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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 conventionnelsThis 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 photorécepteursThis 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 techniqueESEM (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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Pan, Zhipeng. "Advanced optical microscopy for three dimensional deformation, profile and tomography measurement." Thesis, Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54908.
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Deformation, profile and tomography measurement is critical for engineering materials characterization and engineering structure component design, analysis and biomedical application. The current existing 3D measurement method, such as stylus based profilometry, 3D optical stereo imaging and focus stacking, either suffers from low sampling speed from spatial scanning or maximum thickness of the specimen that could be imaged due to physical constraints. This thesis is dedicated to develop a hybrid 3D measurement method that can be easily implemented with fast imaging speed for dynamic process at the microscale. Also, at the microscale, the reduced depth of focus of existing microscope system greatly limits the maximum depth of the specimen that could be imaged, especially at high magnification. In this study, a 3D tomography system will be developed with extended depth of focus and improved axial resolution.
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Krehl, Jonas. "Incorporating Fresnel-Propagation into Electron Holographic Tomography." Master's thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-217919.
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Tomographic electron holography combines tomography, the reconstruction of three-dimensionally resolved data from multiple measurements with different specimen orientations, with electron holography, an interferometrical method for measuring the complex wave function inside a transmission electron microscope (TEM). Due to multiple scattering and free wave propagation conventional, ray projection based, tomography does perform badly when approaching atomic resolution. This is remedied by incorporating propagation effects into the projection while maintaining linearity in the object potential. Using the Rytov approach an approximation is derived, where the logarithm of the complex wave is linear in the potential. The ray projection becomes a convolution with a Fresnel propagation kernel, which is considerably more computationally expensive. A framework for such calculations has been implemented in Python. So has a multislice electron scattering algorithm, optimised for large fields of view and high numbers of atoms for simulations of scattering at nanoparticles. The Rytov approximation gives a remarkable increase in resolution and signal quality over the conventional approach in the tested system of a tungsten disulfide nanotube. The response to noise seems to be similar as in conventional tomography, so rather benign. This comes at the downside of much longer calculation time per iterationTomographische Elektronenholographie kombiniert Tomographie, die Rekonstruktion dreidimensional aufgelößter Daten aus einem Satz von mehreren Messungen bei verschiedenen Objektorientierungen, mit Elektronenholographie, eine interferrometrische Messung der komplexen Elektronenwelle im Transmissionselektronenmikroskop (TEM). Wegen Mehrfachstreuung und Propagationseffekten erzeugt konventionelle, auf einer Strahlprojektion basierende, Tomography ernste Probleme bei Hochauflösung hin zu atomarer Auflösung. Diese sollen durch ein Modell, welches Fresnel-Propagation beinhaltet, aber weiterhin linear im Potential des Objektes ist, vermindert werden. Mit dem Rytov-Ansatz wird eine Näherung abgeleitet, wobei der Logarithmus der komplexen Welle linear im Potential ist. Die Strahlen-Projektion ist dann eine Faltung mit dem Fresnel-Propagations-Faltungskernel welche rechentechnisch wesentlich aufwendiger ist. Ein Programm-Paket für solche Rechnungen wurde in Python implementiert. Weiterhin wurde ein Multislice Algorithmus für große Gesichtsfelder und Objekte mit vielen Atomen wie Nanopartikel optimiert. Die Rytov-Näherung verbessert sowohl die Auflösung als auch die Signalqualität immens gegenüber konventioneller Tomographie, zumindest in dem getesteten System eines Wolframdisulfid-Nanoröhrchens. Das Rauschverhalten scheint ähnlich der konventionallen Tomographie zu sein, also eher gutmütig. Im Gegenzug braucht die Tomographie basierend auf der Rytov-Näherung wesentlich mehr Rechenzeit pro Iteration
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Sandin, Sara. "Cryo-electron tomography of individual protein molecules /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-462-7/.
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Ren, Christopher Xiang. "Multi-microscopy characterisation of III-nitride devices and materials." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/264158.
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III-nitride optoelectronic devices have become ubiquitous due to their ability to emit light efficiently in the blue and green spectral ranges. Specifically, III-nitride light emitting diodes (LEDs) have become widespread due to their high brightness and efficiency. However, III-nitride devices such as single photon sources are also the subject of research and are promising for various applications. In order to improve design efficient devices and improve current ones, the relationship between the structure of the constituent materials and their optical properties must be studied. The optical properties of materials are often examined by photoluminescence or cathodoluminescence, whilst traditional microscopy techniques such a transmission electron microscopy and scanning electron microscopy are used to elucidate their structure and composition. This thesis describes the use of a dual-beam focussed ion beam/scanning electron microscope (FIB/SEM) in bridging the gap between these two types of techniques and providing a platform on which to perform correlative studies between the optical and structural properties of III-nitride materials. The heteroepitaxial growth of III-nitrides has been known to produce high defect densities, which can harm device performance. We used this correlative approach to identify hexagonal defects as the source of inhomogeneous electroluminescence (EL) in LEDs. Hyperspectral EL mapping was used to show the local changes in the emission induced by the defects. Following this the FIB/SEM was used to prepare TEM samples from the apex of the defects, revealing the presence of p-doped material in the active region caused by the defect. APSYS simulations confirmed that the presence of p-doped material can enhance local EL. The deleterious effects of defects on the photoelectrochemical etching of cavities were also studied. We performed TEM analysis of an edge-defect contained in unetched material on the underside of a microdisk using FIB/SEM sample preparation methods. The roughness and morphology of microdisk and nanobeam cavities was studied using FIB-tomography (FIBT), demonstrating how the dual-beam instrument may be used to access the 3D morphology of cavities down to the resolution of the SEM and the slicing thickness of the FIB. This tomography approach was further extended with electron tomography studies of the nanobeam cavities, a technique which provided fewer issues in terms of image series alignment but also the presence of reconstruction artefacts which must be taken into account when quantitatively analysing the data. The use of correlative techniques was also used to establish the link between high Si content in an interlayer running along the length of microrods with changes in the optical emission of these rods. The combination of CL, FIB/SEM and TEM-based techniques has made it possible to gain a thorough understanding of the link between the structural and optical properties in a wide variety of III-nitride materials and devices.
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Risi, Matthew D. "Advances In Combined Endoscopic Fluorescence Confocal Microscopy And Optical Coherence Tomography." Diss., The University of Arizona, 2014. http://hdl.handle.net/10150/332772.
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Confocal microendoscopy provides real-time high resolution cellular level images via a minimally invasive procedure. Results from an ongoing clinical study to detect ovarian cancer with a novel confocal fluorescent microendoscope are presented. As an imaging modality, confocal fluorescence microendoscopy typically requires exogenous fluorophores, has a relatively limited penetration depth (100μm), and often employs specialized aperture configurations to achieve real-time imaging in vivo. Two primary research directions designed to overcome these limitations and improve diagnostic capability are presented. Ideal confocal imaging performance is obtained with a scanning point illumination and confocal aperture, but this approach is often unsuitable for real-time, in vivo biomedical imaging. By scanning a slit aperture in one direction, image acquisition speeds are greatly increased, but at the cost of a reduction in image quality. The design, implementation, and experimental verification of a custom multi-point-scanning modification to a slit-scanning multi-spectral confocal microendoscope is presented. This new design improves the axial resolution while maintaining real-time imaging rates. In addition, the multi-point aperture geometry greatly reduces the effects of tissue scatter on imaging performance. Optical coherence tomography (OCT) has seen wide acceptance and FDA approval as a technique for ophthalmic retinal imaging, and has been adapted for endoscopic use. As a minimally invasive imaging technique, it provides morphological characteristics of tissues at a cellular level without requiring the use of exogenous fluorophores. OCT is capable of imaging deeper into biological tissue (~1-2 mm) than confocal fluorescence microscopy. A theoretical analysis of the use of a fiber-bundle in spectral-domain OCT systems is presented. The fiber-bundle enables a flexible endoscopic design and provides fast, parallelized acquisition of the optical coherence tomography data. However, the multi-mode characteristic of the fibers in the fiber-bundle affects the depth sensitivity of the imaging system. A description of light interference in a multi-mode fiber is presented along with numerical simulations and experimental studies to illustrate the theoretical analysis.
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Vitry, Pauline. "Applications and development of acoustic and microwave atomic force microscopy for high resolution tomography analysis." Thesis, Dijon, 2016. http://www.theses.fr/2016DIJOS046/document.
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La microscopie à force atomique (AFM) est un outil de caractérisation d’échantillons tant organiques qu’inorganiques d’intérêt en physique, en biologie et en métallurgie. Le champ d’investigation de la microscopie AFM reste néanmoins restreint à l’étude des propriétés surfaciques des échantillons et la caractérisation sub-surfacique à l’échelle nanométrique n’est pas envisageable au-delà de la nano-indentation. Lors de ce travail, nous nous sommes intéressés à deux techniques de sonde locale complémentaires pour l’investigation volumique haute résolution.La première technique proposée est la microscopie de champ proche ultrasonore (MS-AFM), mise en place et exploitée en collaboration avec Dr. L. Tétard de l’Université Centrale de Floride. Cette technique fournie des informations localisées en profondeur en utilisant des ondes acoustiques dans la gamme de fréquences du MHz. Une étude complète de l’influence des paramètres de fréquences a été réalisée sur des échantillons de calibration et a permis de valider un modèle d’interprétation numérique. Cette technique ultrasonore, non invasive, a été appliquée à la caractérisation de vésicules lipidiques au sein de bactéries lors d’une collaboration avec les Pr. A. Dazzi et M.-J. Virolle, de l’Université Paris Sud Orsay. Un couplage a été réalisé avec la microscopie AFM infra-rouge (AFM-IR). Cette étude a démontré le potentiel d’investigation et d’analyse volumique et chimique d’échantillons biologiques.La seconde technique étudiée est la microscopie micro-onde (SMM), développée en collaboration avec la société Keysight. Cette technique, tout comme la microscopie acoustique, est non invasive et conduit à une caractérisation physico-chimique basée sur l’interaction de micro-ondes (0.2-16 GHz) avec la matière. Dans le cas de métaux, un lien entre la fréquence et la profondeur d’investigation a été mis en évidence. Cette technique a été appliquée à l’étude de la diffusion d’élément chimique léger au sein de métaux et à la mesure des propriétés mécaniques des matériaux. L’ensemble de ces résultats ouvre un nouveau champ d’investigation de la tomographie 3D dans l’analyse volumique à l’échelle nanométrique que ce soit dans le domaine de la biologie ou de la métallurgieThe atomic force microscope (AFM) is a powerful tool for the characterization of organic and inorganic materials of interest in physics, biology and metallurgy. However, conventional scanning probe microscopy techniques are limited to the probing surface properties, while the subsurface analysis remains difficult beyond nanoindentation methods. Thus, the present thesis is focused on two novel complementary scanning probe techniques for high-resolution volumetric investigation that were develop to tackle this persisting challenge in nanometrology. The first technique considered, called Mode Synthesizing Atomic Force Microscopy (MSAFM), has been exploited in collaboration with Dr. Laurene Tetard of University of Central Florida to explore the volume of materials with high spatial resolution by means of mechanical actuation of the tip and the sample with acoustic waves of frequencies in the MHz range. A comprehensive study of the impact of the frequency parameters on the performance of subsurface imaging has been conducted through the use of calibrated samples and led to the validation of a numerical model for quantitative interpretation. Furthermore, this non-invasive technique has been utilized to locate lipid vesicles inside bacteria (in collaboration with Pr. A. Dazzi and M.-J. Virolle of Université Paris Sud, Orsay). Furthermore, we have combined this ultrasonic approach with infra-red microscopy, to add chemical speciation aimed at identifying the subsurface features, which represents a great advance for volume and chemical characterization of biological samples. The second technique considered is the Scanning Microwave Microscopy, which was developed in collaboration with Keysight society. Similar to acoustic-based microscopy, this non-invasive technique provided physical and chemical characterizations based on the interaction of micro-waves radiations with the matter (with frequency ranging from 0.2 and 16 GHz). Particularly, for metallic samples we performed volumetric characterization based on the skin effect of the materials. On the other hand, we have used this technique to analyze the diffusion of light chemical elements in metals and measured the effect of changes in mechanical properties of materials on their conductivity.Overall, these results constitute a new line of research involving non-destructive subsurface high resolution analysis by means of the AFM of great potential for several fields of research
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Zhou, Yifeng. "Design and application of combined multiphoton microscopy and optical coherence tomography system." Thesis, University of British Columbia, 2012. http://hdl.handle.net/2429/43195.
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Optical coherence tomography (OCT) is a non-invasive optical tomographic technique based on the principle of interferometry. It can capture micrometer-resolution, three-dimensional images of tissues over millimeter field-of-view at a fast speed. Multiphoton microscopy (MPM) is an emerging imaging modality based on the excitation of nonlinear signals from fluorescent molecules and the induction of second harmonic generation (SHG). It is capable of en-face high-resolution imaging with sub-micron resolution. Although OCT and MPM are essential imaging tools for disease diagnosis, each one of them has shortages, such as the low resolution of OCT and the low depth penetration of MPM. The purpose of this study is to design a multimodal imaging system by combining MPM and OCT into a single platform so that the two modalities can complement and overcome the shortages of each other.
The design consists of two parts: hardware and software. For hardware, the two modalities are integrated into a single platform, sharing the laser source, the controlling scanners and the sample arm. In addition, the OCT has a reference arm for interference and a custom-built spectrometer for signal detection, whereas the MPM uses two photomultiplier tubes (PMT) for photon detection. For software, two user interfaces are specially designed to control beam scanning and data acquisition of the MPM and OCT respectively.
The performance of this mutlimodal system is demonstrated by imaging biological samples. The results indicate that our system is capable of multiscale imaging of multilayered tissues with clear structures. One of the important applications of the multimodal system is measuring the refractive index (RI) and thickness of biological tissues. This capability is demonstrated on fish cornea. The results show our system is capable of imaging as well as quantitative characterization of RI and thickness of multilayered biological tissues. This system can potentially be a powerful tool for disease detection and surgery treatment.
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Nam, Ahhyun. "Development and translation of label-free functional microscopy based on optical coherence tomography." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/108851.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2017.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
Optical coherence tomography (OCT), an imaging modality based on low coherence interferometry, can be extended to obtain various endogenous functional contrasts. This thesis focuses on the development and translation of angiographic and polarization sensitive (PS) OCT techniques for clinical and preclinical applications. This goal includes four specific aims. The first aim is to develop a clinical imaging system to image the anatomy and microvasculature of human skin. The second aim is to develop a high performance post-processing algorithm for angiographic OCT. Towards this aim, we developed a processing algorithm based on complex differential variance (CDV) and confirmed its performance by benchmarking it against other published algorithms. The third aim is to develop a new approach for achieving high spatial resolution with an extended depth of focus for angiographic imaging. To achieve this aim, we have designed and built a triband wavelength system in which each spectrum is tightly focused at displaced focal planes to yield high transverse resolution over an effectively extended depth range. The fourth aim is to provide an imaging platform for preclinical study of peripheral nerve injury and repair. The vascularization is assessed by angiographic OCT, and the degree of myelination is measured by PS-OCT. These results confirm that the OCT platform can reveal new insights into preclinical studies of nerve regeneration and may ultimately provide a means for clinical intraoperative assessment of peripheral nerve health.
by Ahhyun Stephanie Nam.
Ph. D.
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Aguirre, Aaron Dominic 1977. "Advances in Optical Coherence Tomography and Microscopy for endoscopic applications and functional neuroimaging." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43740.
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Thesis (Ph. D.)--Harvard-MIT Division of Health Sciences and Technology, 2008.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Includes bibliographical references.
Optical Coherence Tomography (OCT) is a developing medical imaging technology that generates micron resolution cross-sectional images of subsurface internal tissue structure in situ and in real time, without the need to remove and process specimens. Previous studies have suggested that OCT holds great potential for use in laparoscopic and endoscopic applications to detect early stage neoplastic pathologies. A minimally invasive imaging modality capable of identifying pre-malignant tissues in vivo could be used to guide conventional excisional biopsy and histology, thereby reducing sampling error and enabling earlier detection and treatment. One limitation of prior endoscopic OCT imaging methods is the inability to visualize cellular features characteristic of early disease states such as neoplasia. This thesis seeks to demonstrate that advances in OCT resolution and in miniaturized imaging devices will lead to enhanced visualization of pathologic changes in vivo at both the tissue architectural and cellular levels. Toward this goal, three technological advances are made. First, compact and portable laser light sources for clinical ultrahigh resolution OCT are demonstrated based on supercontinuum generation in highly nonlinear optical fibers. Second, an extension of OCT called optical coherence microscopy (OCM) is developed for in vivo cellular imaging. High speed OCM system designs are demonstrated and characterization of OCM imaging parameters is performed. Importantly, this work demonstrates that OCM can make use of broadband laser sources to image cellular features with reduced numerical aperture compared to confocal microscopy, thereby facilitating the development of small diameter endoscopic probes.
(cont.) Third, two-axis scanning catheters based on micromirror technology are designed and demonstrated for ultrahigh resolution three-dimensional and en face OCT imaging. To demonstrate feasibility of these advances in future clinical applications, ex vivo imaging studies of endoscopically accessible human gastrointestinal tissues including key pathologies are performed. Results demonstrate that three-dimensional and cellular resolution optical coherence imaging can significantly improve performance over conventional OCT methods for gastrointestinal endoscopy. Finally, this thesis also explores a new application for optical coherence tomography in neuroscience. Optical methods are currently being used to study the neurovascular response to functional activation, but most existing techniques lack depth resolution. Through correlation with video microscopy, OCT is shown to enable depth-resolved cross-sectional imaging of functional activation in the important rat somatosensory cortex model system. With further development, OCT may offer a new tool for basic and applied neuroscience research.
by Aaron Dominic Aguirre.
Ph.D.
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Müller, Paul. "Optical Diffraction Tomography for Single Cells." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-202261.
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Analyzing the structure of a single cell based on its refractive index (RI) distribution is a common and valued approach, because it does not require any artificial markers. The RI is an inherent structural marker that can be quantified in three dimensions with optical diffraction tomography (ODT), an inverse scattering technique. This work reviews the theory of ODT and its implementation with an emphasis on single-cell analysis, identifying the Rytov approximation as the most efficient descriptor for light propagation. The accuracy of the reconstruction method is verified with in silico data and imaging artifacts associated with the inverse scattering approach are addressed. Furthermore, an experimental ODT setup is presented that consists of a bright-field microscope, a phase-imaging camera, and an optical trap combined with a microfluidic chip. A novel image analysis pipeline is proposed that addresses image corrections and frame alignment of the recorded data prior to the RI reconstruction. In addition, for a rotational axis that is tilted with respect to the image plane, an improved reconstruction algorithm is introduced and applied to single, suspended cells in vitro, achieving sub-cellular resolution.
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Butts, Mark D. "Nondestructive examination of nicalon fiber composite preforms using x-ray tomographic microscopy." Thesis, Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/19959.
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Zhang, Daliang. "3D Electron crystallography real space reconstruction and reciprocal space tomography /." Doctoral thesis, Stockholm : Department of Materials and Environmental Chemistry (MMK), Stockholm University, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-39034.
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Chen, Yi-Sheng. "Characterisation of hydrogen trapping in steel by atom probe tomography." Thesis, University of Oxford, 2017. http://ora.ox.ac.uk/objects/uuid:9d8ee66f-176d-4ac1-aad6-ccb33efc924d.
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Hydrogen embrittlement (HE), which results in an unpredictable failure of metals, has been a major limitation in the design of critical components for a wide range of engineering applications, given the near-ubiquitous presence of hydrogen in their service environments. However, the exact mechanisms that underpin HE failure remain poorly understood. It is known that hydrogen, when free to diffuse in these materials, can tend to concentrate at a crack tip front. In turn, this facilitates crack propagation. Hence one of the proposed strategies for mitigating HE is to limit the content of freely diffusing hydrogen within the metal atomic lattice via the introduction of microstructural hydrogen traps. Further, it is empirically known that the introduction of finely-dispersed distribution of nano-sized carbide hydrogen traps in ferritic steel matrix can improve resilience to HE. This resilience has been attributed to the effective hydrogen trapping of the carbides. However, conclusive atomic-scale experimental evidence is still lacking as to the manner by which these features can impede the movement of the hydrogen. This lack of insight limits the further progress for the optimisation of the microstructural design of this type of HE-resistant steel. In order to further understand the hydrogen trapping phenomenon of the nano-sized carbide in steel, an appropriate characterisation method is required. Atom probe tomography (APT) has been known for its powerful combination of high 3D spatial and chemical resolution for the analysis of very fine precipitates. Furthermore, previous studies have shown that the application of isotopic hydrogen (2H) loading techniques, combined with APT, facilitates the hydrogen signal associated to fine carbides to be unambiguously identified. However, the considerable experimental requirements as utilised by these previous studies, particularly the instrumental capability necessary for retention of the trapped hydrogen in the needle-shaped APT specimen, limits the study being reproduced or extended. In this APT study, a model ferritic steel with finely dispersed V-Mo-Nb carbides of 10-20 nm is investigated. Initially, existing specialised instrumentation formed the basis of a cryogenic specimen chain under vacuum, so as to retain loaded hydrogen after an electrolytic charging treatment for APT analysis. This work confirms the importance of cryogenic treatment for the retention of trapped hydrogen in APT specimen. The quality of the obtained experimental data allows a quantitative analysis on the hydrogen trapping mechanism. Thus, it is conclusively determined that interior of the carbides studied in this steel acts as the hydrogen trapping site as opposed to the carbide/matrix interface as commonly expected. This result supports the theoretical investigations proposing that the hydrogen trapping within the carbide interior is enabled by a network of carbon vacancies. Based on the established importance of the specimen cold chain in these APT experiments, this work then successfully develops a simplified approach to cryo-transfer which requires no instrumental modification. In this approach there is no requirement for the charged specimen to be transferred under vacuum conditions. The issue of environmental-induced ice contamination on the cryogenic sample surface in air transfer is resolved by its sublimation in APT vacuum chamber. Furthermore, the temperature of the transferred sample is able to be determined independently by both monitoring changes to vacuum pressure in the buffer chamber and also the thermal response of the APT sample stage in the analysis chamber. This simplified approach has the potential to open up a range of hydrogen trapping studies to any commercial atom probe instrument. Finally, as an example of the use of this simplified cryo-transfer technique, targeted studies for determining the source of hydrogen adsorption during electropolishing and electrolytic loading process are demonstrated. This research provides a critical verification of hydrogen trapping mechanism of fine carbides as well as an achievable experimental protocol for the observation of the trapping of individual hydrogen atoms in alloy microstructures. The methods developed here have the potential to underpin a wide range of possible experiments which address the HE problem, particularly for the design of new mitigation strategies to prevent this critical issue.
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Liu, Yang. "‘Tri-3D’ electron microscopy tomography by FIB, SEM and TEM : Application to polymer nanocomposites." Thesis, Lyon, INSA, 2013. http://www.theses.fr/2013ISAL0076/document.
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Ce travail a porté sur la caractérisation et la quantification en 3D de la répartition de charges de différents types (nanoparticules, nanotubes, etc.) dans des matrices polymères. Nous nous focalisons sur les techniques de tomographie en microscopie électronique. Une approche multiple en tomographie électronique a été réalisée : la tomographie en FIB/MEB (faisceau d’ions focalisé/microscope électronique à balayage), la tomographie en MEB et la tomographie en MET (microscope électronique en transmission). Les nanocomposites polymère sont généralement élaborés aux fins d’améliorer les propriétés physiques (mécanique, électrique, etc.) du matériau polymère constituant la matrice, grâce à une addition contrôlée de charges nanométriques. La caractérisation de tels matériaux, et l’établissement de corrélations précises entre la microstructure et les propriétés d’usage, requièrent une approche tri-dimensionnelle. En raison de la taille nanométrique des charges, la microscopie électronique est incontournable. Deux systèmes de nanocomposite polymère ont été étudiés par une approche multiple de tomographie électronique : P(BuA-stat-S)/MWNTs (copolymère statistique poly (styrène-co-acrylate de butyl) renforcé par des nanotubes de carbone multi-parois), et P(BuA-stat-MMA)/SiO2 (copolymère statistique poly(butyl acrylate-co-methyl methacrylate) renforcé par des nanoparticules de silice). Par combinaison de divers techniques, la caractérisation et la quantification des nanocharges ont été possibles. En particulier, la taille, la fraction volumique et la distribution des charges ont été mesurées. Cette étude a ainsi fourni des informations en 3D qui contribuent à mieux comprendre les propriétés des nanocomposites. Une attention particulière a été portée aux artefacts et causes d’erreur possibles durant l’étape de traitement 3D. Nous avons également essayé de comparer les différentes techniques utilisées du point de vue de leurs avantages et inconvénients respectifs, en dégageant des possibilités d’amélioration futureThis work is focused on the characterization and quantification of the 3D distribution of different types of fillers (nanoparticles, nanotubes, etc.) in polymer matrices. We have essentially used tomography techniques in electron microscopy. Multiple approaches to electron tomography were performed: FIB-SEM (focused ion beam/scanning electron microscope) tomography, SEM tomography and TEM (transmission electron microscope) tomography. Polymer nanocomposites are basically synthesized in order to improve the physical properties (mechanical, electric, etc.) of the pure polymer constituting the matrix, by a controlled addition of fillers at the nanoscale. The characterization of such materials and the establishment of accurate correlations between the microstructure and the modified properties require a three-dimensional approach. According to the nanometric size of the fillers, electron microscopy techniques are needed. Two systems of polymer nanocomposites have been studied by multiple electron tomography approaches: P(BuA-stat-S)/MWNTs (statistical copolymer poly(styrene-co-butyl acrylate) reinforced by multi-walled carbon nanotubes) and P(BuA-stat-MMA)/SiO2 (statistical copolymer poly(butyl acrylate-co-methyl methacrylate) reinforced by silica nanoparticles). By combining various techniques, the characterization and the quantification of nanofillers were possible. In particular, statistics about size, distribution and volume fraction of the fillers were measured. This study has then provided 3D information, which contributes to a better understanding of properties of the nanocomposites. Attention has been paid to analyze carefully original data, and artifacts and causes of errors or inaccuracy were considered in the 3D treatments. We also attempted to compare benefits and drawbacks of all techniques employed in this study, and perspectives for future improvements have been proposed
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Bennett, Samantha. "Nitride semiconductors studied by atom probe tomography and correlative techniques." Thesis, University of Cambridge, 2011. https://www.repository.cam.ac.uk/handle/1810/236685.
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Optoelectronic devices fabricated from nitride semiconductors include blue and green light emitting diodes (LEDs) and laser diodes (LDs). To design efficient devices, the structure and composition of the constituent materials must be well-characterised. Traditional microscopy techniques used to examine nitride semiconductors include transmission electron microscopy (TEM), and atomic force microscopy (AFM). This thesis describes the study of nitride semiconductor materials using these traditional methods, as well as atom probe tomography (APT), a technique more usually applied to metals that provides three-dimensional (3D) compositional information at the atomic scale. By using both APT and correlative microscopy techniques, a more complete understanding of the material can be gained, which can potentially lead to higher-efficiency, longer-lasting devices. Defects, such as threading dislocations (TDs), can harm device performance. An AFM-based technique was used to show that TDs affect the local electrical properties of nitride materials. To investigate any compositional changes around the TD, APT studies of TDs were attempted, and evidence for oxygen enrichment near the TD was observed. The dopant level in nitride devices also affects their optoelectronic properties, and the combination of APT and TEM was used to show that Mg dopants were preferentially incorporated into pyramidal inversion domains, with a Mg content two orders of magnitude above the background level. Much debate has been focused on the microstructural origin of charge carrier localisation in InGaN. Alloy inhomogeneities have often been suggested to provide this localisation, yet APT has revealed InGaN quantum wells to be a statistically random alloy. Electron beam irradiation in the TEM caused damage to the InGaN, however, and a statistically significant deviation from a random alloy distribution was then observed by APT. The alloy homogeneity of InAlN was also studied, and this alloy system provided a unique opportunity to study gallium implantation damage to the APT sample caused during sample preparation by the focused ion beam (FIB). The combination of APT with traditional microscopy techniques made it possible to achieve a thorough understanding of a wide variety of nitride semiconductor materials.
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Federici, Antoine. "Développement de systèmes de microscopie par cohérence optique plein champ étendus spatialement et spectralement." Thesis, Université Paris-Saclay (ComUE), 2015. http://www.theses.fr/2015SACLS024/document.
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La tomographie par cohérence optique plein champ (OCT plein champ) est une technique de microscopie interférométrique basée sur l’utilisation d’une source de lumière faiblement cohérente, telle qu’une lampe halogène. Elle permet de réaliser, de façon non invasive, des images tomographiques à plusieurs centaines de micromètres de profondeur dans les tissus biologiques et avec une résolution spatiale isotrope de l’ordre de 1 µm. Ces travaux de thèse concernent le développement de plusieurs systèmes d'OCT plein champ, dans le but de proposer de nouvelles performances et de nouveaux contrastes destinés à l’imagerie en trois dimensions de tissus biologiques. Nous avons dans un premier temps exploité la large bande spectrale d’émission d’une lampe halogène, afin d’apporter une information spectroscopique et d’être capable de distinguer et de caractériser des zones d’un échantillon qui seraient sinon indiscernables. Puis nous avons optimisé la résolution spatiale d’un montage d’OCT plein champ pour atteindre une valeur record de 0,5 µm (dans l’eau) dans les trois directions de l’espace, notamment grâce à l’utilisation d’une bande spectrale adaptée à l’imagerie de tissus, tels que la peau. Un montage dont le champ de vision est élargi à 18 mm x 18 mm a ensuite été développé et appliqué à l’imagerie du signal d’amplitude ainsi qu’à la mesure quantitative du signal de phase résolu en profondeur. Enfin un système utilisant un laser à balayage spectral comme source de lumière combiné à un traitement numérique de correction de la focalisation a été mis en œuvre. Nous avons ainsi démontré la possibilité de réaliser des images en trois dimensions avec une résolution latérale relativement élevée, sans utiliser le moindre déplacement mécanique durant l’acquisitionFull-field optical coherence tomography (FF-OCT) is an optical technology based on low-coherence interference microscopy for tomographic imaging of semitransparent samples. Non-invasive three-dimensional imaging can be performed with an isotropic spatial resolution of the order of 1 µm. During the PhD thesis, several FF-OCT systems have been reported achieving extended performances or contrast enhanced images relevant for biological tissues imaging. Firstly, a three-band, 1.9-μm axial resolution FF-OCT system has been implemented to perform spectroscopic contrast enhanced imaging of biological tissues over a 530-1700 nm wavelength range. Then, a study of the FF-OCT axial response has been carried out for maximizing the axial resolution of the system. An isotropic spatial resolution of 0.5 µm (in water) has been obtained by combining 1.2-NA microscope objectives with an optimized broad spectral band adapted to biological tissues imaging, such as skin samples. A set-up with an extended field of view of 18 mm x 18 mm has been also designed and applied to amplitude signal detection as well as depth-resolved quantitative phase signal measurement. At last, we developed a technique based on the combination of full-field swept-source optical coherence tomography (FF-SSOCT) with low spatial coherence illumination and a special numerical processing that allows for numerically focused mechanical motion-free three-dimensional imaging
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Fogelqvist, Emelie. "Laboratory Soft X-Ray Cryo Microscopy: Source, System and Bio Applications." Doctoral thesis, KTH, Biomedicinsk fysik och röntgenfysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-206428.
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Soft x-ray microscopes routinely perform high-resolution 3D imaging of biological cells in their near-native environment with short exposure times at synchrotron radiation facilities. Some laboratory-sized microscopes are aiming to make this imaging technique more accessible to a wider scientific community. However, these systems have been hampered by source instabilities hindering routine imaging of biological samples with short exposure times. This Thesis presents work performed on the Stockholm laboratory x-ray microscope. A novel heat control system has been implemented, improving the stability of the laser-produced plasma source. In combination with recent upgrades to the imaging system and an improved cryofixation method, the microscope now has the capability to routinely produce images with 10-second exposure time of cryofixed biological samples. This has allowed for tomographic imaging of cell autophagy and cell-cell interactions. Furthermore, a numerical 3D image formation model is presented as well as a novel reconstruction approach dealing with the limited depth of focus in x-ray microscopes.QC 20170505
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Eavis, Joe. "An investigation of soft tissue ultrasonic microimaging." Thesis, University of Bristol, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.310800.
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Su, Zhongyi. "Performance enhancement of all-solid-state batteries by optimizing the electrolyte through advanced microscopy and tomography techniques." Thesis, The University of Sydney, 2020. https://hdl.handle.net/2123/22112.
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NASICON-structured electrolytes of Li1+xAlxGe2−x(PO4)3, abbreviated as LAGP, are relatively stable in ambient air, also show good performance regarding Li+ conductivity (up to10-3 S·cm-1 at room temperature), thus are promising applications in ASSLIBs. To understand the ion transport mechanism of LAGP and the Al/Ge exchange system, a detailed study of SEM, Nano-SIMS, TEM and APT characterization applied for LGP and LAGP(X=0.1,0.3,0.5).It was confirmed that, by doping aluminum, the substitution: LiGe2(PO4)3 → Li1+xAlxGe2−x(PO4)3, can be accomplished. Al3+ ions partially substitute Ge4+ ions, introducing extra Li+ ions inside the grain. Moreover, an amorphous phase forms along the grain boundaries as LiAlPO4, which contributes to the increase of the density and the improvement of the lithium ion mobility along the grain boundary. Doping extra aluminum enhances the electrochemical performance of the lithium battery by providing more lithium ion channels both inside the grain and along the grain boundaries. We also proved the feasibility of applying atom probe tomography for the ceramic solid electrolyte to study their atomic scale chemical composition.
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Barnett, Brett William. "RECONSTRUCTION TECHNIQUES FOR OBTAINING ARTERIAL CONTOURS FROM DATA ACQUIRED IN VIVO (BLOOD FLOW, MICROSCOPY, TOMOGRAPHY)." Thesis, The University of Arizona, 1986. http://hdl.handle.net/10150/275488.
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Jahr, Wiebke. "Spectrally resolved, three-dimensional widefield microscopy." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-225963.
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A major goal in biological imaging is to visualize interactions of different tissues, often fluorescently labeled, during dynamic processes. Only a few of these labels fit into the available spectral range without overlap, but can be separated computationally if the full spectrum of every single pixel is known. In medical imaging, hyperspectral techniques show promise to identify different tissue types without any staining. Yet, microscopists still commonly acquire spectral information either with filters, thus integrating over a few broad bands only, or point-wise, dispersing the spectra onto a multichannel detector, which is inherently slow. Light sheet fluorescence microscopy (LSFM) and optical projection tomography (OPT) are two techniques to acquire 3D microscopic data fast, photon-efficiently and gently on the specimen. LSFM works in fluorescence mode and OPT in transmission. Both are based on a fast widefield detection scheme where a 2D detector records the spatial information but leaves no room to acquire dispersed spectra. Hyperspectral imaging had not yet been demonstrated for either technique. In this work, I developed a line-scanning hyperspectral LSFM and an excitation scanning OPT to acquire 5D data (3D spatial, 1D temporal, 1D spectral) and optimized the performance of both setups to minimize acquisition times without sacrificing image contrast, spatial or spectral information. I implemented and assessed different evaluation pipelines to classify and unmix relevant features. I demonstrate the efficiency of my workflow by acquiring up to five fluorescent markers and the autofluorescence in \\zf and fruit fly embryos on my hyperspectral LSFM. I extracted both concentration maps and spectra for each of these fluorophores from the multidimensional data. The same methods were applied to investigate the transmission data from my spectral OPT, where I found evidence that OPT image formation is governed by refraction, whereas scattering and absorption only play a minor role. Furthermore, I have implemented a robust, educational LSFM on which laymen have explored the working principles of modern microscopies. This eduSPIM has been on display in the Technische Sammlungen Dresden for one year during the UNESCO international year of lightEin wichtiges Ziel biologischer Bildgebung ist die Visualisierung des Zusammenspiels von verschiedenen, meist fluoreszent markierten, Geweben bei dynamischen Prozessen. Nur wenige dieser Farbstoffe passen ohne Überlapp in das zur Verfügung stehende Spektrum. Sie können jedoch rechnerisch getrennt werden, wenn das gesamte Spektrum jedes Pixels bekannt ist. In medizinischen Anwendungen versprechen hyperspektrale Techniken, verschiedene Gewebetypen markierungsfrei zu identifizieren. Dennoch ist es in der Mikroskopie noch immer üblich, spektrale Information entweder mit Filtern über breiten Bändern zu integrieren, oder Punktspektren mithilfe von Dispersion zu trennen und auf einem Multikanaldetektor aufzunehmen, was inhärent langsam ist. Light Sheet Fluorescence Microscopy (LSFM) und Optical Projection Tomography (OPT) nehmen 3D Mikroskopiedaten schnell, photoneneffizient und sanft für die Probe auf. LSFM arbeitet mit Fluoreszenz, OPT in Transmission. Beide basieren auf schneller Weitfelddetektion, wobei die räumliche Information mit einem 2D Detektor aufgenommen wird, der keinen Raum lässt, um die getrennten Spektren zu messen. Hyperspektrale Bildgebung wurde bis jetzt für keine der zwei Techniken gezeigt. Ich habe ein hyperspektrales LSFM mit Linienabtastung und ein OPT mit Wellenlängenabtastung entwickelt, um 5D Daten (3D räumlich, 1D zeitlich, 1D spektral) aufzunehmen. Beide Aufbauten wurden hinsichtlich minimaler Aufnahmezeit optimiert, ohne dabei Kontrast, räumliche oder spektrale Auflösung zu opfern. Ich habe verschiedene Abläufe zum Klassifizieren und Trennen der Hauptkomponenten implementiert. Ich nehme bis zu fünf Fluorophore und Autofluoreszenz in Zebrafisch- und Fruchtfliegenembryos mit dem hyperspektralen LSFM auf und zeige die Effizienz des gesamten Ablaufes, indem ich Spektren und räumliche Verteilung aller Marker extrahiere. Die Transmissionsdaten des spektralen OPT werden mit denselben Methoden untersucht. Ich konnte belegen, dass die Bildformation im OPT massgeblich von Brechung bestimmt ist, und Streuung und Absorption nur einen geringen Beitrag leisten. Außerdem habe ich ein robustes, didaktisches LSFM gebaut, damit Laien die Funktionsweise moderner Mikroskopie erkunden können. Dieses eduSPIM war ein Jahr lang in den Technischen Sammlungen Dresden ausgestellt
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Leary, Rowan Kendall. "Atomic-scale and three-dimensional transmission electron microscopy of nanoparticle morphology." Thesis, University of Cambridge, 2015. https://www.repository.cam.ac.uk/handle/1810/246903.
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The burgeoning field of nanotechnology motivates comprehensive elucidation of nanoscale materials. This thesis addresses transmission electron microscope characterisation of nanoparticle morphology, concerning specifically the crystal- lographic status of novel intermetallic GaPd2 nanocatalysts and advancement of electron tomographic methods for high-fidelity three-dimensional analysis. Going beyond preceding analyses, high-resolution annular dark-field imaging is used to verify successful nano-sizing of the intermetallic compound GaPd2. It also reveals catalytically significant and crystallographically intriguing deviations from the bulk crystal structure. So-called ‘non-crystallographic’ five-fold twinned nanoparticles are observed, adding a new perspective in the long standing debate over how such morphologies may be achieved. The morphological complexity of the GaPd2 nanocatalysts, and many cognate nanoparticle systems, demands fully three-dimensional analysis. It is illustrated how image processing techniques applied to electron tomography reconstructions can facilitate more facile and objective quantitative analysis (‘nano-metrology’). However, the fidelity of the analysis is limited ultimately by artefacts in the tomographic reconstruction. Compressed sensing, a new sampling theory, asserts that many signals can be recovered from far fewer measurements than traditional theories dictate are necessary. Compressed sensing is applied here to electron tomographic reconstruction, and is shown to yield far higher fidelity reconstructions than conventional algorithms. Reconstruction from extremely limited data, more robust quantitative analysis and novel three-dimensional imaging are demon- strated, including the first three-dimensional imaging of localised surface plasmon resonances. Many aspects of transmission electron microscopy characterisation may be enhanced using a compressed sensing approach.
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Samudrala, Saritha Kowmudy. "Atomic scale analysis of nanocrystalline materials by advanced microscopy." Thesis, The University of Sydney, 2015. http://hdl.handle.net/2123/13655.
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In this thesis, relatively new and advanced microscopy techniques are used to overcome many challenging problems in characterisation of nanocrystalline (nc-) materials. They include grain boundaries’ orientation and misorientation evaluation by transmission Kikuchi diffraction (TKD) and atomic scale analysis of segregation at grain boundaries by atom probe microscopy (APM). For each of these techniques, systematic investigations were carried out to optimise specimen preparation methods, data acquisition and analysis parameters. This resulted in fundamental knowledge that could be adopted to study a wide range of nc- materials. Two different sets of nc- materials are considered in this work: (i) bulk engineering materials (duplex stainless steels (DSS)) processed by high pressure torsion (HPT); and (ii) novel binary thin film systems including Al-O, Ni-P and Cu synthesized by direct current (DC) - magnetron sputtering and electron beam evaporation methods. In DSS samples, TKD work with the support of high resolution transmission electron microscopy has shown deformation twinning in body centred cubic ferrite phase, which is a significant experimental finding in contrast to the abundant theoretical modelling work in literature. Further, ferrite-ferrite grain boundaries and ferrite-austenite interphase boundaries are captured in APM experiments for studying segregation of alloying elements. This provided a way to calculate interfacial excess of segregating elements such as Mo, P, B, and W. Even in Al-O thin films, solute excess of O atoms and O rich clusters at grain boundaries is directly evidenced by APM and quantified by advanced computational methods. APM data also showed that O and P additions in Al-O and Ni-P led to a reduction in grain size of the as-deposited films. AP results facilitated and led to the studies of grain boundary pinning effect on stress coupled grain boundary mediated deformation mechanisms in these films.
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Paradiso, Nicola. "Tomography and manipulation of quantum Hall edge channels." Doctoral thesis, Scuola Normale Superiore, 2012. http://hdl.handle.net/11384/85830.
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Bilal, Huma. "Atomic Scale Microscopy of Zr-based Bulk Metallic Glasses Processed by Various Routes." Thesis, The University of Sydney, 2022. https://hdl.handle.net/2123/29908.
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Bulk metallic glasses (BMGs) exhibit a rare combination of strength and toughness that is difficult to achieve by other materials. These properties make them favourable for a diverse range of engineering applications. However, their disordered amorphous structure invokes catastrophic failure with shear bands localisation, limiting their industrial development as structural materials. Moreover, it is not yet clear how to quantitatively link their microstructural features to processing and mechanical properties. The aim of this thesis was to quantitatively analyse the structural features contributing to local hardness variations in thermomechanically processed zirconium (Zr)-based BMGs. Advanced atom probe tomography (APT) techniques were used to observe structural and chemical changes in these BMGs. APT operational parameters were optimised and tested for robust data outcomes. APT cluster analysis was effectively utilised in the characterisation of nanoscale heterogeneities in the BMG microstructure. The chemical composition of the nanoscale heterogeneities was roughly Zr27Cu29Al21Ni19Nb4 (at. %) in Zr63.96Cu13.36Ni10.29Al11.04Nb1.25 (at. %), and Zr22Cu29Al17Ni23Ti9 (at. %) in Zr52.5Cu17.9Ni14.6Al10Ti5 (at. %). Their chemistry was experimentally reported herein for the first time. Additionally, an ab-initio molecular dynamic (AIMD) simulation was used to simulate the atomistic distribution in a Zr-based BMG. Clusters observed in APT assigned as MRO regions were found synonymous to the shear band nucleation zones. Beyond the novel methodological rigor introduced here, the findings provide a new, independent validation of the inverse correlation between local hardness and size of the MRO regions, with their chemical compositions, providing a novel handle on the quest for understanding microstructure- property-processing relationship in BMGs.
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Niehle, Michael [Verfasser], Henning [Gutachter] Riechert, Eric [Gutachter] Tournié, and Günter [Gutachter] Möbus. "Electron tomography and microscopy on semiconductor heterostructures / Michael Niehle ; Gutachter: Henning Riechert, Eric Tournié, Günter Möbus." Berlin : Mathematisch-Naturwissenschaftliche Fakultät, 2016. http://d-nb.info/1116433931/34.
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La, Fontaine Alexandre Jacques. "Understanding the structure of minerals at the atomic scale: a new perspective enabled by advanced microscopy." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/15484.
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From oxides to ores and rocks, minerals are the most prevalent materials on Earth. The majority of their properties are the direct result of their microstructure. The investigation of their structure at the nano and micron scale is routinely carried out using techniques such as optical and electron microscopy, X-ray diffraction or secondary ion mass spectrometry. However, these techniques are usually limited in resolution, either spatially or chemically. More recently, atom probe tomography (APT) has emerged as a powerful microscopy technique that can provide 3D maps showing the position and atomic mass of individual atoms with sub-nanometre resolution. The non-conductive character of most minerals, both thermally and electrically, makes their investigation by APT challenging, from sample preparation to data interpretation. However, with the relatively recent development of focused ion beam sample preparation techniques and ultra-violet laser-assisted local electrode atom probe, the APT study of large band gap materials such as oxides has become more successful in the last decade. Advanced microscopy techniques such as transmission Kikuchi diffraction (TKD) or electron backscattered diffraction (EBSD) can also be used in combination with APT, and bring a new perspective to the investigation of the atomic scale structure of minerals, leading to a better understanding of their structure – properties relationships. The overall purpose of this thesis is to develop and apply new methods and techniques for the characterization of the structure of minerals at the atomic scale. This is achieved by means of various advanced microscopy techniques, which are applied to a selection of important scientific questions. By using a combination of APT, TKD, EBSD and transmission electron microscopy we investigate intergranular corrosion in stainless steels, the atomic structure of dental enamel and the robustness of zircon as a geological dating accessory. In this work, intergranular corrosion mechanisms in a commercial austenitic stainless steel (ASS) were revealed using EBSD and correlative TKD/TEM. Characterization by APT of the intergranular iron-chromium spinel formed during corrosion of the ASS revealed new insights at the atomic scale on its role towards the fast corrosion rate of the ASS. With the combined use of EBSD, TKD and APT, the atomic scale distribution of trace elements within dislocations in deformed mineral zircons was investigated for the first time to review the robustness of zircon for radiogenic dating. By using APT and TEM, new structural and elemental analysis of human dental enamel at the atomic scale provided unprecedented information for our understanding of human tooth decay.
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Koneti, Siddardha. "In situ and 3D environmental transmission electron microscopy of Pd-Al2O3 nano catalysts : Fast tomography with applications to other catalytic systems in operando conditions and to electron beam sensitive nanomaterials." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEI123/document.
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Au début du XXIème siècle, la Microscopie Electronique à Transmission en mode Environnemental (ETEM) est devenue l’une des techniques les plus fiables de caractérisation de nanomatériaux dans des conditions simulant leur vie réelle. L’ETEM est maintenant en mesure de suivre l’évolution dynamique des nanomatériaux dans des conditions variables comme l’exposition à des températures élevées, l’observation en milieux liquide ou gazeux à diverses pressions. Parmi différents domaines de recherche et développement concernés, la catalyse peut bénéficier de manière significative des avancées permises par la microscopie électronique environnementale. Cette thèse, dédiée au développement de l’ETEM au laboratoire MATEIS, a commencé avec l’étude du système catalytique Pd-alumine. Les nanoparticules de Pd déposées sur alpha -Al2O3 et delta-Al2O3 sont très utilisées en physicochimie avec un impact environnemental important : en particulier dans le domaine de l’hydrogénation sélective, pour la synthèse de polymères ou l’hydrogénation de CO2 pour la production de méthane. Nous avons tout d’abord effectué des analyses 2D aux différentes étapes du processus de synthèse du catalyseur : imprégnation du précurseur, séchage et chauffage pour la calcination dans l’air à la pression atmosphérique. La motivation de cette approche a été de comparer des analyses post mortem avec des traitements en ETEM où l’évolution des nanoparticules peut être mesurée in situ et pas seulement « avant » et « après ». De manière générale, les études faites en ETEM en 2D donnent un aperçu limité sur la morphologie des objets et la distribution spatiale des nanoparticules supportées. Nous avons développé une nouvelle approche d’acquisition rapide pour collecter dans des temps très courts des séries d’images sous différents angles de vue pour la tomographie électronique, la rapidité de cette acquisition étant un prérequis pour appréhender correctement la morphologie d’un nano-système au cours de son évolution dynamique in situ. La technique a ensuite été utilisée pour l’étude de plusieurs systèmes où une acquisition tridimensionnelle rapide est indispensable, notamment sur un sujet concernant un enjeu sociétal important, la dépollution des moteurs diesel : l’oxydation de la suie a été étudiée in situ sur des supports à base de zircone entre 400 et 600°C et une pression de 2 mbar d’oxygène à différents degrés de combustion, ce qui a permis d’extraire des données cinétiques telle que l’énergie d’activation du processus. La tomographie électronique rapide a été également appliquée à des matériaux sensibles au faisceau électronique, comme des nanocomposites polymères et des objets biologiques, montrant le large spectre d’applications possibles pour cette technique, qui constitue un pas important vers la caractérisation operando 3D de nanomatériaux en temps réelIn the beginning of the XXIst century, Environmental Transmission Electron Microscopy has become one of the reliable characterization techniques of nanomaterials in conditions mimicking their real life. ETEM is now able to follow the dynamic evolution of nanomaterials under various conditions like high temperature, liquid or various gas pressures. Among various fields of research, catalysis can benefit significantly from Environmental Microscopy. This contribution starts with the study of the Palladium-Alumina catalytic system. Pd nanoparticles supported by α-Al2O3 and δ-Al2O3 are of an important physicochemical and environmental interest, particularly in the field of selective hydrogenation in petrochemistry, for the synthesis of polymers or CO2 hydrogenation for methane production. We first performed 2D analyses at different steps of the synthesis process, then the same synthesis steps were performed under in situ conditions. The motivation of this approach was to compare post mortem treatments with ETEM observations. In general, 2D data provide limited insights on, for example, the morphology and position of supported nanoparticles. We have then developed a new fast acquisition approach to collect tomographic tilt series in very short times, enabling to reconstruct nano-systems in 3D during their dynamical evolution. Taking advantage of this approach, we have determined the activation energy for soot combustion on YSZ oxidation catalysts for diesel motors from volumetric data extracted from in situ experiments. Fast electron tomography was also applied to electron beam sensitive materials, like polymer nanocomposites and biological materials, showing the wide spectrum of possible applications for rapid 3D characterization of nanomaterials
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Grandfield, Kathryn. "Nanoscale Osseointegration : Characterization of Biomaterials and their Interfaces with Electron Tomography." Doctoral thesis, Uppsala universitet, Tillämpad materialvetenskap, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-179445.
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Bone response is one of the key determining factors in the overall success of biomaterials intended for bone regeneration and osseointegration. Understanding the formation of bone at an implant surface may lead to the improved design of biomaterials for the future. However, due to the inhomogeneity of bone tissue at an interface, two-dimensional images often lack detail on the interfacial complexity. Furthermore, the increasing use of nanotechnology in the design and production of biomaterials demands characterization techniques on a similar nano length scale. While current analysis methods, such as X-ray tomography, transmission electron microscopy, focused ion beam microscopy and scanning electron microscopy, provide a basis for analysing biomaterials and biointerfaces, they are incapable of doing so with both nanometre resolution and three-dimensional clarity. In contrast, electron tomography may be used to characterize the three-dimensional structure of biomaterials and their interfaces to bone with nanometre resolution. In this work, hydroxyapatite scaffolds, and laser-modified titanium and Ti6Al4V implants were studied in contact with human or rabbit bone. Z-contrast electron tomography revealed that the orientation of collagen in bone apposing hydroxyapatite, titanium and Ti6Al4V implants is consistently parallel to the implant surface, where the bioactive layer that precipitates on HA is oriented perpendicular to the implant surface. With this method, complete three-dimensional nanoscale osseointegration of titanium-based implants was also established. The extension of this technique from interfacial analyses to the design of biomaterials provided an understanding of the pore structure of mesoporous titania. In further investigations, the open three-dimensional pore network, as revealed by electron tomography, showed promise as a coating that improves implant osseointegration and enables site-specific drug-delivery from an implant surface. In summary, it was demonstrated that two-dimensional characterization techniques were insufficient for the investigation of nanostructured biomaterials, as well as their interfaces to bone. Visualizing biointerfaces and biomaterials with nanometre precision in three-dimensions can expose new fundamental information on materials properties and bone response, enabling better design of biomaterials for the future.
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Liu, Xiaojing. "Optical Coherence Photoacoustic Microscopy (OC-PAM) for Multimodal Imaging." FIU Digital Commons, 2016. http://digitalcommons.fiu.edu/etd/3189.
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Optical coherence tomography (OCT) and Photoacoustic microscopy (PAM) are two noninvasive, high-resolution, three-dimensional, biomedical imaging modalities based on different contrast mechanisms. OCT detects the light backscattered from a biological sample either in the time or spectral domain using an interferometer to form an image. PAM is sensitive to optical absorption by detecting the light-induced acoustic waves to form an image. Due to their complementary contrast mechanisms, OCT and PAM are suitable for being combined to achieve multimodal imaging.
In this dissertation, an optical coherence photoacoustic microscopy (OC-PAM) system was developed for in vivo multimodal retinal imaging with a pulsed broadband NIR light source. To test the capabilities of the system on multimodal ophthalmic imaging, the retina of pigmented rats was imaged. The OCT images showed the retinal structures with quality similar to conventional OCT, while the PAM images revealed the distribution of melanin in the retina since the NIR PAM signals are generated mainly from melanin in the posterior segment of the eye.
By using the pulsed broadband light source, the OCT image quality highly depends on the pulse-to-pulse stability of the light source without averaging. In addition, laser safety is always a concern for in vivo applications, especially for eye imaging with a pulsed light source. Therefore, a continuous wave (CW) light source is desired for OC-PAM applications. An OC-PAM system using an intensity-modulated CW superluminescent diode was then developed. The system was tested for multimodal imaging the vasculature of a mouse ear in vivo by using Gold Nanorods (GNRs) as contrast agent for PAM, as well as excised porcine eyes ex vivo.
Since the quantitative information of the optical properties extracted from the proposed NIR OC-PAM system is potentially able to provide a unique technique to evaluate the existence of melanin and lipofuscin specifically, a phantom study has been conducted and the relationship between image intensity of OCT and PAM was interpreted to represent the relationship between the optical scattering property and optical absorption property. It will be strong evidence for practical application of the proposed NIR OC-PAM system.
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Perrot, Jean-Luc. "Explorations optiques multimodales et multiéchelles non invasives appliquées au revêtement cutanéomuqueux , étendues à l'appareil oculaire antérieur." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSES010/document.
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Après une introduction brève de l’historique de l’imagerie dermatologique non invasive, ce travail est divisé 3 parties. 1) Présentation d’un projet de développement d’un tomographe à cohérence optique miniaturisé, peu onéreu devant permettre une diffusion de cette technique aux dermatologues exerçant en dehors des hôpitaux. Il s’agi d’un projet ANR DOCT-VCSEL Portable Optical Coherence Tomography with MEMS-VCSEL swept- sources for skin analysis ANR 2015 / Défi sociétal « Vie, Santé et Bien-Etre » Axe 13 « Technologies pour la santé » 2) Présentation d’un projet dont le but est l’identification de lésions cutanées cancéreuses au moyen d’un nouvel OCT haute définition développé par la société DAMAE, issue de l’Institut supérieur d’Optique de Palaiseau. Il s’agit d’un dispositif qui sera dans un premier temps réservé aux centre d’excellence en imagerie dermatologique. 3) la reprise des 52 publications ayant trait à l’imagerie cutanée auxquelles j’ai participé et référencées dans les bases de données internationales au 31 décembre 2016. Ce travail couvre l’ensemble de l’imagerie non invasive dermatologique moderne et aborde des sujets qui n’avaient jamais été étudié de la sorte. Notamment les muqueuses et l’appareil oculaire antérieur mais aussi l’identification par microscopie confocale des marge chirurgicales ou l’association microscopie confocale spectrométrie RamanAfter a brief introduction to the history of non-invasive dermatological imaging, this work is divided into 3 parts. 1) Presentation of a project for the development of a low-cost miniaturized optical coherence tomograph to allow dissemination of this technique to dermatologists practicing outside hospitals. This is an ANR project: DOCT-VCSEL Portable Optical Coherence Tomography with MEMS-VCSEL swept-sources for skin analysis ANR 2015 / Societal Challenge "Life, Health and Welfare" Axis 13 “Technologies for Health" 2) Presentation of a project whose goal is the identification of cancer skin lesions by means of a new high definition OCT developed by the company DAMAE, resulting from the Higher Institute of Optics of Palaiseau. It is a device that will initially be reserved for centers of excellence in dermatological imaging. 3) Presentation of 52 publications related to skin imaging, in which I participated, and referenced in the international databases as of December 31, 2016. This work covers all modern dermatological non-invasive imaging and addresses Subjects that had never been studied in this way. Notably the mucous membranes and the anterior ocular apparatus but also the identification by confocal microscopy of the surgical margins or the association confocal microscopy Raman spectrometry
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Ogien, Jonas. "Développement de systèmes de microscopie par cohérence optique pour l'imagerie de la peau." Thesis, Université Paris-Saclay (ComUE), 2017. http://www.theses.fr/2017SACLO011/document.
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La microscopie par cohérence optique (OCM) est une technique d'imagerie tomographique basée sur l'interférométrie en lumière blanche permettant d'imager les milieux biologiques à l'échelle microscopique. L'OCM est une méthode particulièrement adaptée à l'imagerie dermatologique, en particulier pour le diagnostic du cancer de la peau, car elle permet d'obtenir des images similaires aux images histologiques sans nécessiter d'effectuer de biopsie.Ces travaux de thèse portent sur le développement de la microscopie par cohérence optique pour l'imagerie de la peau, dans le but de fournir au dermatologue un outil d'imagerie compact, adapté à l'imagerie dermatologique in vivo, et permettant d'obtenir des images à la fois structurelles et fonctionnelles.Un dispositif de microscopie par cohérence optique plein champ (FF-OCM) compact, à éclairage par LED blanche, a tout d'abord été développé, permettant d'obtenir des images tomographiques à très haute résolution (0.7 μm × 1.8 μm) jusqu’à ∼200 μm de profondeur dans la peau. En utilisant une LED de haute puissance, des images de peau in vivo ont pu être obtenues.A partir de ce dispositif de FF-OCM, des méthodes d'imagerie fonctionnelle permettant de cartographier les écoulements sanguins (angiographie) ont été mises en oeuvre. Quatre méthodes, basées sur une analyse du signal interférométrique (temporelle ou fréquentielle), d'images de phase ou d'images d'amplitude ont permis d'imager de l'intralipide s'écoulant dans un modèle de capillaire sanguin.L'imagerie fonctionnelle polarimétrique a aussi été explorée en FF-OCM. Une optimisation du contraste des images polarimétriques a été obtenue en modifiant les composants polarisants d'un montage conventionnel de FF-OCM polarimétrique en fonction de l'échantillon imagé. Cette méthode a été testée sur un échantillon polarisant simple.Finalement, une nouvelle méthode d'OCM, la microscopie par cohérence optique confocale à éclairage « ligne » (LC-OCM) a été étudiée, dans le but de développer un système permettant d'imager la peau in vivo, avec une plus grande profondeur de pénétration dans les tissus que la FF-OCM. Ce système, combinant un filtrage interférométrique et un filtrage confocal, a permis d'obtenir des images de peau in vivo en coupe verticale et en coupe en face, avec une résolution spatiale similaire à celle de la FF-OCM, mais à une profondeur supérieure atteignant 300 μmOptical coherence microscopy (OCM) is a technique for tomographic imaging based on white light interferometry, making it possible to image biological media with micrometer-scale spatial resolution. OCM is particularly well-suited to dermatological imaging, especially skin cancer diagnosis, since it provides images that are similar to histological images without the need for biopsy.This PhD thesis focuses on the development of OCM for skin imaging, with the aim of providing a compact, in vivo imaging tool for the dermatologist, capable of acquiring structural and functional images of the skin.A compact, full-field OCM (FF-OCM) system illuminated by a white LED was first developed, making it possible to obtain tomographic images at an ultra-high resolution (0.7 μm × 1.8 μm), up to ∼200 μm in depth within the skin. Using a high power LED, in vivo skin images could be obtained.Using this FF-OCM setup, functional imaging methods for blood flow mapping (angiography) were implemented. Four methods, based on temporal or frequency analysis of the interferometric signal, phase images or amplitude images, have been shown to be able to image intralipid flow within a model blood capillary.Functional polarimetric imaging has also been explored in FF-OCM. Contrast optimization in polarimetric images has been obtained by modifying the polarizing components of the conventional polarization sensitive FF-OCM setup depending on the sample to be imaged. This method has been tested on a simple polarizing sample.Finally, a new OCM method, line-field confocal OCM (LC-OCM), has been studied. The goal here was to develop a system capable of imaging the skin in vivo, with a tissue penetration depth greater than what is possible for FF-OCM. This system, which combines interferometric filtering and confocal filtering, makes it possible to obtain in vivo skin images in vertical and en face slices, with a spatial resolution similar to that of FF-OCM, but with a greater penetration depth of 300 μm
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Barbieri, Francesco. "INVESTIGATING THE FUNCTIONAL MORPHOLOGY OF IN SITU IFT TRAINS BY CORRELATIVE LIGHT-ELECTRON MICROSCOPY." Doctoral thesis, Università di Siena, 2018. http://hdl.handle.net/11365/1052316.
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Cilia and flagella are cellular organelles involved in several and crucial aspects for the cell, tissue and organs normal physiology. Cilia can be classified according to their ability to perform a movement or not. Eukaryotic unicellular organisms and particular cells of mostly evolved organisms, i. e. spermatozoa, have evolved motile cilia for the cell propulsion in liquid media. Ciliated epithelia direct the movement of fluids by the ciliary beating. The primary cilium is an immotile cilium present in all the so far studied metazoan. This organelle is ubiquitous in human somatic cells when they are in G0 and G1 phases. Primary cilium and motile cilia work as sensory antennae highly specialized in receiving and secreting molecular signals. Such signal pathways regulate many aspects of the cellular metabolism, the cellular life-cycle, and the eventual cellular differentiations. Thus, ciliary alterations trigger severe consequences in human health causing a group of diseases known as ciliopathies. Such alterations in ciliary integrity are generated also from mutations affecting peptides involved in the intra-flagellar transport system (IFT), a selective and specific system of flagellar proteins transport, delivery, and recycling in which are employed proteic complexes (IFT trains) able to move bi-directionally along the flagellar axoneme. IFT trains transport into the ciliary compartment all the components needed for a correct ciliary assembly and maintenance i.e. peptide and proteic complexes of the ciliary axoneme, and several membrane-associated receptors. Analysis directed to better understand all the IFT features are thus of primary importance. Many analyses have been performed by studying the green algae model organism Chlamydomonas reinhardtii. Studies on IFT dynamics were performed in vivo, lacking in high resolution imaging. Other studies oriented in the determination of IFT trains ultrastructural morphology, and 3D-modeling digital reconstruction were performed ex vivo by transmission electron microscopy (TEM) imaging. A very recent work by Stepanek and Pigino (2017) revealed new insights in IFT system by using the correlative light electron microscopy (CLEM), which combines in vivo dynamics observed by florescence microscopy with ex vivo high-resolution analysis by electron microscopy. This study tough providing interesting anew clues about IFT functioning, left other important questions open on the motility direction of the different IFT trains categories present in Chlamydomonas flagella. In the present thesis we aimed at providing deeper insights in IFT system by using CLEM, in order to correlate a specific function to a specific ultrastructural category of IFT train. The reported results highlighted “short narrow IFT trains” moving in both anterograde and retrograde directions along the axoneme, while “short wide IFT trains” and “long IFT trains” were observed to remain static during in vivo observation.
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Cimalla, Peter, Theresa Werner, Kai Winkler, Claudia Mueller, Sebastian Wicht, Maria Gaertner, Mirko Mehner, et al. "Imaging of nanoparticle-labeled stem cells using magnetomotive optical coherence tomography, laser speckle reflectometry, and light microscopy." SPIE, 2015. https://tud.qucosa.de/id/qucosa%3A35268.
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Cell transplantation and stem cell therapy are promising approaches for regenerative medicine and are of interest to researchers and clinicians worldwide. However, currently, no imaging technique that allows three-dimensional in vivo inspection of therapeutically administered cells in host tissues is available. Therefore, we investigate magnetomotive optical coherence tomography (MM-OCT) of cells labeled with magnetic particles as a potential noninvasive cell tracking method. We develop magnetomotive imaging of mesenchymal stem cells for future cell therapy monitoring. Cells were labeled with fluorescent iron oxide nanoparticles, embedded in tissue-mimicking agar scaffolds, and imaged using a microscope setup with an integrated MM-OCT probe. Magnetic particle-induced motion in response to a pulsed magnetic field of 0.2 T was successfully detected by OCT speckle variance analysis, and cross-sectional and volumetric OCT scans with highlighted labeled cells were obtained. In parallel, fluorescence microscopy and laser speckle reflectometry were applied as two-dimensional reference modalities to image particle distribution and magnetically induced motion inside the sample, respectively. All three optical imaging modalities were in good agreement with each other. Thus, magnetomotive imaging using iron oxide nanoparticles as cellular contrast agents is a potential technique for enhanced visualization of selected cells in OCT.
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Beasley, Daniel. "3D quantitative elemental mapping of biological tissues using proton induced X-ray emission tomography (PIXE-T) and on/off-axis scanning transmission ion microscopy tomography (STIM-T)." Thesis, University of Surrey, 2006. http://epubs.surrey.ac.uk/843466/.
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A novel experimental set-up was installed at the University of Surrey Ion Beam Centre for the purpose of producing 3D quantitative elemental maps of biological samples by combining simultaneous Proton Induced X-Ray Emission Tomography (PIXE- T), on/off-Axis Scanning Transmission Ion Microscopy-Tomography (STIM-T) and Rutherford Backscatter Spectrometry (RBS). A tomographic sample holder was designed and built and a scattering system developed for On/Off-Axis STIM. 2D PIXE and off-STIM analysis of leukocytes was performed to complement concurrent research and to identify problems with the very recently installed proton microbeam at the Ion Beam Centre. The other major aim was to see if a leukocyte would be a suitable sample for tomographic analysis and to study the damage induced by the beam on biological samples. Instrumental Neutron Activation Analysis (INAA) was performed on hair samples collected from MSc students at the University of Surrey and a database compiled of all elemental analysis of hair performed at the University. This complemented the tomographic analysis performed on a section of a strand of hair. Si, S, Cl, K, Ca, Fe and Zn were mapped using simultaneous PIXE-T, On/Off- Axis STIM-T and RBS.
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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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Moore, Chad Lewis. "Insights into the three-dimensional ultrastructure of uterine epithelial cells during pregnancy." Thesis, The University of Sydney, 2020. https://hdl.handle.net/2123/22010.
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To initialise implantation in pregnancy, the blastocyst must first attach to the luminal uterine epithelial cells (UECs), which undergo extensive morphological changes from the time of fertilisation to implantation collectively known as the Plasma Membrane Transformation (PMT). This thesis utilises 3-Dimensional Scanning Electron Microscopy (3DSEM) and Correlative Light and Electron Microscopy (CLEM) to investigate UECs during the PMT in the rat. 3DSEM revealed that following mating, neutrophils and macrophages are internalised within UECs, crossing the apical plasma membrane, representing the first evidence of cell-in-cell structures in the uterine epithelium. 3DSEM then quantified morphological changes in UECs during early pregnancy, revealing that at the time of implantation there is a significant reduction in cell volume, with a concurrent significant increase in the mean lipid droplet volume and the total lipid droplet volume. A novel CLEM protocol was utilised to investigate the actin cytoskeleton of UECs, confirming that the terminal web becomes disorganised at the time of implantation, with a thin, inconsistent actin fluorescence signal corresponding with remaining irregular membrane protrusions. CLEM was applied to investigate the actin terminal web in a rat model of Ovarian Hyperstimulated pregnancy (OH), which revealed the actin terminal web was also disrupted at the time of implantation. The apical actin cytoskeleton regulator Keratin 19 was then investigated. Keratin 19 was significantly greater in abundance at the time of implantation in OH pregnancy compared to normal pregnancy, while a 26 kDa fragment was significantly increased in abundance at the time of implantation in normal pregnancy. Experiments in ovariectomised rats showed that Keratin 19 expression is regulated by oestrogen. This thesis utilised 3DSEM and CLEM to derive novel insights into the changes that occur in UECs required for the development of uterine receptivity in early pregnancy.
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Korde, Vrushali Raj. "OPTICAL IMAGING MODALITIES: FROM DESIGN TO DIAGNOSIS OF SKIN CANCER." Diss., The University of Arizona, 2009. http://hdl.handle.net/10150/193716.
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This study investigates three high resolution optical imaging modalities to better detect and diagnose skin cancer. The ideal high resolution optical imaging system can visualize pre-malignant tissue growth non-invasively with resolution comparable to histology. I examined 3 modalities which approached this goal. The first method examined was high magnification microscopy of thin stained tissue sections, together with a statistical analysis of nuclear chromatin patterns termed Karyometry. This method has subcellular resolution, but it necessitates taking a biopsy at the desired tissue site and imaging the tissue ex-vivo. My part of this study was to develop an automated nuclear segmentation algorithm to segment cell nuclei in skin histology images for karyometric analysis. The results of this algorithm were compared to hand segmented cell nuclei in the same images, and it was concluded that the automated segmentations can be used for karyometric analysis.The second optical imaging modality I investigated was Optical Coherence Tomography (OCT). OCT is analogous to ultrasound, in which sound waves are delivered into the body and the echo time and reflected signal magnitude are measured. Due to the fast speed of light and detector temporal integration times, low coherence interferometry is needed to gate the backscattered light. OCT acquires cross sectional images, and has an axial resolution of 1-15 µm (depending on the source bandwidth) and a lateral resolution of 10-20 µm (depending on the sample arm optics). While it is not capable of achieving subcellular resolution, it is a non-invasive imaging modality. OCT was used in this study to evaluate skin along a continuum from normal to sun damaged to precancer. I developed algorithms to detect statistically significant differences between images of sun protected and sun damaged skin, as well as between undiseased and precancerous skin.An Optical Coherence Microscopy (OCM) endoscope was developed in the third portion of this study. OCM is a high resolution en-face imaging modality. It is a hybrid system that combines the principles of confocal microscopy with coherence gating to provide an increased imaging depth. It can also be described as an OCT system with a high NA objective. Similar to OCT, the axial resolution is determined by the source center wavelength and bandwidth. The NA of the sample arm optics determines the lateral resolution, usually on the order of 1-5 µm. My effort on this system was to develop a handheld endoscope. To my knowledge, an OCM endoscope has not been developed prior to this work. An image of skin was taken as a proof of concept. This rigid handheld OCM endoscope will be useful for applications ranging from minimally invasive surgical imaging to non-invasively assessing dysplasia and sun damage in skin.
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Kong, Jun. "A Study of Computer Vision and Pattern Recognition in Medical Image Analysis: Digital Microscopy and Optical Coherent Tomography." Columbus, Ohio : Ohio State University, 2008. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1228075056.
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Robles, Victor Adrian. "Automated image analysis of corneal structures in anterior-segment optical coherence tomography and in-vivo confocal microscopy images." Diss., University of Iowa, 2017. https://ir.uiowa.edu/etd/5988.
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Optical Coherence Tomography (OCT) is a noninvasive imaging modality that has significantly contributed to the quantitative assessment of ocular diseases. Another tool available to ophthalmic clinicians is in-vivo confocal microscopy, which allows anatomical structures to be observed live at the cellular level. Incorporating both of these modalities for imaging the cornea allows us to take structural measurements to characterize disease-related changes in corneal anatomy.
Notable diseases that directly impact or correlate with corneal structures include glaucoma and diabetic neuropathy. Given glaucoma's impact as the second leading cause of blindness in the world, great efforts have been made in researching and understanding the disease. Correlations have been found between the central corneal thickness (CCT) and the risk of developing visual field loss in patients diagnosed with glaucoma. It should come as no surprise that measuring CCT among glaucoma suspects has also now become a clinical standard of practice. Diabetes is a group of metabolic diseases where the body experiences high blood sugar levels over prolonged periods of time. It is a prominent disease that affects millions of Americans each day. While not necessarily an ocular disease in its own right, it has been shown that diabetes can still affect the corneal structures. Diabetics have decreased corneal sensitivity and a significant link has been established between neuropathic severity in diabetic patients and corneal nerve fiber density.
Given the availability of these imaging tools and the significant impact these prominent diseases have on society a growing focus has developed on relating corneal structure measurements and ophthalmic diseases. However, manually acquiring structural measures of the cornea can be a labor intensive and daunting task. Hence, experts have sought to develop automatic alternatives. The goals of our work includes the ability to automatically segment the corneal structures from anterior segment-optical coherence tomography (AS-OCT) and in-vivo confocal microscopy (IVCM) to provide useful structural information from the cornea.
The major contributions of this work include 1) utilizing the information of AS-OCT imagery to segment the cornea layers simultaneously in 3D, 2) increasing the region-of-interest of IVCM imagery using a feature-based registration approach to develop a panorama from the images, 3) incorporating machine-learning techniques to segment the corneal nerves in the IVCM imagery, and 4) extracting structural measurements from the segmentation results to determine correlations between the structural measurements known to differ from the corneal structures in various subject groups.