy (STEM) detector and image processing chain. A thorough statistical investigation over a hundred of morphological and structural characteristics of CB was performed on a set of 6000 STEM images. This study has introduced 7 new features and selected the 37 most discriminating descriptors to create the final model. An unsupervised segmentation algorithm has been developed and evaluated in order to build an automatic process as efficient as possible. Then, five classifiers were trained and compared on a base of nearly 65,000 aggregates. It appears that the most suitable descriptor is the Neuron networks as it gives a perfect recognition. As the recognition model is based on 2D projections of CB aggregates, it is necessary to verify that the chosen descriptors are indeed able to correctly characterize the three dimensional structure of CB. The statistical comparison of the 2D descriptors with 3D descriptors extracted from electronic tomography images has been successful, and therefore demonstrates the relevance of the model. The proposed approach, starting from the sample preparation and STEM acquisitions to their classification and through the image analysis steps, offers a new and innovative method for the reliable characterization of CB. This method can be used routinely on raw CB or CB extracted from vulcanizes rubbers
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Louys, Mireille. "Traitement d'images de microscopie électronique appliqué à l'étude structurale de macromolécules biologiques." Université Louis Pasteur (Strasbourg) (1971-2008), 1988. http://www.theses.fr/1988STR13153.
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Wahl, Reiner. "Reguläre bakterielle Zellhüllenproteine als biomolekulares Templat." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2003. http://nbn-resolving.de/urn:nbn:de:swb:14-1055925295812-40846.
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Bacterial cell wall proteins (S-layer) are - due to both the capability to self-assemble into two-dimensional crystals and their distinct chemical and structural properties - suitable for the deposition of metallic particles at their surface . The cluster growth is subject of this thesis. The binding of metal complexes to S-layers of Bacillus sphaericus and Sporosarcina ureae and their subsequent reduction leads to the formation of regularly arranged platinum or palladium cluster arrays on the biomolecular template. A heterogeneous nucleation mechanism is proposed for this process consisting of the binding of metal complexes and their subsequent reduction. The kinetics of the process and the binding of the complexes to the protein are characterized by UV/VIS spectroscopy. This thesis focuses on structural investigations by means of transmission electron microscopy, electron holography, scanning force microscopy, image analysis, and image processing. Preferred cluster-deposition sites are determined by correlation averaging. A more precise determination and quantification is obtained by Multivariate Statistical Analysis. Furthermore a method for the electron beam induced formation of highly-ordered metallic cluster arrays in the transmission electron microscope and a fast screening method for surface layers of Gram-positive bacteria are presentedBakterielle Zellhüllenproteine (S-Layer) eignen sich durch ihre Fähigkeit zur Selbstassemblierung zu zweidimensionalen Kristallen und durch ihre besonderen chemischen und strukturellen Eigenschaften zur Abscheidung regelmäßiger metallischer Partikel auf ihrer Oberfläche. In dieser Arbeit wird das Clusterwachstum auf S-Layern untersucht. Die Anbindung von Metallkomplexen an S-Layer von Bacillus sphaericus und Sporosarcina ureae und deren Reduktion führt zur Abscheidung periodisch angeordneter metallischer Platin- bzw. Palladiumcluster auf dem Biotemplat. Für diese Clusterbildung wird ein heterogener Keimbildungsmechanismus vorgeschlagen, bestehend aus Komplexanbindung und Reduktion. Die Bestimmung der Prozeßkinetik und die Charakterisierung der Anbindung der Komplexe an das Protein erfolgt mittels UV/VIS-Spektroskopie. Den Schwerpunkt dieser Arbeit bilden strukturelle Untersuchungen mit Hilfe der Transmissionselektronenmikroskopie, der Elektronenholographie, der Rasterkraftmikroskopie und der Bildanalyse und Bildverarbeitung. Durch Korrelationsmittelung werden Strukturinformationen gewonnen, die eine Bestimmung der lateral bevorzugten Clusterpositionen ermöglichen. Für die auf S-Layern erzeugten Clusterarrays wird die Belegung der einzelnen Positionen mittels Multivariater Statistischer Analyse genauer quantifiziert. Außerdem werden eine Methode zur Erzeugung hochgeordneter metallischer Partikelarrays unter dem Einfluß des Elektronenstrahles im Transmissionselektronenmikroskop und eine Methode zum schnellen Test Gram-positiver Bakterienstämme auf die Existenz von S-Layern vorgestellt
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Sobola, Dinara. "Nedestruktivní lokální diagnostika optoelektronických součástek." Doctoral thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2015. http://www.nusl.cz/ntk/nusl-233678.
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Chceme-li využít nové materiály pro nová optoelektronická zařízení, potřebujeme hlouběji nahlédnout do jejich struktury. K tomu, abychom toho dosáhli, je však nutný vývoj a aplikace přesnějších diagnostických metod. Předložená disertační práce, jako můj příspěvek k částečnému dosažení tohoto cíle, se zabývá metodami lokální diagnostiky povrchu optoelektronických zařízení a jejich materiálů, většinou za využití nedestruktivních mechanických, elektrických a optických technik. Tyto techniky umožňují jednak pochopit podstatu a jednak zlepšit celkovou účinnost a spolehlivost optoelektronických struktur, které jsou obecně degradovány přítomností malých defektů, na nichž dochází k absorpci světla, vnitřnímu odrazu a dalším ztrátovým mechanismům. Hlavní úsilí disertační práce je zaměřeno na studium degradačních jevů, které jsou nejčastěji způsobeny celkovým i lokálním ohřevem, což vede ke zvýšené difúze iontů a vakancí v daných materiálech. Z množství optoelektronických zařízení, jsem zvolila dva reprezentaty: a) křemíkové solární články – součástky s velkým pn přechodem a b) tenké vrstvy – substráty pro mikro optoelektronická zařízení. V obou případech jsem provedla jejich detailní povrchovou charakterizaci. U solárních článků jsem použila sondovou mikroskopii jako hlavní nástroj pro nedestruktivní charakterizaci povrchových vlastností. Tyto metody jsou v práci popsány, a jejich pozitivní i negativní aspekty jsou vysvětleny na základě rešerše literatury a našich vlastních experimentů. Je také uvedeno stanovisko k použití sondy mikroskopických aplikací pro studium solárních článků. V případě tenkých vrstev jsem zvolila dva, z hlediska stability, zajímavé materiály, které jsou vhodnými kandidáty pro přípravu heterostruktury: safír a karbid křemíku. Ze získaných dat a analýzy obrazu jsem našla korelaci mezi povrchovými parametry a podmínkami růstu heterostruktur studovaných pro optoelektronické aplikace. Práce zdůvodňuje používání těchto perspektivních materiálů pro zlepšení účinnosti, stability a spolehlivosti optoelektronických zařízení.
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Verguet, Amandine. "Développements méthodologiques et informatiques pour la microscopie électronique en transmission appliqués à des échantillons biologiques Alignment of Tilt Series (Chapter 7 of the Book: Cellular Imaging: Electron Tomography and Related Techniques, Hanssen Eric) An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI) Comparison of methods based on feature tracking for fiducial-less image alignment in electron tomography." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS487.
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La microscopie électronique en transmission est une technique pertinente pour les études structurales en biologie. Certaines méthodes d’acquisition et d’analyse doivent être améliorées pour permettre l’observation d’échantillons sensibles aux doses d’électrons dans de bonnes conditions de contraste et de rapport signal sur bruit. Au cours de cette thèse, j’ai exploré différentes approches méthodologiques et informatiques dans le but d’améliorer la qualité des images. J’ai ainsi évalué la pertinence de la combinaison de l’imagerie en énergie filtrée avec le mode STEM. Je montre que cette combinaison est prometteuse puisqu’elle permet d’améliorer le rapport signal sur bruit des images. Par ailleurs, j’ai collaboré à des développements algorithmiques et logiciels pour la reconstitution d’images de contraste de phase. Ceci permet l’amélioration du contraste par rapport à une acquisition classique. Je montre aussi qu’à cette fin, la phase plate tout comme les séries focales sont des outils efficaces. En étudiant une approche logicielle pour l’exploitation des séries focales, nous avons déterminé qu’il est possible d’obtenir, en plus de données quantitatives, un résultat qualitatif à partir d’une seule image. J’ai ainsi développé le plugin SPCI pour le logiciel ImageJ, qui permet de traiter de une à trois images focales. Je m’intéresse également à l’optimisation du processus de reconstruction tomographique, tant à l’alignement qu’à la reconstruction proprement dite. L’approche évaluée pour l’alignement utilise des points caractéristiques associés à des descripteurs locaux. Elle s’est montrée performante et permet de traiter des images sans marqueurs fiduciaires. Enfin, je propose une nouvelle méthode unifiée de reconstruction tridimensionnelle de séries tomographiques parcimonieuses. Il en découle une approche innovante mélangeant reconstruction et alignement dont l’ébauche servira de base à des travaux futurs pour le traitement de séries tomographiques parcimonieuses. L’ensemble des méthodes évoquées ici, leur validation, ainsi que les perspectives d’évolution associées sont décrites dans ce manuscritTransmission Electron Microscopy is a major tool for performing structural studies in biology. Some methods used for image sampling and analysis need to be improved in order to observe electron dose sensitive samples with good contrast and good signal to noise ratio. During this thesis, various methodological and computational approaches have been studied which aim to improve image quality. First, I evaluated the relevance of combining energy filtered imaging with the STEM mode. I show that this allows an improvement of the signal to noise ratio of images. Then, I devised an algorithm that generates an image from phase data. This approach allows improving the image contrast over direct imaging. The use of a phase plate and focal tilt series are both efficient tools to achieve this goal. While working on the software approach for processing of tilt series, we found that a qualitative result can be obtained from a single image. I developped the SPCI plugin for the ImageJ software. It allows processing between one and three focal images. My work involves optimization of the tomographic reconstruction process, including working with both alignment algorithms and reconstruction algorithms. I expose my studies on image alignment methods used on tilt series. These methods do rely on the use of key points and associated local descriptors. They have proved to be efficient to process images lacking fiducial markers. Finally, I propose a new unified algorithmic approach for 3D reconstruction of tomographic tilt series acquired with sparse sampling. I then derived another novel method that integrates the image alignment step in the process. Studies and developments will continue on both methods in futur work
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Wu, Yimin A. "Towards large area single crystalline two dimensional atomic crystals for nanotechnology applications." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:bdb827e5-f3fd-4806-8085-0206e67c7144.
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Nanomaterials have attracted great interest due to the unique physical properties and great potential in the applications of nanoscale devices. Two dimensional atomic crystals, which are atomic thickness, especially graphene, have triggered the gold rush recently due to the fascinating high mobility at room temperature for future electronics. The crystal structure of nanomaterials will have great influence on their physical properties. Thus, this thesis is focused on developing the methods to control the crystal structure of nanomaterials, namely quantum dots as semiconductor, boron nitride (BN) as insulator, graphene as semimetal, with low cost for their applications in photonics, structural support and electronics. In this thesis, firstly, Mn doped ZnSe quantum dots have been synthesized using colloidal synthesis. The shape control of Mn doped ZnSe quantum dots has been achieved from branched to spherical by switching the injection temperature from kinetics to thermodynamics region. Injection rates have been found to have effect on controlling the crystal phase from zinc blende to wurtzite. The structural-property relationship has been investigated. It is found that the spherical wurtzite Mn doped ZnSe quantum dots have the highest quantum yield comparing with other shape or crystal phase of the dots. Then, the Mn doped ZnSe quantum dots were deposited onto the BN sheets, which were micron-sized and fabricated by chemical exfoliation, for high resolution imaging. It is the first demonstration of utilizing ultrathin carbon free 2D atomic crystal as support for high resolution imaging. Phase contrast images reveal moiré interference patterns between nanocrystals and BN substrate that are used to determine the relative orientation of the nanocrystals with respect to the BN sheets and interference lattice planes using a newly developed equation method. Double diffraction is observed and has been analyzed using a vector method. As only a few microns sized 2D atomic crystal, like BN, can be fabricated by the chemical exfoliation. Chemical vapour deposition (CVD) is as used as an alternative to fabricate large area graphene. The mechanism and growth dynamics of graphene domains have been investigated using Cu catalyzed atmospheric pressure CVD. Rectangular few layer graphene domains were synthesized for the first time. It only grows on the Cu grains with (111) orientation due to the interplay between atomic structure of Cu lattice and graphene domains. Hexagonal graphene domains can form on nearly all non-(111) Cu surfaces. The few layer hexagonal single crystal graphene domains were aligned in their crystallographic orientation over millimetre scale. In order to improve the alignment and reduce the layer of graphene domains, a novel method is invented to perform the CVD reaction above the melting point of copper (1090 ºC) and using molybdenum or tungsten to prevent the balling of the copper from dewetting. By controlling the amount of hydrogen during the growth, individual single crystal domains of monolayer over 200 µm are produced determined by electron diffraction mapping. Raman mapping shows the monolayer nature of graphene grown by this method. This graphene exhibits a linear dispersion relationship and no sign of doping. The large scale alignment of monolayer hexagonal graphene domains with epitaxial relationship on Cu is the key to get wafer-sized single crystal monolayer graphene films. This paves the way for industry scale production of 2D single crystal graphene.
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Lara, Alexandre Guilherme de. "Metodologia para análise na perícia criminal de microvestígios forenses: fios de cabelo." Universidade Tecnológica Federal do Paraná, 2016. http://repositorio.utfpr.edu.br/jspui/handle/1/2006.
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A presente dissertação expositiva teve por objetivo o desenvolvimento de metodologia para análise forense de fios de cabelos. Considerado um microvestígio comum de ser encontrado em locais de crime contra pessoa (DOREA, 2010), fios de cabelo são capazes de fornecer informações úteis na identificação da autoria do crime, ou a entender a dinâmica de um crime violento (ROBERTSON, 1999). As fibras compostas por fio de cabelo deterioram-se lentamente (ROBBINS, 2012), e podem ser analisadas mesmo transcorrido longo período de tempo, tornando-se ainda mais relevante em locais de crime que são examinados tardiamente. Os equipamentos utilizados no presente estudo são de uso comum em laboratórios, permitindo que a metodologia seja amplamente empregada. O presente estudo buscou desenvolver metodologias para análise por microscopia ótica de fios de cabelo, identificando as características de interesse forense passíveis de serem estudadas. Utilizaram-se amostras de fios de cabelo para análise das seções transversais e longitudinais, de forma destrutiva e não destrutiva, com preparação de lâminas de forma permanente e não permanente. Como resultado obteve-se uma metodologia de baixo custo descrita para aplicações forenses em vestígios coletados em locais de crime, em armas de crimes ou em suspeitos, de forma a combater a criminalidade face o poder probatório da prova material. Constatou-se a possibilidade de identificação de características macroscópicas e microscópicas de fios de cabelo, que revelam atributos do doador e, em alguns casos, auxiliar no entendimento da dinâmica do crime. A agilidade observada no método permite ainda a obtenção de informações durante a fase preliminar ou de investigação em curtos espaços de tempo.This monographic dissertation aimed to develop standards of microscopic forensic hair analysis. A very common trace to be found in certain crimes (DOREA, 2010), hair can be helpful to provide information regarding the perpetrator or the way that the crime was committed (ROBERTSON, 1999). Once hair is a low degradation fiber (ROBBINS, 2012), it can be analyzed long after the fact, becoming even more relevant in crime scenes processed after elapse time. The equipment’s used for this study are commonly found in forensic labs, allowing broad use. The study was restricted to literature review and further elaboration of preparation and analysis by optical microscopy of hairs methods, identifying the characteristics of forensic interest that can be studied. Samples of hair for cross section and longitudinal sections analysis had been used. Destructive and non-destructive methods in permanent and non-permanent blades where tested. As a result a low cost methodology was obtained for forensic applications in traces collected from crime scenes, weapons used in crimes or suspects, in order to combat crime by using the probative power of physical evidence.
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CORREA, EDUARDO DE L. "Produção, caracterização e aplicação de nanopartículas de Gd2O3 e Er2O3 como radiossensibilizadores em feixes de Radioterapia." reponame:Repositório Institucional do IPEN, 2017. http://repositorio.ipen.br:8080/xmlui/handle/123456789/27968.
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Submitted by Marco Antonio Oliveira da Silva (maosilva@ipen.br) on 2017-11-08T16:29:11Z
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Nesse trabalho foram produzidas nanopartículas (NPs) de Gd2O3 e Er2O3 para aplicação como radiossensibilizadores em feixes de radioterapia. Elas foram sintetizadas no Laboratório de Interações Hiperfinas do IPEN pelo método da decomposição térmica e caracterizadas utilizando difração de raios-X, para verificar a estrutura cristalina, microscopia eletrônica de transmissão, para obter informações sobre forma, tamanho e distribuição de tamanho, análise por ativação neutrônica, por meio da qual foi possível determinar a pureza das amostras e calcular a concentração de gadolínio e érbio. Medições de magnetização e de espectroscopia de correlação angular γ-γ perturbada (PAC) foram realizadas a fim de estudar o comportamento magnético e a interação quadrupolar das partículas, respectivamente. Os resultados da caracterização mostram a formação de uma estrutura cristalina do tipo bixbyite, com aproximadamente 5 nm de diâmetro e estreita distribuição de tamanho, para as amostras pós-síntese. A determinação da massa de terra-rara em cada amostra foi importante para realizar a normalização nas medições de susceptibilidade magnética, tornando possível a visualização de um grande aumento na magnetização abaixo de 30 K, nas amostras pós-síntese, o que não é observado em partículas maiores, além de um aumento no momento magnético efetivo das NPs em relação aos respectivos bulks e uma mudança na temperatura de ordenamento antiferromagnético para o Er2O3. Os resultados da espectroscopia PAC evidenciam possíveis efeitos de superfície. A falta de uma frequência bem definida nas amostras de 5 nm indicam que a quantidade de 111In(111Cd) na superfície da partícula é maior do que no interior da mesma, fazendo com que a interação hiperfina do núcleo de prova com o host não seja evidente. Já a união da técnica de difração de raios-X com a espectroscopia PAC foi fundamental para o entendimento do dano causado às partículas pela irradiação com 60Co. Quanto às medições de radiossensibilização a dosimetria Fricke gel foi fundamental para a verificação de um fator de aumento de dose (DEF) de até 1,67 e 1,09 para NPs de Gd2O3 irradiadas com 60Co e 6MV, respectivamente. Nas mesmas condições, para as amostras de Er2O3, foram encontrados valores de DEF de até 1,37 e 1,06. Isso comprova os efeitos radiossensibilizadores dessas NPs. Os resultados alcançados nesse trabalho não apenas fornecem dados importantes para o estudo de NPs de terra-rara na área de física da matéria condensada como também uma base sólida para a aplicação desses elementos como radiossensibilizadores em feixes de radioterapia, possibilitando a utilização da imagem por ressonância magnética para localizar e obter a concentração dessas NPs dentro do paciente, aumentando assim a eficiência do tratamento do câncer.
Tese (Doutorado em Tecnologia Nuclear)
IPEN/T
Instituto de Pesquisas Energéticas e Nucleares - IPEN-CNEN/SP
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Guiral, Vega Juan Sebastian. "Textural and Mineralogical Characterization of Li-pegmatite Deposit: Using Microanalytical and Image Analysis to Link Micro and Macro Properties of Spodumene in Drill Cores. : Keliber Lithium Project, Finland." Thesis, Luleå tekniska universitet, Mineralteknik och metallurgi, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:ltu:diva-70422.
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Lithium represents one of the strategic elements for the rest of the 21st century due to its increasing demand in technological applications. Therefore, new efforts should be focused on the optimization of mineral characterization processes, which link the ore properties with its behaviour during downstream processes. These efforts should result in reducing operational risks and increasing resources utilization. The methodology presented in this study is based on the application of several classification techniques, aiming the mineral and textural characterization of two spodumene pegmatite deposits within the Keliber Lithium Project. Twelve textural classes have been proposed for the textual classification of the ore, which have been defined through the recognition of the main mineral features at macro- and micro-scale. The textural classification was performed through the application of drill core logging and scanning electron microscopy. Six classes are proposed to describe the characteristics of the spodumene ore. Six additional classes describe the main properties of the rocks surrounding the ore zone. Image analysis was implemented for the generation of mineral maps and the subsequent quantification of spodumene and Li2O within the analysed drill core images. The image segmentation process was executed in Fiji-ImageJ and is based on eight mineral classes and a set of seven feature extraction procedures. Thus, quantification of spodumene and Li2O is estimated by textural class. Hyperspectral images were used as a reference for assessing the estimations made through images analysis. A machine learning model in Weka allowed forecasting the behaviour of the twelve textural classes during spodumene flotation. This model is fed by metallurgical data from previous flotation tests and uses Random Forest classifier. The proposed methodology serves as an inexpensive but powerful approach for the complete textural characterization of the ore at Keliber Lithium Project. It provides information about: (1) mineral features at different scales, (2) spatial distribution of textures within the pegmatite body, (3) quantification of spodumene and Li2O within the drill cores and (4) processing response of each textural class. However, its application requires wide knowledge and expertise in the mineralogy of the studied deposits.Thesis Presentation.
Textural and Mineralogical Characterization of Li-pegmatite Deposit: Using Microanalytical and Image Analysis to Link Micro and Macro Properties of Spodumene in Drill Cores. Keliber Lithium Project, Finland.
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Thomas, Gareth James. "Advanced materials for plasma facing components in fusion devices." Thesis, University of Oxford, 2009. http://ora.ox.ac.uk/objects/uuid:f8ba1ae1-f303-4c32-877e-dca421a3cb5c.
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This thesis describes the design, manufacture and characterisation of thick vacuum plasma sprayed tungsten (W) coatings on steel substrates. Fusion is a potentially clean, sustainable, energy source in which nuclear energy is generated via the release of internal energy from nuclei. In order to fuse nuclei the Coulomb barrier must be breached - requiring extreme temperatures or pressures – akin to creating a ‘star in a box’. Tungsten is a promising candidate material for future fusion reactors due to a high sputtering threshold and melting temperature. However, the large coefficient of thermal expansion mismatch with reactor structural steels such as the low activation steel Eurofer’97 is a major manufacturing and in-service problem. A vacuum plasma spraying approach for the manufacture of tungsten and tungsten/steel graded coatings has been developed successfully. The use of graded coatings and highly textured 3D interface surfi-sculpt substrates has been investigated to allow the deposition of thick plasma sprayed tungsten coatings on steel substrates. Finite element models have been developed to understand the residual stresses that develop in W/steel systems and made use of experimental measurements of coating thermal history during manufacture and elastic moduli measured by nano-indentation. For both the graded and surfi-sculpt coating, the models have been used to understand the mechanism of residual stress redistribution and relief in comparison with simple W on steel coatings, particularly by consideration of stored strain energy. In the case of surfi-sculpt W coatings, the patterned substrate gave rise to regular stress concentrating features, and allowed 2mm thick W coatings to be produced reproducibly without delamination. Preliminary through thickness residual stress measurements were compared to model predictions and provided tentative evidence of significant W coating stress relief by regulated coating segmentation.
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Dohet-Eraly, Jérôme. "Méthodes de microscopie par holographie numérique interférentielle en couleurs avec un éclairage partiellement cohérent." Doctoral thesis, Universite Libre de Bruxelles, 2017. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/250123.
Full textAbstract:
La présente thèse traite de méthodes en microscopie holographique numérique (MHN) en couleurs, avec un éclairage de cohérence spatiale partielle. Le principal inconvénient de la microscopie optique classique est sa faible profondeur de champ, rendant difficile l’observation de phénomènes dynamiques dans des échantillons épais. Au contraire, la MHN offre une reconstruction en profondeur grâce à la propagation numérique de l’hologramme. La MHN interférométrique donne aussi le contraste quantitatif de la phase, utile pour analyser des objets transparents. Un éclairage à plusieurs longueurs d’onde dans une configuration appropriée permet la MHN en couleurs. L’imagerie en flux et en couleurs de particules en MHN est ici développée, avec une méthode pour la correction automatique de la balance des couleurs et des défauts permanents. Elle est appliquée pour l’analyse du plancton dans des échantillons d’eau de surface et fournit des images de haute qualité pour les intensité et phase optiques. En outre, la réduction du bruit obtenue en diminuant la cohérence spatiale de l’éclairage en MHN est également étudiée, avec deux modèles évaluant quantitativement ce phénomène en fonction de la cohérence spatiale de la lumière et de la distance entre la source de bruit et le plan d’enregistrement. De plus, la MHN différentielle est aussi abordée. Celle-ci fournit les phases différentielles, la phase étant calculée par intégration. Cependant, les défauts présents conduisent à des aberrations lors du calcul de la phase, qui affectent sa qualité et empêchent la reconstruction holographique. Un traitement spécifique est développé, permettant la reconstruction numérique en profondeur. Enfin, en MHN, un critère est essentiel pour déterminer automatiquement la distance de netteté de l’objet. Deux critères de netteté sont ici mis au point, fonctionnant indépendamment de la nature de l’objet observé (amplitude, phase ou mixte). L’un, monochromatique, est basé sur l’analyse de l’amplitude et sur un filtrage passe-haut ;l’autre, qui détecte rapidement le plan de netteté en MHN en couleurs, compare la phase dans le domaine de Fourier entre les couleurs. Les méthodes développées dans la thèse montrent le potentiel élevé de la MHN en couleurs avec un éclairage partiellement cohérent spatialement, suggérant un avenir prometteur pour cette technique.The thesis deals with methods and developments in color digital holographic microscopy (DHM), with a partial spatial coherence illumination. The principal drawback of classical optical microscopy is its poor depth of field, which makes difficult the observation of dynamic phenomena in thick samples. On the contrary, DHM provides reconstruction in depth thanks to numeric propagation of the recorded hologram. Another feature of interferometric DHM is the quantitative phase contrast imaging, useful for analyzing transparent objects. Usual DHM is limited to monochromatic case, but multispectral illumination in an appropriate setup leads to color DHM. Color in-flow imaging of particles in DHM is developed in the thesis, with a method for the automatic correction of color balance and permanent defects. It is applied to analyze plankton microorganisms in untreated pond water samples, and provides high quality images, for both optical phase and intensity. Moreover, noise reduction obtained when decreasing the spatial coherence of the illumination in DHM is also investigated in the thesis, with the development of two models that quantitatively assess the noise reduction as a function of both the spatial coherence of the illumination, and the defocus distance of the noise source. Furthermore, differential DHM (DDHM) is also studied in the thesis. As DHM gives the optical phase, DDHM provides differential phases, from which phase is retrieved by integration. However, misalignments and defects give some aberrations, which affect phase quality and hinder refocusing. A specific hologram processing is developed, giving an accurate phase image and enabling holographic reconstruction in depth. Finally, in DHM, a criterion is essential to automatically achieve the refocusing distance of the object. Two refocusing criteria are developed in the thesis, both working independently of the nature of the observed object (amplitude, phase, or both mixed). The first one, monochromatic, is based on amplitude analysis and on a high-pass filtering process. The second one, which gives fast refocusing in multispectral DHM, compares the phase in the Fourier domain among wavelengths. Methods developed in the thesis show the high potential of color DHM with a partial spatial coherence illumination, suggesting a promising future for this technique.
Doctorat en Sciences de l'ingénieur et technologie
info:eu-repo/semantics/nonPublished
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Viljanen-Rollinson, S. L. H. "Expression and detection of quantitative resistance to Erysiphe pisi DC. in pea (Pisum sativum L.)." Lincoln University, 1996. http://hdl.handle.net/10182/1657.
Full textAbstract:
Characteristics of quantitative resistance in pea (Pisum sativum L.) to Erysiphe pisi DC, the pathogen causing powdery mildew, were investigated. Cultivars and seedlines of pea expressing quantitative resistance to E. pisi were identified and evaluated, by measuring the amounts of pathogen present on plant surfaces in field and glasshouse experiments. Disease severity on cv. Quantum was intermediate when compared with that on cv. Bolero (susceptible) and cv. Resal (resistant) in a field experiment. In glasshouse experiments, two groups of cultivars, one with a high degree of resistance and the other with nil to low degrees of resistance to E. pisi, were identified. This indicated either that a different mechanism of resistance applied in the two groups, or that there has been no previous selection for intermediate resistance. Several other cultivars expressing quantitative resistance were identified in a field experiment. Quantitative resistance in Quantum did not affect germination of E. pisi conidia, but reduced infection efficiency of conidia on this cultivar compared with cv. Pania (susceptible). Other epidemiological characteristics of quantitative resistance expression in Quantum relative to Pania were a 33% reduction in total conidium production and a 16% increase in time to maximum daily conidium production, both expressed on a colony area basis. In Bolero, the total conidium production was reduced relative to Pania, but the time to maximum spore production on a colony area basis was shorter. There were no differences between the cultivars in pathogen colony size or numbers of haustoria produced by the pathogen. Electron microscope studies suggested that haustoria in Quantum plants were smaller and less lobed than those in Pania plants and the surface area to volume ratios of the lobes and haustorial bodies were larger in Pania than in Quantum. The progress in time and spread in space of E. pisi was measured in field plots of cultivars Quantum, Pania and Bolero as disease severity (proportion of leaf area infected). Division of leaves (nodes) into three different age groups (young, medium, old) was necessary because of large variability in disease severity within plants. Disease severity on leaves at young nodes was less than 4% until the final assessment at 35 days after inoculation (dai). Exponential disease progress curves were fitted for leaves at medium nodes. Mean disease severity on medium nodes 12 dai was greatest (P<0.001) on Bolero and Pania (9.3 and 6.8% of leaf area infected respectively), and least on Quantum (1.6%). The mean disease relative growth rate was greatest (P<0.001) for Quantum, but was delayed compared to Pania and Bolero. Gompertz growth curves were fitted to disease progress data for leaves at old nodes. The asymptote was 78.2% of leaf area infected on Quantum, significantly lower (P<0.001) than on Bolero or Pania, which reached 100%. The point of inflection on Quantum occurred 22.8 dai, later (P<0.001) than on Pania (18.8 dai) and Bolero (18.3 dai), and the mean disease severity at the point of inflection was 28.8% for Quantum, less (P<0.00l) than on Pania (38.9%) or Bolero (38.5%). The average daily rates of increase in disease severity did not differ between the cultivars. Disease progress on Quantum was delayed compared with Pania and Bolero. Disease gradients from inoculum foci to 12 m were detected at early stages of the epidemic but the effects of background inoculum and the rate of disease progress were greater than the focus effect. Gradients flattened with time as the disease epidemic intensified, which was evident from the large isopathic rates (between 2.2 and 4.0 m d⁻¹) Some epidemiological variables expressed in controlled environments (low infection efficiency, low maximum daily spore production and long time to maximum spore production) that characterised quantitative resistance in Quantum were correlated with disease progress and spread in the field. These findings could be utilised in pea breeding programmes to identify parent lines from which quantitatively resistant progeny could be selected.
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Driss, Khodja Kouider. "Etude expérimentale et modélisation de la fonction diélectrique des milieux inhomogènes 2D et 3D." Rouen, 1989. http://www.theses.fr/1989ROUES018.
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Pour prendre en compte la structure réelle des milieux inhomogènes, nous avons proposé une théorie de milieu effectif à 2D et 3D basée sur une procédure de renormalisation dans l'espace réel. Ces modèles utilisent la technique des blocs de Kadanoff. Dans un premier temps cette approche a été appliquée à des réseaux carrés générés par ordinateur dont les sites sont occupés aléatoirement pour une concentration donnée. Dans une deuxième étape nous avons appliqué cette procédure à des images réelles constituées de micrographies de microscopie électronique par transmission digitalisées puis binarisées de systèmes 2D et 3D. On présente également une interprétation des similarités et des différences entre la théorie et l'expérience. Les résultats obtenus sur des réseaux simulés rendent compte à la fois de l'anomalie diélectrique et de la percolation optique. Notre approche est ainsi l'une des rares théories à modéliser la transition métal-non métal. Nous avons montré que la fonction diélectrique effective obéit à des lois d'échelle avec des exposants critiques S3D et S2D pour la polarisation et T3D et T2D pour la conduction, valeurs proches des estimations théoriques. Les fonctions diélectriques obtenues par l'application de ces modèles à des micrographies de microscopie électronique par transmission digitalisées puis binarisées sont en bon accord avec la plupart des résultats expérimentaux
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Gopinath, Ajay 1980. "Feature modeling and tomographic reconstruction of electron microscopy images." Thesis, 2012. http://hdl.handle.net/2152/ETD-UT-2012-05-4972.
Full textAbstract:
This work introduces a combination of image processing and analysis
methods that perform feature extraction, shape analysis and tomographic reconstruction of Electron Microscopy images. These have been implemented on
images of the AIDS virus interacting with neutralizing molecules. The AIDS
virus spike is the primary target of drug design as it is directly involved in
infecting host cells. First, a fully automated technique is introduced that can
extract sub-volumes of the AIDS virus spike and be used to build a statistical
model without the need for any user supervision. Such an automatic feature
extraction method can significantly enhance the overall process of shape analysis
of the AIDS virus spike imaged through the electron microscope. Accurate
models of the virus spike will help in the development of better drug design
strategies.
Secondly, a tomographic reconstruction method implemented using a
shape based regularization technique is introduced. Spatial models of known
features in the structure being reconstructed are integrated into the reconstruction
process as regularizers. This regularization scheme is driven locally
through shape information obtained from segmentation and compared with a
known spatial model. This method shows reduced blurring, and an improvement
in the resolution of the reconstructed volume was also measured. It performs better than popular current techniques and can be extended to other tomographic modalities. Improved Electron Tomography reconstructions will provide better structure elucidation and improved feature visualization, which can aid in solving key biological issues.text
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"Development of histologic color image analysis system." Chinese University of Hong Kong, 1994. http://library.cuhk.edu.hk/record=b5888199.
Full textAbstract:
by Chung-fai Kwok.Thesis (M.Sc.)--Chinese University of Hong Kong, 1994.
Includes bibliographical references (leaves 65).
Contents --- p.i
Table of Figures --- p.iii
Abstract --- p.v
Acknowledgment --- p.vii
Introduction --- p.viii
Chapter 1. --- Overview : Medical image network system --- p.1
Chapter 1.1 --- MAGNET --- p.1
Chapter 1.2 --- Medical image --- p.2
Chapter 2. --- System configuration --- p.4
Chapter 2.1 --- Hardware setting --- p.4
Chapter 2.2 --- Software functions design --- p.5
Chapter 3. --- Color handling --- p.7
Chapter 3.1 --- Color --- p.7
Chapter 3.2 --- Colormap and color display --- p.9
Chapter 3.3 --- Static and dynamic color mapping --- p.10
Chapter 4. --- Color image processing --- p.11
Chapter 4.1 --- Color image quantization --- p.11
Chapter 4.1.1 --- Pre-quantization --- p.13
Chapter 4.1.2 --- Median cut Algorithm --- p.15
Chapter 4.1.3 --- Remapping colors --- p.16
Chapter 4.1.4 --- Hashing --- p.17
Chapter 4.1.5 --- Distortion Measures --- p.21
Chapter 4.1.6 --- Experiment results and Discussion --- p.22
Chapter 4.2 --- Intensity mapping --- p.30
Chapter 4.2.1 --- Graylevel image contrast enhancement and reduction --- p.30
Chapter 4.2.2 --- Graylevel image brightness increment and reduction --- p.36
Chapter 4.2.3 --- Contrast enhancement and reduction on color components --- p.40
Chapter 4.2.4 --- Brightness increment and reduction on color components --- p.41
Chapter 4.3 --- Pseudocoloring --- p.45
Chapter 5. --- Color image analysis --- p.47
Chapter 5.1 --- Region Measures --- p.47
Chapter 5.1.1 --- Region measures function design --- p.47
Chapter 5.1.2 --- Region growing mechanism --- p.48
Chapter 5.1.3 --- Region smoothing --- p.49
Chapter 5.2 --- Distance measures --- p.53
Chapter 5.3 --- Statistical analysis --- p.53
Chapter 6. --- Summary and future work --- p.57
Appendix : User interfaces and functions --- p.58
Bibliography --- p.65
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Hons, Michael. "Structural Survey on Cohesin and Viomycin Inhibited 70S Ribosome by Single Particle Electron Microscopy." Doctoral thesis, 2015. http://hdl.handle.net/11858/00-1735-0000-0028-8739-5.
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Aksoylar, Aydan. "Modeling and model-aware signal processing methods for enhancement of optical systems." Thesis, 2016. https://hdl.handle.net/2144/19504.
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Theoretical and numerical modeling of optical systems are increasingly being utilized in a wide range of areas in physics and engineering for characterizing and improving existing systems or developing new methods. This dissertation focuses on determining and improving the performance of imaging and non-imaging optical systems through modeling and developing model-aware enhancement methods. We evaluate the performance, demonstrate enhancements in terms of resolution and light collection efficiency, and improve the capabilities of the systems through changes to the system design and through post-processing techniques. We consider application areas in integrated circuit (IC) imaging for fault analysis and malicious circuitry detection, and free-form lens design for creating prescribed illumination patterns.
The first part of this dissertation focuses on sub-surface imaging of ICs for fault analysis using a solid immersion lens (SIL) microscope. We first derive the Green's function of the microscope and use it to determine its resolution limits for bulk silicon and silicon-on-insulator (SOI) chips. We then propose an optimization framework for designing super-resolving apodization masks that utilizes the developed model and demonstrate the trade-offs in designing such masks. Finally, we derive the full electromagnetic model of the SIL microscope that models the image of an arbitrary sub-surface structure.
With the rapidly shrinking dimensions of ICs, we are increasingly limited in resolving the features and identifying potential modifications despite the resolution improvements provided by the state-of-the-art microscopy techniques and enhancement methods described here. In the second part of this dissertation, we shift our focus away from improving the resolution and consider an optical framework that does not require high resolution imaging for detecting malicious circuitry. We develop a classification-based high-throughput gate identification method that utilizes the physical model of the optical system. We then propose a lower-throughput system to increase the detection accuracy, based on higher resolution imaging to supplement the former method.
Finally, we consider the problem of free-form lens design for forming prescribed illumination patterns as a non-imaging application. Common methods that design free-form lenses for forming patterns consider the input light source to be a point source, however using extended light sources with such lenses lead to significant blurring in the resulting pattern. We propose a deconvolution-based framework that utilizes the lens geometry to model the blurring effects and eliminates this degradation, resulting in sharper patterns.
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Mohale, Given Terrance Mpho. "SEM image processing as an alternative method to determine chromite pre-reduction / Given Terrance Mpho Mohale." Thesis, 2015. http://hdl.handle.net/10394/15423.
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Ferrochrome (FeCr) is a crude alloy containing chromium (Cr) and iron (Fe). FeCr is mainly used for the production of stainless steel, which is an important modern-day alloy. FeCr is produced from chromite ore through various smelting methods. In this study, the focus was on the pelletised chromite pre-reduction process, which is also referred to as the solid state reduction of chromite. In this process, fine chromite ore, a clay binder and a carbon reductant are dry milled, agglomerated (pelletised) and pre-reduced (solid state reduction) in a rotary kiln. The pre-reduced pellets are then charged hot, immediately after exiting the rotary kiln, into a closed submerged arc furnace (SAF). This production process option has the lowest specific energy consumption (SEC), i.e. MWh/ton FeCr produced, of all the FeCr production processes that are commercially applied. Other advantages associated with the application of the pelletised chromite pre-reduction process are that it eliminates the use of chromite fines, has a high Cr recovery, and produces low sulphur- (S) and silicon (Si)-containing FeCr. The main disadvantage of the pelletised chromite pre-reduction process is that it requires extensive metallurgical control due to the variances in the levels of pre-reduction achieved and carbon content of the pre-reduced pelletised furnace feed material. This implies that the metallurgical carbon balance has to be changed regularly to prevent the process from becoming carbon deficient (also referred to as ‘under coke’) or over carbon (also referred to as ‘over coke’). The analytical technique currently applied to determine the level of chromite pre-reduction is time consuming, making it difficult and expensive to deal with large numbers of samples. In an attempt to develop a technique that would be faster to determine the level of chromite pre-reduction, a new analytical method using a combination of scanning electron microscopy (SEM), image processing and computational techniques was investigated in this study.
Metallurgical grade chromite (<1 mm), anthracite breeze (<1 mm), and fine FeCr (<1 mm) that were used to prepare pellets in the laboratory, as well as industrially produced pre-reduced pellets that had already been milled in preparation for the determination of the pre-reduction level with wet chemical analysis were received from a large South African FeCr producer. These laboratory prepared pellets and the industrially produced pellet mixtures were considered in this investigation. Samples were moulded in resin and polished in order to obtain SEM micrographs of the polished cross sections. Elements with higher molecular weights are indicated by lighter greyscale, while elements with lower molecular weights are indicated by darker greyscale in SEM micrographs. This basic principle was applied in the development of the new analytical technique to determine the level of chromite pre-reduction, with the hypothesis that the pixel count of white pixels (representing metallised particles), divided by the combined pixel count of white (representing metallised particles) and grey (representing chromite particles) pixels would be directly related to the level of chromite pre-reduction determined with the current wet chemical method. This hypothesis can be mathematically expressed as:
The newly-developed analytical method was validated by correlating the white pixel% calculated with the chromite pre-reduction levels (%) determined with wet chemical analysis of laboratory prepared and industrially produced pellet mixtures, which had R2 values of 0.998 and 0.919, respectively. This suggests that the method can be used to determine chromite pre-reduction accurately.MSc (Engineering Sciences in Chemical Engineering), North-West University, Potchefstroom Campus, 2015
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Ullberg, Nathan. "Characterizing optical and electrical properties of monolayer MoS2 by backside absorbing layer microscopy." Thesis, 2020. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-419630.
Full textAbstract:
Nanomaterials are playing an increasing role in novel technologies, and it is important to develop optical methods to characterize them in situ. To that end, backside absorbing layer microscopy (BALM) has emerged as a powerful tool, being capable to resolve sub-nanometer height profiles, with video-rate acquisition speeds and a suitable geometry to couple live experiments. In the internship, several techniques involving BALM were developed, and applied to study optical and electrical properties of the transition metal dichalcogenide (TMD) monolayer MoS2, a type of 2-dimensional (2D) crystalline semiconductor. A simulations toolkit was created in MATLAB to model BALM, a workflow to reliably extract linear intensities from the CMOS detector was realized, and 2D MoS2 was synthesized by chemical vapor deposition followed by transfer to appropriate substrates. BALM data of the 2D MoS2 was acquired and combined with simulations, giving a preliminary result for its complex refractive index at 5 optical wavelengths. In addition, the first steps towards coupling BALM with a gate biased 2D MoS2 field-effect transistor were explored. To complement BALM measurements, the grown samples were also characterized by conventional optical microscopy, scanning electron microscopy, atomic force microscopy, photoluminescence spectroscopy, and Raman spectroscopy. This work provides new additions to an existing platform of BALM techniques, enabling novel BALM experiments with nanomaterial systems. In particular, it introduces a new alternative for local extraction of optical parameters and for probing of electrical charging effects, both of which are vital in the research and development of nano-optoelectronics.
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(6591728), Rui Yan. "The Development of Image Processing Algorithms in Cryo-EM." Thesis, 2019.
Find full textAbstract:
Cryo-electron microscopy (cryo-EM) has been established as the leading imaging technique for structural studies from small proteins to whole cells at a molecular level. The great advances in cryo-EM have led to the ability to provide unique insights into a wide variety of biological processes in a close to native, hydrated state at near-atomic resolutions. The developments of computational approaches have significantly contributed to the exciting achievements of cryo-EM. This dissertation emphasizes new approaches to address image processing problems in cryo-EM, including tilt series alignment evaluation, simultaneous determination of sample thickness, tilt, and electron mean free path based on Beer-Lambert law, Model-Based Iterative Reconstruction (MBIR) on tomographic data, minimization of objective lens astigmatism in instrument alignment and defocus and magnification dependent astigmatism of TEM images. The final goal of these methodological developments is to improve the 3D reconstruction of cryo-EM and visualize more detailed characterization.
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Thiessen, Jonathan. "Development and application of quantitative MRI methods for assessing white matter integrity in the mouse brain." 2012. http://hdl.handle.net/1993/9221.
Full textAbstract:
Healthy white matter in the brain and spinal cord is composed primarily of myelinated axons and glial cells. Myelinated axons transfer information between the peripheral nervous system and the central nervous system (CNS) as well as between centres within the CNS. Demyelination, a hallmark of neurodegenerative autoimmune diseases such as multiple sclerosis (MS), can cause nerve damage and degrade signal propagation. Magnetic resonance imaging (MRI) methods thought to assess myelin integrity and the structural integrity of axons are improving both the diagnosis and understanding of white matter diseases such as MS. Current methods, however, are sensitive to many different pathologies, making the interpretation of individual MRI results difficult. For this dissertation, several quantitative MRI methods were developed and compared, including single component T1 and T2 relaxometry, multicomponent T2 relaxometry, diffusion tensor imaging (DTI), and quantitative magnetization transfer imaging (qMTI). These methods were tested on agarose gels, fixed rat spinal cords, healthy control mice, and the cuprizone mouse model of demyelination.
Quantitative MRI measurements were correlated to ultrastructural measurements of white matter to determine the influence myelin content and axonal structure have on different MRI methods. Cellular distributions measured in electron micrographs of the corpus callosum correlated strongly to several different quantitative MRI metrics. The largest Spearman correlation coefficient varied depending on cellular type: longitudinal relaxation rates (RA/T1) vs. the myelinated axon fraction ( r = 0.90/-0.90), the qMTI-derived bound pool fraction (f) vs. the myelin sheath fraction ( r = 0.93), and the DTI-derived axial diffusivity vs.
the non-myelinated cell fraction (r = 0.92). Using Pearson’s correlation coefficient, f was strongly correlated to the myelin sheath fraction (r = 0.98) with a linear equation predicting myelin content (5.37f −0.25). Of the calculated MRI metrics, f was the strongest indicator of myelin content while longitudinal relaxation rates and diffusivity measurements were the strongest indicators of changes in tissue structure. Multiparametric MRI measurements of relaxation, diffusion, and magnetization transfer give a more complete picture of white matter integrity.
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Heisen, Burkhard Clemens. "New Algorithms for Macromolecular Structure Determination." Doctoral thesis, 2009. http://hdl.handle.net/11858/00-1735-0000-0006-B503-3.
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