Relevant bibliographies by topics / Microscopy and tomography

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Microscopy and tomography'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "Microscopy and tomography"

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van der Krift, Theo, Ulrike Ziese, Willie Geerts, and Bram Koster. "Computer-Controlled Transmission Electron Microscopy: Automated Tomography." Microscopy and Microanalysis 7, S2 (August 2001): 968–69. http://dx.doi.org/10.1017/s1431927600030919.

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The integration of computers and transmission electron microscopes (TEM) in combination with the availability of computer networks evolves in various fields of computer-controlled electron microscopy. Three layers can be discriminated: control of electron-optical elements in the column, automation of specific microscope operation procedures and display of user interfaces. The first layer of development concerns the computer-control of the optical elements of the transmission electron microscope (TEM). Most of the TEM manufacturers have transformed their optical instruments into computer-controlled image capturing devices. Nowadays, the required controls for the currents through lenses and coils of the optical column can be accessed by computer software. The second layer of development is aimed toward further automation of instrument operation. For specific microscope applications, dedicated automated microscope-control procedures are carried out. in this paper, we will discuss our ongoing efforts on this second level towards fully automated electron tomography. The third layer of development concerns virtual- or telemicroscopy. Most telemicroscopy applications duplicate the computer-screen (with accessory controls) at the microscope-site to a computer-screen at another site. This approach allows sharing of equipment, monitoring of instruments by supervisors, as well as collaboration between experts at remote locations.Electron tomography is a three-dimensional (3D) imaging method with transmission electron microscopy (TEM) that provides high-resolution 3D images of structural arrangements. with electron tomography a series of images is acquired of a sample that is tilted over a large angular range (±70°) with small angular tilt increments.
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Wang, Xinkun, Kedi Xiong, Xin Jin, and Sihua Yang. "Tomography-assisted Doppler photoacoustic microscopy: proof of concept." Chinese Optics Letters 18, no. 10 (2020): 101702. http://dx.doi.org/10.3788/col202018.101702.

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Butz, T., D. Lehmann, T. Reinert, D. Spemann, and J. Vogt. "Ion Microscopy and Tomography." Acta Physica Polonica A 100, no. 5 (November 2001): 603–13. http://dx.doi.org/10.12693/aphyspola.100.603.

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Wang, Lihong V. "Photoacoustic Tomography and Microscopy." Optics and Photonics News 19, no. 7 (July 1, 2008): 36. http://dx.doi.org/10.1364/opn.19.7.000036.

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Xiu, Peng, Xin Zhou, Cuifang Kuang, Yingke Xu, and Xu Liu. "Controllable tomography phase microscopy." Optics and Lasers in Engineering 66 (March 2015): 301–6. http://dx.doi.org/10.1016/j.optlaseng.2014.10.001.

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Borg, Thomas K., James A. Stewart, and Michael A. Sutton. "Imaging the Cardiovascular System: Seeing Is Believing." Microscopy and Microanalysis 11, no. 3 (May 12, 2005): 189–99. http://dx.doi.org/10.1017/s1431927605050439.

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From the basic light microscope through high-end imaging systems such as multiphoton confocal microscopy and electron microscopes, microscopy has been and will continue to be an essential tool in developing an understanding of cardiovascular development, function, and disease. In this review we briefly touch on a number of studies that illustrate the importance of these forms of microscopy in studying cardiovascular biology. We also briefly review a number of imaging modalities such as computed tomography, (CT) Magnetic resonance imaging (MRI), ultrasound, and positron emission tomography (PET) that, although they do not fall under the realm of microscopy, are imaging modalities that greatly complement microscopy. Finally we examine the role of proper imaging system calibration and the potential importance of calibration in understanding biological tissues, such as the cardiovascular system, that continually undergo deformation in response to strain.
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Carlson, David B., Jeff Gelb, Vadim Palshin, and James E. Evans. "Laboratory-Based Cryogenic Soft X-Ray Tomography with Correlative Cryo-Light and Electron Microscopy." Microscopy and Microanalysis 19, no. 1 (January 18, 2013): 22–29. http://dx.doi.org/10.1017/s1431927612013827.

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AbstractHere we present a novel laboratory-based cryogenic soft X-ray microscope for whole cell tomography of frozen hydrated samples. We demonstrate the capabilities of this compact cryogenic microscope by visualizing internal subcellular structures of Saccharomyces cerevisiae cells. The microscope is shown to achieve better than 50 nm half-pitch spatial resolution with a Siemens star test sample. For whole biological cells, the microscope can image specimens up to 5 μm thick. Structures as small as 90 nm can be detected in tomographic reconstructions following a low cumulative radiation dose of only 7.2 MGy. Furthermore, the design of the specimen chamber utilizes a standard sample support that permits multimodal correlative imaging of the exact same unstained yeast cell via cryo-fluorescence light microscopy, cryo-soft X-ray microscopy, and cryo-transmission electron microscopy. This completely laboratory-based cryogenic soft X-ray microscope will enable greater access to three-dimensional ultrastructure determination of biological whole cells without chemical fixation or physical sectioning.
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Smallwood, R., P. Metherall, D. Hose, M. Delves, H. Pollock, A. Hammiche, C. Hodges, V. Mathot, and P. Willcocks. "Tomographic imaging and scanning thermal microscopy: thermal impedance tomography." Thermochimica Acta 385, no. 1-2 (March 2002): 19–32. http://dx.doi.org/10.1016/s0040-6031(01)00705-5.

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Ko, Dae-Sik. "Multiple-Transducer Scheme for Scanning Tomographic Acoustic Microscopy Using Transverse Waves." Ultrasonic Imaging 19, no. 4 (October 1997): 294–304. http://dx.doi.org/10.1177/016173469701900405.

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We propose a new type of multiple-transducer scheme with functions of multiple-angle and multiple-frequency tomography for scanning tomographic acoustic microscopy (STAM) using transverse waves. We review the data acquisition system and mode conversion of the acoustic waves for STAM and the multiple-angle and multiple-frequency tomography. Our multiple-transducer scheme has three insonification angles and three resonance frequencies in order to operate, in the transverse wave mode, multiple-angle and multiple frequency tomography for STAM. In order to evaluate the performance of our transducer scheme, we have simulated tomographic reconstruction with a back-and-forth propagation algorithm. Simulation results show that our multiple-transducer scheme is capable of obtaining good resolution with transverse wave mode and multiple-frequency tomography. We also show that our multiple-transducer scheme is an efficient rotation tool for a number of projections.
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Qin, Wei, Qian Chen, and Lei Xi. "A handheld microscope integrating photoacoustic microscopy and optical coherence tomography." Biomedical Optics Express 9, no. 5 (April 16, 2018): 2205. http://dx.doi.org/10.1364/boe.9.002205.

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Dissertations / Theses on the topic "Microscopy and tomography"

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Godavarthi, Charankumar. "Optical diffraction tomography microscopy : towards 3D isotropic super-resolution." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM4337/document.

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Cette thèse vise à améliorer la résolution en trois dimensions grâce à une technique récente d’imagerie : la microscopie tomographique diffractive (MTD). Son principe est d’éclairer l’objet successivement sous différents angles en lumière cohérente, de détecter le champ diffracté en phase et en amplitude, et de reconstruire la carte 3D de permittivité de l’objet par un algorithme d’inversion. La MTD s’est avérée capable de combiner plusieurs modalités utiles pour la microscopie sans marquage, telles que plein champ, champ sombre, à contraste de phase, confocale, ou encore la microscopie à synthèse d’ouverture 2D ou 3D. Toutes sont basées sur des approximations scalaires et linéaires, ce qui restreint leur domaine d’application pour restituer l’objet de manière quantitative. A l’aide d’une inversion numérique rigoureuse prenant en compte la polarisation du champ et le phénomène de diffusion multiple, nous sommes parvenus à reconstruire la carte 3D de permittivité d’objets avec une résolution de λ/4. Une amélioration supplémentaire la portant à λ/10 a été rendue possible par l’insertion d’information a priori sur l’objet dans l’algorithme d’inversion. Enfin, la résolution axiale est moins bonne du fait de l’asymétrie des schémas d’illumination et de détection dans les microscopes. Pour s’affranchir de cette limitation, une configuration de tomographie assistée par miroir a été implémentée et a mis en évidence un pouvoir de séparation axial meilleur que λ/2. Au final, la MTD s’est illustrée comme un outil de caractérisation puissant pour reconstruire en 3D les objets ainsi que leurs indices optiques, à des résolutions bien supérieures à celles des microscopes conventionnels
This PhD thesis is devoted to the three-dimensional isotropic resolution improvement using optical tomographic diffraction microscopy (TDM), an emerging optical microscope technique. The principle is to illuminate the sample successively with various angles of coherent light, collect the complex (amplitude and phase) diffracted field and reconstruct the sample 3D permittivity map through an inversion algorithm. A single TDM measurement was shown to combine several popular microscopy techniques such as bright-field microscope, dark-field microscope, phase-contrast microscope, confocal microscope, 2D and 3D synthetic aperture microscopes. All rely on scalar and linear approximations that assume a linear link between the object and the field diffracted by it, which limit their applicability to retrieve the object quantitatively. Thanks to a rigorous numerical inversion of the TDM diffracted field data which takes into account the polarization of the field and the multiple scattering process, we were able to reconstruct the 3D permittivity map of the object with a λ/4 transverse resolution. A further improvement to λ/10 transverse resolution was achieved by providing a priori information about the sample to the non-linear inversion algorithm. Lastly, the poor axial resolution in microscopes is due to the fundamental asymmetry of illumination and detection. To overcome this, a mirror-assisted tomography configuration was implemented, and has demonstrated a sub-λ/2 axial resolution capability. As a result, TDM can be seen as a powerful tool to reconstruct objects in three-dimensions with their optical material properties at resolution far superior to conventional microscopes
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Bertilson, Michael. "Laboratory soft x-ray microscopy and tomography." Doctoral thesis, KTH, Biomedicinsk fysik och röntgenfysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-29950.

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Soft x-ray microscopy in the water-window (λ = 2.28 nm – 4.36 nm) is based on zone-plate optics and allows high-resolution imaging of, e.g., cells and soils in their natural or near-natural environment. Three-dimensional imaging is provided via tomographic techniques, soft x-ray cryo tomography. However, soft x-ray microscopes with such capabilities have been based on large-scale synchrotron x‑ray facilities, thereby limiting their accessibility for a wider scientific community. This Thesis describes the development of the Stockholm laboratory soft x-ray microscope to three-dimensional cryo tomography and to new optics-based contrast mechanisms. The microscope relies on a methanol or nitrogen liquid-jet laser-plasma source, normal-incidence multilayer or zone-plate condenser optics, in-house fabricated zone-plate objectives, and allows operation at two wavelengths in the water-window, λ = 2.48 nm and λ = 2.48 nm. With the implementation of a new state-of-the-art normal-incidence multilayer condenser for operation at λ = 2.48 nm and a tiltable cryogenic sample stage the microscope now allows imaging of dry, wet or cryo-fixed samples. This arrangement was used for the first demonstration of laboratory soft x-ray cryo microscopy and tomography. The performance of the microscope has been demonstrated in a number of experiments described in this Thesis, including, tomographic imaging with a resolution of 140 nm, cryo microscopy and tomography of various cells and parasites, and for studies of aqueous soils and clays. The Thesis also describes the development and implementation of single-element differential-interference and Zernike phase-contrast zone-plate objectives. The enhanced contrast provided by these optics reduce exposure times or lowers the dose in samples and are of major importance for harder x-ray microscopy. The implementation of a high-resolution 50 nm compound zone-plate objective for sub-25-nm resolution imaging is also described. All experiments are supported by extensive numerical modelling for improved understanding of partially coherent image formation and stray light in soft x-ray microscopes. The models are useful tools for studying effects of zone plate optics or optical design of the microscope on image formation and quantitative accuracy in soft x-ray tomography.
QC 20110221
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Balakishan, Harishankar. "Nanoscale Tomography Based in Electrostatic Force Microscopy." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/671789.

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The ability to characterize the elements beneath the surface has been a dire necessity in the fields of materials science, polymer technology, biology, and medical sciences. Scanning Probe Microscopies are the family of microscopies that scans the surface using a nanometric probe and the acquired data is used to reconstruct the physical properties of the samples in nanometric resolution (e.g., topography). Since the measurements could be carried out in non-contact mode, the ability to study tomography have made them a better contender. SPM also possess the relative advantage of being non-invasive, non-destructive, requires relatively minimal sample preparation, can be extended into any environment (inert, ambient vacuum), and also be measured in air, water, or any biological medium. Among them, Electrostatic Force Microscopy, has been successfully used in subsurface investigations to study the compositional modifications below the organic layers, imaging below the organic layers, imaging water molecules in confined nanometric channels, imaging of carbon nanotubes, graphene networks and nanoparticles inside the polymeric nanocomposites. Nanocomposites, which consist of nanostructures in their bulk matrix to improve the matrix efficiency, have been one of the successfully incorporated material science application of the last two decades. Silver nanoparticle especially have a barrage of applications to its credit ranging from solar cell applications, touch screens, LEDs to flexible wearable devices. Understanding the subsurface features or tomography of these nanocomposites could help us in understanding their properties, interpreting them based on their parametric dependence which would later aid us in tuning them for our desired applications. In this thesis. Individual computational studies have been carried out of nanowires buried in a dielectric matrix to observe the effects of various parameters influencing the subsurface imaging. Spatial resolution is given prime importance as its behavior of two parallel nanowires is studied along with two nanowires overlapped one on top of each other. Also, the analysis of silver nanowire nanocomposites has been investigated with the help of Scanning Dielectric Force Volume Microscopy, a technique proposed recently with EFM. The bulk matrix is composed of gelatin which can offer a range of permittivities depending on the degree of hydration, for e.g., here εr ~ 5 to εr ~ 14 . This sample is experimentally analyzed, imaged and the depth of nanowires in the matrix inside the bulk matrix is mapped with the theoretical analysis. This thesis research provides us with subsurface information that would help us in understanding and tuning the parameters to achieve desired applications.
La capacidad de caracterizar los elementos debajo de la superficie ha sido una necesidad imperiosa en los campos de la ciencia de los materiales, la tecnología de polímeros, la biología y las ciencias médicas. La microscopía de sonda de barrido (SPM por sus siglas en inglés) es una técnica de microscopía que permite exploran la superficie de una muestra a nano escala utilizando una sonda nanométrica, donde los datos adquiridos se utilizan para reconstruir las propiedades físicas de las muestras en resolución nanométrica (por ejemplo, topografía). Dado que las mediciones se pueden realizar sin contacto, los diferentes tipos de SPM se han convertido en candidatos óptimos para el estudio de propiedades sin necesidad de destruir la muestra. El SPM también posee la ventaja relativa de ser no invasivo, no destructivo, requiere una preparación de muestra relativamente sencilla, puede extenderse a cualquier ambiente (inerte, vacío ambiental), y también medirse en aire, agua o cualquier medio biológico. Entre ellos, la microscopía de fuerza electrostática, se ha utilizado con éxito en investigaciones del subsuelo para estudiar las modificaciones de composición debajo de las capas orgánicas, obtener imágenes debajo de las capas orgánicas, obtener imágenes de moléculas de agua confinada en canales nanométricos, imágenes de nanotubos de carbono, redes de grafeno y nanopartículas dentro de polímeros. Los nanocompuestos, que consisten en nanoestructuras en gran parte de su matriz para mejorar la eficiencia de la matriz, han sido una de las aplicaciones de la ciencia de materiales incorporadas con éxito en las últimas dos décadas. Las nanopartículas de plata tienen especialmente un aluvión de aplicaciones en su haber que van desde aplicaciones de células solares, pantallas táctiles, LED hasta dispositivos portátiles flexibles. Comprender las características del subsuelo o la tomografía de estos nanocompuestos podría ayudarnos a comprender sus propiedades, interpretándolas en función de su dependencia paramétrica, lo que luego nos ayudaría a ajustarlos para otras aplicaciones. En esta tesis, se han realizado estudios computacionales individuales de nano cables enterrados en una matriz dieléctrica para observar los efectos de varios parámetros que influyen en las imágenes del subsuelo. La resolución espacial tiene una importancia primordial, ya que se estudia su comportamiento de dos nano cables paralelos junto con dos nano cables superpuestos uno encima del otro. Además, el análisis de nanocompuestos de nano cables de plata se han investigado con la ayuda de la microscopía de barrido volumen de fuerza dieléctrica, una técnica propuesta recientemente con el EFM. La mayor parte de la matriz está compuesta de gelatina que puede ofrecer un rango de permitividades dependiendo del grado de hidratación, por ejemplo, aquí εr ~ 5 a εr ~ 14. Esta muestra se analiza experimentalmente, se obtienen imágenes y la profundidad de los nano cables en la matriz se mapean con el análisis teórico. Esta tesis nos proporciona nueva información y técnicas avanzadas a nivel tomográfico que ayudaran a la realización de imágenes de nanoestructuras de nuevos nanomateriales para aplicaciones en Salud y Electrónica.
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Niehle, Michael. "Electron tomography and microscopy on semiconductor heterostructures." Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät, 2016. http://dx.doi.org/10.18452/17607.

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Elektronentomographie erlaubt die dreidimensionale (3D) Charakterisierung von Kristalldefekten auf der Nanometerskala. Die Anwendung in der Forschung an epitaktischen Halbleiterheterostrukturen ist bisher nicht durchgesetzt worden, obwohl kleiner werdende Bauteile mit zunehmend dreidimensionaler Struktur entsprechende Untersuchungen verlangen, um die Beziehung von Struktur und physikalischen Eigenschaften in entsprechenden Materialsystemen zu verstehen. Die vorliegende Arbeit demonstriert die konsequente Anwendung der Elektronentomographie auf eine III-Sb basierte Laser- und eine 3D (In,Ga)N/GaN Nanosäulenheterostruktur. Die unerlässliche Zielpräparation von Proben mittels FIB-SEM-Zweistrahlmikroskops wird herausgestellt. Die kontrollierte Orientierung der Probe während der Präparation und die sorfältige Auswahl eines Abbildungsverfahrens im STEM werden detailliert beschrieben. Die umfassende räumliche Mikrostrukturanalyse einer antimonidbasierten Schichtstruktur folgt der Dimensionalität von Kristalldefekten. Die Facettierung und Lage einer Pore (3D Defekt), deren Auftreten in der MBE gewachsenen GaSb-Schicht untypisch ist, werden bestimmt. Das Zusammenspiel von anfänglich abgeschiedenen AlSb-Inseln auf dem Si-Substrat, der Ausbildung eines Fehlversetzungsnetzwerkes an der Grenzfläche der Heterostruktur (2D Defekt) und dem Auftreten von Durchstoßversetzungen wird mit Hilfe der Kombination tomographischer und komplementärer TEM-/STEM-Ergebnisse untersucht. Die räumliche Anordnung von Versetzungen (1D Defekte), die das ganze Schichtsystem durchziehen, wird mit Elektronentomographie offenbart. Die Wechselwirkung dieser Versetzungen mit Antiphasengrenzen und anderen Liniendefekten sind ein einzigartiges Ergebnis der Elektronentomographie. Abschließend sind Unterschiede im Indiumgehalt und in der Schichtdicke von (In,Ga)N-Einschlüssen auf verschiedenen Facetten schief aufgewachsener GaN-Nanosäulen einmalig per Elektronentomographie herausgearbeitet worden.
Electron tomography exhibits a very poor spread in the research field of epitaxial semiconductor heterostructures in spite of the ongoing miniaturization and increasing three-dimensional (3D) character of nano-structured devices. This necessitates a tomographic approach at the nanometre scale in order to characterize and understand the relation between structure and physical properties of respective material systems. The present work demonstrates the rigorous application of electron tomography to an III-Sb based laser and to an (In,Ga)N/GaN nanocolumn heterostructure. A specific target preparation using a versatile FIB-SEM dual-beam microscope is emphasized as indispensable. The purposeful orientation of the specimen during preparation and the careful selection of an imaging mode in the scanning-/transmission electron microscope (S/TEM) are regarded in great detail. The comprehensive spatial microstructure characterization of the antimonide based heterostructure follows the dimensionality of crystal defects. The facetting and position of a pore (3D defect) which is unexpected in the MBE grown GaSb layer, is determined. The interplay of the initially grown AlSb islands on Si, the formation of a misfit dislocation network at the heterostructure interface (2D defect) and the presence of threading dislocations is investigated by the correlation of tomographic and complementary S/TEM results. The spatial arrangement of dislocations (1D defects) penetrating the whole stack of antimonide layers is revealed by electron tomography. The interaction of these line defects with anti-phase boundaries and with other dislocations is exclusively observed in the 3D result. The insertion of (In,Ga)N into oblique GaN nanocolumns is uniquely accessed by electron tomography. The amount of incorporated indium and the (In,Ga)N layer thickness is shown to vary on the different facets of the GaN core.
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Ford, Bridget K. "Computed tomography based spectral imaging for fluorescence microscopy." Diss., The University of Arizona, 2002. http://hdl.handle.net/10150/280122.

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Multispectral imaging has been used for decades in remote sensing to enhance the classification, discrimination and characterization of materials. Only recently has this same technology been similarly applied to fixed biological samples in cytogenetics, pathology and medicine. A further extension to in vivo studies is often limited by the low levels of associated fluorescence as well as the increased temporal resolution required to analyze physiological changes. In addition, the cellular response to a specific agonist is often heterogeneous across the cellular field requiring a combination of sufficient spatial and temporal resolutions. A computed tomography imaging spectrometer (CTIS) has been developed which overcomes these limitations by simultaneously collecting extended range spectral information (470-740 nm, 5 nm sampling) across a 2-D field of view (200 μm x 200 μm, 0.96 μm sampling). The CTIS uses a computer generated hologram to produce a 5 x 5 array of images with differing amounts and directions of dispersion. This set of images allows the 3-D signal (x, y, λ) from a fluorescent sample to be mapped onto a 2-D detector array. In this way, the full spectral and spatial information is acquired for a 2-D cellular field during a single integration time (presently 2 sec for biological specimens). The CTIS's design, calibration, and underlying theory are described in detail. In addition, the capability of the CTIS to simultaneously collect the fluorescence emission of multiple fluorophores across a 2-D cellular field is demonstrated. Specifically, the combined spectral variations of seminapthorhodafluor-I and enhanced green fluorescent protein were followed in rat insulinoma cells in order to extend the linear range of intracellular pH detection.
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Swinford, Richard William. "An AFM-SIMS Nano Tomography Acquisition System." PDXScholar, 2017. https://pdxscholar.library.pdx.edu/open_access_etds/3485.

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An instrument, adding the capability to measure 3D volumetric chemical composition, has been constructed by me as a member of the Sánchez Nano Laboratory. The laboratory's in situ atomic force microscope (AFM) and secondary ion mass spectrometry systems (SIMS) are functional and integrated as one instrument. The SIMS utilizes a Ga focused ion beam (FIB) combined with a quadrupole mass analyzer. The AFM is comprised of a 6-axis stage, three coarse axes and three fine. The coarse stage is used for placing the AFM tip anywhere inside a (13x13x5 mm3) (xyz) volume. Thus the tip can be moved in and out of the FIB processing region with ease. The planned range for the Z-axis piezo was 60 µm, but was reduced after it was damaged from arc events. The repaired Z-axis piezo is now operated at a smaller nominal range of 18 µm (16.7 µm after pre-loading), still quite respectable for an AFM. The noise floor of the AFM is approximately 0.4 nm Rq. The voxel size for the combined instrument is targeted at 50 nm or larger. Thus 0.4 nm of xyz uncertainty is acceptable. The instrument has been used for analyzing samples using FIB beam currents of 250 pA and 5.75 nA. Coarse tip approaches can take a long time so an abbreviated technique is employed. Because of the relatively long thro of the Z piezo, the tip can be disengaged by deactivating the servo PID. Once disengaged, it can be moved laterally out of the way of the FIB-SIMS using the coarse stage. This instrument has been used to acquire volumetric data on AlTiC using AFM tip diameters of 18.9 nm and 30.6 nm. Acquisition times are very long, requiring multiple days to acquire a 50-image stack. New features to be added include auto stigmation, auto beam shift, more software automation, etc. Longer term upgrades to include a new lower voltage Z-piezo with strain-gauge feedback and a new design to extend the life for the coarse XY nano-positioners. This AFM-SIMS instrument, as constructed, has proven to be a great proof of concept vehicle. In the future it will be used to analyze micro fossils and it will also be used as a part of an intensive teaching curriculum.
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Selin, Mårten. "3D X-ray microscopy: image formation, tomography and instrumentation." Doctoral thesis, KTH, Biomedicinsk fysik och röntgenfysik, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-184095.

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Tomography in soft X-ray microscopy is an emerging technique for obtaining quantitative 3D structural information about cells. One of its strengths, compared with other techniques, is that it can image intact cells in their near-native state at a few 10 nm’s resolution, without staining. However, the methods for reconstructing 3D-data rely on algorithms that assume projection data, which the images are generally not due to the imaging systems’ limited depth of focus. To bring out the full potential of tomography in soft X-ray microscopy an improved understanding of the image formation is desired. This Thesis reviews zone plate-based X-ray microscopy for biological imaging and the theory necessary for a numerical implementation of a 3D image formation model. Furthermore, a novel reconstruction approach is proposed that improves the overall resolution in a reconstruction of a tomographically imaged object. This is demonstrated by simulations and experiments. Finally, this Thesis covers work on the Stockholm X-ray microscope, including an upgrade of the X-ray source yielding unprecedented brightness for a compact system. With this upgrade it was possible to do high-quality imaging of cells in their near-native state with only 10 second exposures.
Tomografi i mjukröntgenmikroskopi är en ny teknik för att få ut kvantitativ strukturell 3D information om celler. Dess styrka jämfört med andra tekniker är att den kan avbilda intakta celler i deras nära naturliga tillstånd med ett par 10 nm upplösning, utan omfattande preparering. Dock är metoderna för att rekonstruera 3D-data beroende av algoritmer som antar projektionsdata, vilket bilderna i allmänhet inte är på grund av avbildningsystemens begränsade skärpedjup. För att få ut den fulla potentialen av tomografi i röntgenmikroskopi behövs en ökad förståelse för avbildningsprocessen. Denna avhandling behandlar zonplatte-baserad röntgenmikroskopi för biologisk avbildning och den nödvändiga teorin för en numerisk implementering av en avbildningsmodell i 3D. En ny rekonstruktionsmetod föreslås som förbättrar upplösningen i rekonstruktionen för ett tomografiskt avbildat objekt. Detta visas i simuleringar och experiment. Slutligen omfattar denna avhandling arbete på Stockholms mjukröntgenmikroskop, inklusive en uppgradering av röntgenkällan som ger oöverträffad ljusstyrka för ett kompakt system. Denna uppgradering möjliggör högkvalitativ avbildning av celler i deras nästan naturliga tillstånd med endast 10 sekunders exponering.

QC 20160324

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Sharp, Joanne. "Electron tomography of defects." Thesis, University of Cambridge, 2010. https://www.repository.cam.ac.uk/handle/1810/228638.

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Tomography of crystal defects in the electron microscope was first attempted in 2005 by the author and colleagues. This thesis further develops the technique, using a variety of samples and methods. Use of a more optimised, commercial tomographic reconstruction program on the original GaN weak beam dark-field (WBDF) tilt series gave a finer reconstruction with lower background, line width 10-20 nm. Four WBDF tilt series were obtained of a microcrack surrounded by dislocations in a sample of indented silicon, tilt axes parallel to g = 220, 220, 400 and 040. Moiré fringes in the defect impaired alignment and reconstruction. The effect on reconstruction of moiré fringe motion with tilt was simulated, resulting in an array of rods, not a flat plane. Dislocations in a TiAl alloy were reconstructed from WBDF images with no thickness contours, giving an exceptionally clear reconstruction. The effect of misalignment of the tilt axis with systematic row g(ng) was assessed by simulating tilt series with diffraction condition variation across the tilt range of Δn = 0, 1 and 2. Misalignment changed the inclination of the reconstructed dislocation with the foil surfaces, and elongated the reconstruction in the foil normal direction; this may explain elongation additional to the missing wedge effect in experiments. Tomography from annular dark-field (ADF) STEM dislocation images was also attempted. A tilt series was obtained from the GaN sample; the reconstructed dislocations had a core of bright intensity of comparable width to WBDF reconstructions, with a surrounding region of low intensity to 60 nm width. An ADF STEM reconstruction was obtained from the Si sample at the same microcrack as for WBDF; here automatic specimen drift correction in tomography acquisition software succeeded, a significant improvement. The microcrack surfaces in Si reconstructed as faint planes and dislocations were recovered as less fragmented lines than from the WBDF reconstruction. ADF STEM tomography was also carried out on the TiAl sample, using a detector inner angle (βin) that included the first order Bragg spots (in other series βin had been 4-6θ B). Extinctions occurred which were dependent on tilt; this produced only weak lines in the reconstruction. Bragg scattering in the ADF STEM image was estimated by summing simulated dark-field dislocation images from all Bragg beams at a zone axis; a double line was produced. It was hypothised that choosing the inner detector angle to omit these first Bragg peaks may preclude most dynamical image features. Additional thermal diffuse scattering (TDS) intensity due to dilatation around an edge dislocation was estimated and found to be insignificant. The Huang scattering cross section was estimated and found to be 9Å, ten times thinner than experimental ADF STEM dislocation images. The remaining intensity may be from changes to TDS from Bloch wave transitions at the dislocation; assessing this as a function of tilt is for further work. On simple assessment, only three possible axial channeling orientations were found over the tilt range for GaN; if this is typical, dechanneling contrast probably does not apply to defect tomography.
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Mazlin, Viacheslav. "Tomographie optique cohérente pour l’imagerie in vivo de la cornée." Thesis, Paris Sciences et Lettres (ComUE), 2019. http://www.theses.fr/2019PSLET024.

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Ce projet de thèse vise à créer un système optique pour l'imagerie à haute résolution sans contact de la cornée humaine in vivo. Pour y parvenir, le système de tomographie par cohérence optique plein champ travaillant dans le domaine temporel ex vivo par contact (FFOCT) a été transformé en un dispositif d'imagerie in vivo sans contact et a été appliqué pour la première fois à l'œil humain. La FFOCT a permis d’acquérir des images de la cornée, du limbe, de la sclère et du film lacrymal sur des yeux humains, révélant des cellules et des nerfs, pouvant être quantifiés sur un champ de vision millimétrique, bien au-delà des capacités de la microscopie confocale et de la tomographie par cohérence optique (OCT) conventionnelle. Le flux sanguin et la dynamique du film lacrymal ont pu être suivis directement et quantifiés. De plus, la FFOCT a été combinée à un OCT spectral pour effectuer un suivi des mouvements axiaux de l'œil en temps réel et une correction de la défocalisation. Ce dernier ajout a permis l’imagerie et l’affichage FFOCT en temps réel, ce qui ouvre la voie à la mise en œuvre future de dispositifs dans pour la recherche que pour la pratique clinique. Le transfert de FFOCT du laboratoire à l’hôpital est en outre stimulé par plusieurs solutions qui sont proposées dans le manuscrit, dans le but de réduire la complexité instrumentale. Enfin, un dispositif FFOCT apparenté a été appliqué à l’imagerie rétinienne humaine in vivo, révélant des photorécepteurs
This PhD project aimed to create an optical system for non-contact cellular resolution imaging of the human cornea in vivo. To achieve that, the contact ex vivo time-domain full-field optical coherence tomography (FFOCT) system was transformed into a non-contact in vivo imaging device and was for the first time applied to the human eye. FFOCT acquired images from the entire human cornea, limbus, sclera and tear film, revealing cells and nerves, which could be quantified over a millimetric field-of-view, beyond the capability of confocal microscopy and conventional optical coherence tomography (OCT). Blood flow and tear film dynamics could be directly followed and quantified. Furthermore, FFOCT was combined with a conventional OCT to perform real-time axial eye tracking and defocusing correction. The latter enabled real-time FFOCT imaging and display, which opens a path for future device implementation in clinical research and practice. Bench to bedside transfer of FFOCT is further stimulated by several solutions proposed in the manuscript, aiming to reduce the instrumentational complexity. Finally, a related FFOCT device was applied to imaging in vivo human retina, revealing the photoreceptors
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Xiao, Juan. "Development of electron tomography on liquid suspensions using environmental scanning electron microscopy." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEI050/document.

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La Microscopie Electronique à Balayage Environnementale permet l'observation de liquides dans certaines conditions de pression et température. En travaillant en transmission, i.e. en mode STEM (Scanning Transmission Electron Microscopy), des nano-objets présents au sein du liquide peuvent même être analysés (mode « Wet-STEM»). Dans les solutions concentrées, l'arrangement du soluté peut changer être un paramètre microstructural important, qu’il est alors nécessaire de caractériser. Dans ce contexte, le but de ce travail est de développer la tomographie électronique sur des suspensions liquides en utilisant le mode STEM en ESEM, de manière à obtenir la structure 3D de nano-objets dispersés dans un liquide. Dans une première partie, le contraste entre des nanoparticules et le film d’eau est étudié en combinant des images expérimentales Wet-STEM (en 2D) et des simulations Monte Carlo. Deux types de nano-matériaux sont choisis : des nanoparticules d’or sphériques, de diamètre environ 40 nm, dispersées dans l’eau, ainsi qu’une suspension aqueuse de latex SBA-PMMA, contenant 3% de PMMA utilisé comme tensioactif stérique. La comparaison entre les résultats simulés et expérimentaux permet d’estimer comment le contraste entre l’eau et les nanomatériaux est affecté par l’épaisseur du film d’eau. Dans une deuxième partie, des expériences de tomographie sont réalisées à sec sur des films de polyuréthane contenant des nanotubes de carbone multiparois greffés ou non, en utilisant une platine développée précédemment au laboratoire. Le volume a pu être reconstruit correctement. Cependant, en effectuant une acquisition 3D sur des suspensions de latex SBA-PMMA, le contrôle de la température de l’échantillon s’est révélé insuffisant. Nous proposons une amélioration à la fois de la platine et des conditions d’observations permettant de mieux contrôler l’évaporation et la condensation de l’eau sur des échantillons liquides. La troisième partie est dévolue à une analyse approfondie d’une suspension de latex SBA-PMMA, de différentes concentrations (d’un état dilué à très concentré), les acquisitions étant effectuées avec les conditions optimisées. L’arrangement des particules de latex est comparé à des modèles issus de la littérature, et avec des résultats expérimentaux obtenus par cryo-SEM sur suspensions congelées. Nous présentons ensuite une étude du même latex en présence de tensioactif. La couche de tensioactif peut être mise en évidence dans les volumes reconstruits et segmentés. En conclusion, nous résumons les potentialités de la tomographie wet-STEM pour la caractérisation de nanomatériaux solides et liquides. Des perspectives sont proposées pour continuer dans l’exploration de ces potentialités et des limites de la technique
ESEM (Environmental Scanning Electron Microscopy) allows the observation of liquids under specific conditions of pressure and temperature. When working in the transmission mode, i.e. in STEM (Scanning Transmission Electron Microscopy), nano-objects can even be analyzed inside the liquid (“wet-STEM” mode). Moreover, in situ evaporation of water can be performed to study the materials evolution from the wet to the dry state. This work aims at developing electron tomography on liquid suspensions using STEM-in-ESEM, to obtain the 3D structure of nano-objects dispersed in a liquid. In a first part, Monte Carlo simulations and 2D wet-STEM experimental images are combined to study the contrast. Two kinds of liquid nano-materials are chosen as the sample: spherical gold particles (diameter around 40 nm) in suspension in water; latex SBA-PMMA suspension, a copolymer derived from styrene and metacrylic acid esters in aqueous solution, 3% PMMA shell included as steric surfactant. The comparison between simulated and experimental results helps to determine how water can affect the contrast of hydrated nano-materials. Tomography experiments are then performed on dry PU-carbon nanotubes nanocomposites using a previously developed home-made tomography device, and the volume is well reconstructed. When performing tomography on latex suspension, limitations are found on the temperature control of samples. We propose an optimization of the device with new observations conditions to better control water evaporation and condensation of liquid samples. Afterwards, a full 3D analysis on SBA-PMMA latex from dilute suspension to very concentrated one is performed, and a further study is presented in presence of a surfactant. The encouraging reconstruction results are used to model the particles arrangement. This shows the potentialities of wet-STEM tomography for the characterization of both solid and liquid nano-materials
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Books on the topic "Microscopy and tomography"

1

Miller, M. K. Atom probe tomography: Analysis at the atomic level. New York: Kluwer Academic / Plenum Publishers, 2000.

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Larson, David J. Local electrode atom probe tomography: A user's guide. New York: Springer, 2013.

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Atom Probe Tomography: Analysis at the Atomic Level. Boston, MA: Springer US, 2000.

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International, Meeting on Scanning Laser Ophthalmoscopy Tomography and Microscopy (7th 1999). Seventh International Meeting on Scanning Laser Ophthalmoscopy, Tomography, and Microscopy. Boston: Kluwer Academic Publishers, 2001.

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Stock, Stuart R. MicroComputed tomography: Methodology and applications. Boca Raton: CRC Press, 2009.

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1940-, Frank J., ed. Electron tomography: Methods for three-dimensional visualization of structures in the cell. 2nd ed. New York: Springer, 2006.

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Adam, Kruk. Tomografia elektronowa i jej zastosowanie w obrazowaniu i metrologii mikrostruktury materiałów: Electron tomography and its application in imaging and metrology of the microstructure of materials. Kraków: Wydawnictwa AGH, 2012.

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International Conference on Optical Instruments and Technology (2009 Shanghai, China). 2009 International Conference on Optical Instruments and Technology: Optical trapping and microscopic imaging : 19-22 October 2009, Shanghai, China. Edited by Yuan Xiaocong, Zhongguo yi qi yi biao xue hui, Zhongguo guang xue xue hui, SPIE (Society), and Zhongguo yi qi yi biao xue hui. Optoelectronic-Mechanic Technology and System Integration Chapter. Bellingham, Wash: SPIE, 2009.

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K, Miller M., Oak Ridge National Laboratory, and U.S. Nuclear Regulatory Commission. Office of Nuclear Regulatory Research. Division of Engineering Technology., eds. Atom probe tomography characterization of the solute distributions in a neutron-irradiated and annealed pressure vessel steel weld. Washington, DC: U.S. Nuclear Regulatory Commission, 2000.

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L, Ackerman Jerome, Ellingson W. A, and Materials Research Society, eds. Advanced tomographic imaging methods for the analysis of materials: Symposium held November 28-30, 1990, Boston, Massachusetts, U.S.A. Pittsburgh, Pa: Materials Research Society, 1991.

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Book chapters on the topic "Microscopy and tomography"

1

Russ, John C. "Tomography." In Computer-Assisted Microscopy, 419–37. Boston, MA: Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0563-7_13.

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Weyland, Matthew, and Paul Midgley. "Electron Tomography." In Transmission Electron Microscopy, 343–76. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-26651-0_12.

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Aguirre, Aaron D., Chao Zhou, Hsiang-Chieh Lee, Osman O. Ahsen, and James G. Fujimoto. "Optical Coherence Microscopy." In Optical Coherence Tomography, 865–911. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-06419-2_29.

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Aguirre, A. D., and J. G. Fujimoto. "Optical Coherence Microscopy." In Optical Coherence Tomography, 505–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-77550-8_17.

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Miller, M. K. "Field Ion Microscopy." In Atom Probe Tomography, 45–83. Boston, MA: Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4281-0_3.

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Lin, Angela S. P., Stuart R. Stock, and Robert E. Guldberg. "Microcomputed Tomography." In Springer Handbook of Microscopy, 1205–36. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-00069-1_24.

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Midgley, Paul A., and Matthew Weyland. "STEM Tomography." In Scanning Transmission Electron Microscopy, 353–92. New York, NY: Springer New York, 2010. http://dx.doi.org/10.1007/978-1-4419-7200-2_8.

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Carazo, J. M., C. O. Sorzano, E. Rietzel, R. Schröder, and R. Marabini. "Discrete Tomography in Electron Microscopy." In Discrete Tomography, 405–16. Boston, MA: Birkhäuser Boston, 1999. http://dx.doi.org/10.1007/978-1-4612-1568-4_18.

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Kelly, Thomas F. "Atom-Probe Tomography." In Springer Handbook of Microscopy, 715–63. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-00069-1_15.

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Plitzko, Jürgen, and Wolfgang P. Baumeister. "Cryo-Electron Tomography." In Springer Handbook of Microscopy, 189–228. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-00069-1_4.

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Conference papers on the topic "Microscopy and tomography"

1

Colon, Jorge, and Hyungsik Lim. "Adaptive Field Microscopy: Shaping Field for 3D Laser Scanning Microscopy." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/ots.2016.oth4c.8.

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Bell, Kevan, Saad Abbasi, Nicholas Pellegrino, and Parsin Haji Reza. "Hyperspectral Photoacoustic Remote Sensing Microscopy." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2020. http://dx.doi.org/10.1364/ots.2020.sw4d.4.

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Zhang, Hao F. "Optical Ultrasound Detection in Photoacoustic Microscopy." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/ots.2016.oth1c.1.

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Liang, Yizhi, Chao Liu, long jin, and Lidai Wang. "Single-Cell Optical-Resolution Photoacoustic Microscopy." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2018. http://dx.doi.org/10.1364/ots.2018.ow4d.7.

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Wang, Peng. "3D Electron Ptychographical Tomography." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.1146.

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Zhang, Wei, Yanxiu Li, Van Phuc Nguyen, Guan Xu, Yannis M. Paulus, and Xueding Wang. "Integrated photoacoustic microscopy, optical coherence tomography and fluorescence microscopy imaging of rabbit ocular neovascularization in vivo." In Optical Tomography and Spectroscopy. Washington, D.C.: OSA, 2020. http://dx.doi.org/10.1364/ots.2020.sth4d.3.

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Saghi, Zineb. "Workflow for correlative energy-dispersive X-ray tomography and atom probe tomography." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.327.

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Stockton, Patrick A., Keith A. Wernsing, Jeff J. Field, Jeff Squier, and Randy A. Bartels. "Single Pixel Fourier Computed Tomography." In Novel Techniques in Microscopy. Washington, D.C.: OSA, 2019. http://dx.doi.org/10.1364/ntm.2019.nw2c.2.

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Bergoënd, Isabelle, Cristian Arfire, Yann Cotte, and Christian Depeursinge. "Complex field imaging for diffraction tomography." In Novel Techniques in Microscopy. Washington, D.C.: OSA, 2011. http://dx.doi.org/10.1364/ntm.2011.ntuc7.

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Drobek, Dominik. "Correlative 3D characterization of hierarchical zeolite structures linking nano X-ray tomography and 360° electron tomography." In European Microscopy Congress 2020. Royal Microscopical Society, 2021. http://dx.doi.org/10.22443/rms.emc2020.859.

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Reports on the topic "Microscopy and tomography"

1

Edmondson, Philip D. An On-Axis Tomography Holder for Correlative Electron and Atom Probe Microscopy. Office of Scientific and Technical Information (OSTI), October 2018. http://dx.doi.org/10.2172/1479802.

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Knipling, Keith, Fred Meisenkothen, and Eric B. Steel. Proceedings of the International Conference on Atom-Probe Tomography and Microscopy (APT&M 2018). National Institute of Standards and Technology, December 2019. http://dx.doi.org/10.6028/nist.sp.2100-03.

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Riccardella, Scott, and Jason Van Velsor. PR-335-15370-R01 Evaluation of NDE Methodologies for In-Ditch Characterization of ERW Seam Anomalies. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), June 2019. http://dx.doi.org/10.55274/r0011596.

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This work further evaluate and accurately assess the current state (as of 2016) of NDE methodologies for characterizing ERW seam defects. The IM-3C project was conducted as part of a larger program that also incorporated an evaluation of in-line inspection (ILI) technology performance (IM-3-1). The work primarily consisted of a round-robin type study, where service and technology providers were asked to conduct NDE on several blind samples that were known to have ERW seam defects. Following completion of the NDE, the blind samples were destructively tested and the ERW seam defects were characterized in a laboratory using metallurgical microscopy and, in some cases, X-ray computed tomography (XRCT). The results of the destructive were then used to characterize the performance of the NDE methods and technologies applied.
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Riccardella, Scott, and Jason Van Velsor. PR-335-173844-R01 NDE Crack Depth Sizing Performance Validation for Multiple UT Techniques. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), May 2020. http://dx.doi.org/10.55274/r0011676.

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PRCI commissioned this project (NDE-4-6) to further evaluate and accurately assess the current state (as of 2019) of NDE methodologies for characterizing Stress Corrosion Cracking. The NDE-4-6 project also conducted advanced Finite Element Modeling and flaw fabrication to help gain further insight on NDE performance and improve efficiency of conducting round robin evaluations. The project consisted of a round-robin type study, in which service and technology providers were asked to conduct NDE on several blind samples including actual SCC and fabricated flaw samples. Following completion of the NDE, select samples were destructively tested and characterized in a laboratory using metallurgical microscopy and X-ray computed tomography (XRCT). The results of the destructive testing were then used to characterize the performance of the NDE methods and technologies applied.
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Alexander, Chris, and Atul Ganpatye. PR-652-203802-R01 Computed Tomography for the Development of Standards for Anomaly Detection-Characterization. Chantilly, Virginia: Pipeline Research Council International, Inc. (PRCI), December 2022. http://dx.doi.org/10.55274/r0012246.

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This report documents the testing and inspection efforts undertaken to evaluate the capabilities and limitations of X-Ray Computed Tomography (XRCT) technology from the perspective of detection and quantification of flaws in pipelines. The fundamental motivation behind this project is to leverage the capabilities of the XRCT technology for highly accurate detection and characterization of flaws in pipelines. The accurate sizing and characterization of flaws/cracks in pipelines is of great consequence in providing effective and efficient operational and repair decisions in any integrity management program. As is the case with any emerging technology, comprehensive validation is needed before the technology can be considered mature enough to be effectively deployed by operators in the real-world or be used in the development of reference standards. This report discusses a validation approach and compares the XRCT results with those obtained from conventional NDE, and sectioning and microscopy, for synthetic and real-world features. Results are discussed in the context of the development of reference standards using synthetic flaws. The discussion provided in this document will be valuable for operators in understanding applicability, gaps, and future direction for the XRCT technology in the context of accurate flaw detection and characterization in pipelines. Results discussed in the report show that XRCT has the potential to enable the pipeline industry to establish a set of reference standards that can be used for a wide range of purposes, including technology development and qualification, personnel training and competency testing for inspection of flaws in pipelines. Once established as a proxy for "truth", XRCT will significantly minimize the need for frequent destructive testing for the generation of validation data further enabling the use in the development of reference standards. Within the purview of the work scope completed in this project, XRCT showed excellent results with synthetic features confirming that the technology (along with the process of generating synthetic features) is ready to be used in the development of reference standards using synthetic features. This work was funded in part, under the Department of Transportation, Pipeline and Hazardous Materials Safety Administration. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the Pipeline and Hazardous Materials Safety Administration, the Department of Transportation, or the U.S. Government.
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Elbaum, Michael, and Peter J. Christie. Type IV Secretion System of Agrobacterium tumefaciens: Components and Structures. United States Department of Agriculture, March 2013. http://dx.doi.org/10.32747/2013.7699848.bard.

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Objectives: The overall goal of the project was to build an ultrastructural model of the Agrobacterium tumefaciens type IV secretion system (T4SS) based on electron microscopy, genetics, and immunolocalization of its components. There were four original aims: Aim 1: Define the contributions of contact-dependent and -independent plant signals to formation of novel morphological changes at the A. tumefaciens polar membrane. Aim 2: Genetic basis for morphological changes at the A. tumefaciens polar membrane. Aim 3: Immuno-localization of VirB proteins Aim 4: Structural definition of the substrate translocation route. There were no major revisions to the aims, and the work focused on the above questions. Background: Agrobacterium presents a unique example of inter-kingdom gene transfer. The process involves cell to cell transfer of both protein and DNA substrates via a contact-dependent mechanism akin to bacterial conjugation. Transfer is mediated by a T4SS. Intensive study of the Agrobacterium T4SS has made it an archetypal model for the genetics and biochemistry. The channel is assembled from eleven protein components encoded on the B operon in the virulence region of the tumor-inducing plasmid, plus an additional coupling protein, VirD4. During the course of our project two structural studies were published presenting X-ray crystallography and three-dimensional reconstruction from electron microscopy of a core complex of the channel assembled in vitro from homologous proteins of E. coli, representing VirB7, VirB9, and VirB10. Another study was published claiming that the secretion channels in Agrobacterium appear on helical arrays around the membrane perimeter and along the entire length of the bacterium. Helical arrangements in bacterial membranes have since fallen from favor however, and that finding was partially retracted in a second publication. Overall, the localization of the T4SS within the bacterial membranes remains enigmatic in the literature, and we believe that our results from this project make a significant advance. Summary of achievements : We found that polar inflations and other membrane disturbances relate to the activation conditions rather than to virulence protein expression. Activation requires low pH and nutrient-poor medium. These stress conditions are also reflected in DNA condensation to varying degrees. Nonetheless, they must be considered in modeling the T4SS as they represent the relevant conditions for its expression and activity. We identified the T4SS core component VirB7 at native expression levels using state of the art super-resolution light microscopy. This marker of the secretion system was found almost exclusively at the cell poles, and typically one pole. Immuno-electron microscopy identified the protein at the inner membrane, rather than at bridges across the inner and outer membranes. This suggests a rare or transient assembly of the secretion-competent channel, or alternatively a two-step secretion involving an intermediate step in the periplasmic space. We followed the expression of the major secreted effector, VirE2. This is a single-stranded DNA binding protein that forms a capsid around the transferred oligonucleotide, adapting the bacterial conjugation to the eukaryotic host. We found that over-expressed VirE2 forms filamentous complexes in the bacterial cytoplasm that could be observed both by conventional fluorescence microscopy and by correlative electron cryo-tomography. Using a non-retentive mutant we observed secretion of VirE2 from bacterial poles. We labeled the secreted substrates in vivo in order detect their secretion and appearance in the plant cells. However the low transfer efficiency and significant background signal have so far hampered this approach.
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Jackson, J. Wolter X-Ray Microscope Computed Tomography Ray-Trace Model with Preliminary Simulation Results. Office of Scientific and Technical Information (OSTI), February 2006. http://dx.doi.org/10.2172/883616.

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King, W. E., G. H. Campbell, D. L. Haupt, J. H. Kinney, R. A. Riddle, and W. L. Wien. Mechanism of ductile rupture in the Al/sapphire system elucidated using x-ray tomographic microscopy. Office of Scientific and Technical Information (OSTI), December 1995. http://dx.doi.org/10.2172/231570.

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Wendelberger, James. Registration of Laser Confocal Microscope (LCM), Wide Area Measurement System (WAMS), and X-Ray Tomographic (XRAY) Images. Office of Scientific and Technical Information (OSTI), September 2021. http://dx.doi.org/10.2172/1821351.

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Sparks, Paul, Jesse Sherburn, William Heard, and Brett Williams. Penetration modeling of ultra‐high performance concrete using multiscale meshfree methods. Engineer Research and Development Center (U.S.), September 2021. http://dx.doi.org/10.21079/11681/41963.

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Terminal ballistics of concrete is of extreme importance to the military and civil communities. Over the past few decades, ultra‐high performance concrete (UHPC) has been developed for various applications in the design of protective structures because UHPC has an enhanced ballistic resistance over conventional strength concrete. Developing predictive numerical models of UHPC subjected to penetration is critical in understanding the material's enhanced performance. This study employs the advanced fundamental concrete (AFC) model, and it runs inside the reproducing kernel particle method (RKPM)‐based code known as the nonlinear meshfree analysis program (NMAP). NMAP is advantageous for modeling impact and penetration problems that exhibit extreme deformation and material fragmentation. A comprehensive experimental study was conducted to characterize the UHPC. The investigation consisted of fracture toughness testing, the utilization of nondestructive microcomputed tomography analysis, and projectile penetration shots on the UHPC targets. To improve the accuracy of the model, a new scaled damage evolution law (SDEL) is employed within the microcrack informed damage model. During the homogenized macroscopic calculation, the corresponding microscopic cell needs to be dimensionally equivalent to the mesh dimension when the partial differential equation becomes ill posed and strain softening ensues. Results of numerical investigations will be compared with results of penetration experiments.
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