Дисертації: "Cryo-electron microscopy and tomography"

1

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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2

Fatmaoui, Fadwa. "Determination of pericentric heterochromatin structure by in situ cryo-electron tomography." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAJ018.

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L'hétérochromatine constitutive est une forme condensée de chromatine, essentielle au maintien de la stabilité du génome et à la défense contre les rétrotransposons et les rétrovirus endogènes. À l'échelle moléculaire, elle se caractérise par des réseaux réguliers de nucléosomes, la méthylation de l'ADN et des histones et la liaison de protéines spécifiques associées à l'hétérochromatine (famille HP1). Cependant, la manière dont ces caractéristiques moléculaires conduisent à l'état condensé et définissent les propriétés fonctionnelles de l'hétérochromatine constitutive n'est pas encore claire. Le projet abordera cette question en déterminant la structure de l'hétérochromatine constitutive péricentrique directement à l'intérieur de son contenu cellulaire en utilisant la cryotomographie in situ de pointe. Les embryons de drosophile sont utilisés comme modèle expérimental, car dans leurs noyaux, les régions d'hétérochromatine péricentrique coalescent en chromocentres ronds de l'ordre du micron. Nous utilisons la cryosection avec des couteaux diamantés pour l'amincissement de l'échantillon, puis les tomogrammes des chromocentres, ainsi que d'autres domaines de la chromatine, seront enregistrés et reconstruits. Cela nous permettra de définir l'arrangement caractéristique des fibres de nucléosomes pour l'hétérochromatine péricentrique constitutive par comparaison avec l'empaquetage de la chromatine dans d'autres compartiments chromatiniens
Constitutive heterochromatin is a condensed form of chromatin, essential for the maintenance of genome stability and the defense against retrotransposons and endogenous retroviruses. At the molecular scale, it is characterized by regular nucleosome arrays, DNA and histone methylation and binding of specific heterochromatin-associated proteins (HP1 family). However, it remains unclear how these molecular features lead to the condensed state and define the functional properties of constitutive heterochromatin. The project will address this question by determining the structure of pericentric constitutive heterochromatin directly within its cellular content by using state-of-the-art in situ cryo-electron tomography. Drosophila embryos are used as the experimental model, because in their nuclei, the pericentric heterochromatin regions coalesce into round micron-scale chromocenters. We use cryo-sectioning with diamond knives for sample thinning, and then tomograms of chromocenters, as well as other chromatin domains will be recorded and reconstructed. This will enable us to define the characteristic nucleosome fiber arrangement for the constitutive pericentric heterochromatin by comparison with the chromatin packing in other chromatin compartments

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3

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'art
Cryo 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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4

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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5

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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6

Gedda, Magnus. "Contributions to 3D Image Analysis using Discrete Methods and Fuzzy Techniques : With Focus on Images from Cryo-Electron Tomography." Doctoral thesis, Uppsala universitet, Centrum för bildanalys, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-121579.

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With the emergence of new imaging techniques, researchers are always eager to push the boundaries by examining objects either smaller or further away than what was previously possible. The development of image analysis techniques has greatly helped to introduce objectivity and coherence in measurements and decision making. It has become an essential tool for facilitating both large-scale quantitative studies and qualitative research. In this Thesis, methods were developed for analysis of low-resolution (in respect to the size of the imaged objects) three-dimensional (3D) images with low signal-to-noise ratios (SNR) applied to images from cryo-electron tomography (cryo-ET) and fluorescence microscopy (FM). The main focus is on methods of low complexity, that take into account both grey-level and shape information, to facilitate large-scale studies. Methods were developed to localise and represent complex macromolecules in images from cryo-ET. The methods were applied to Immunoglobulin G (IgG) antibodies and MET proteins. The low resolution and low SNR required that grey-level information was utilised to create fuzzy representations of the macromolecules. To extract structural properties, a method was developed to use grey-level-based distance measures to facilitate decomposition of the fuzzy representations into sub-domains. The structural properties of the MET protein were analysed by developing a analytical curve representation of its stalk. To facilitate large-scale analysis of structural properties of nerve cells, a method for tracing neurites in FM images using local path-finding was developed. Both theoretical and implementational details of computationally heavy approaches were examined to keep the time complexity low in the developed methods. Grey-weighted distance definitions and various aspects of their implementations were examined in detail to form guidelines on which definition to use in which setting and which implementation is the fastest. Heuristics were developed to speed up computations when calculating grey-weighted distances between two points. The methods were evaluated on both real and synthetic data and the results show that the methods provide a step towards facilitating large-scale studies of images from both cryo-ET and FM.

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7

Xiao, Juan. "Development of electron tomography on liquid suspensions using environmental scanning electron microscopy." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSEI050/document.

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

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8

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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9

Le, Bihan Olivier. "Etude par microscopie électronique des mécanismes d'action de vecteurs synthétiques pour le transfert de gènes." Thesis, Bordeaux 1, 2009. http://www.theses.fr/2009BOR13972/document.

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La grande majorité des essais cliniques de transfert de gènes in vivo utilise des vecteurs viraux. Si ces derniers sont efficaces, ils présentent des risques immunogènes, toxiques, voire mutagènes avérés. Les vecteurs synthétiques (non viraux), par leur grande modularité et leur faible toxicité représentent une alternative très prometteuse. Le principal frein à leur utilisation est leur manque d’efficacité. L’objectif majeur de ce travail de thèse a été de comprendre le mécanisme de transfert de gènes associé à différents complexes vecteurs synthétiques/ADN plasmidique, ce qui est indispensable pour une conception rationnelle de nouveaux vecteurs. Nous avons étudié, sur cellules en culture, le mécanisme de transfert de gènes associé à deux lipides cationiques ; le BGTC (bis(guanidinium)-tren-cholesterol) et la DOSP (DiOleylamine A-Succinyl-Paromomycine) qui sont connus pour être des vecteurs efficaces in vitro. Nous avons ainsi pu visualiser par microscopie électronique leurs voies d’entrée, leurs remaniements structuraux ainsi que leur échappement endosomal qui représente une étape clé du processus de transfert de gènes. L’identification non ambigüe des lipoplexes tout au long de leur trafic intracellulaire a été rendue possible grâce au marquage de l’ADN par des nanoparticules de silice dotées d’un cœur de maghémite (Fe2O3) dense aux électrons. Cette stratégie de marquage a également été appliquée à l’étude du mécanisme d’action d’un autre vecteur synthétique de type polymère, le copolymère à blocs non ionique P188 ou Lutrol. Contrairement à la plupart des vecteurs synthétiques, celui-ci présente une efficacité de transfection in vivo chez la souris par injection in situ pour le tissu musculaire ou en intra trachéale dans le poumon. En revanche, il est totalement inefficace in vitro. Nous avons montré que le Lutrol permet une augmentation de l’internalisation d’ADN par les cellules mais n’induit pas son échappement endosomal, ce qui expliquerait son absence d’efficacité in vitro. D’autres voies d’entrée sont alors à envisager in vivo pour comprendre son mécanisme d’action
The vast majority of clinical trials of gene transfer in vivo use viral vectors. Although they are effective, they induce immunogenic, toxic or mutagenic risks. Due to their high modularity and low toxicity, synthetic vectors (non viral), represent a promising alternative despite their lack of effectiveness. The major objective of this work was to understand the mechanism of gene transfer using two prototypic synthetic vectors, in the context of a rational design of new vectors. We studied on cultured cells, the mechanism of action of two cationic lipids; BGTC (bis(guanidinium)-tren-cholesterol) and DOSP (DiOleylamine A-Succinyl-Paromomycine) formulated with plasmid DNA (lipoplexes) which are in vitro efficient vectors. We have been able to visualize by electron microscopy, their intracellular pathways, their structural alterations and their endosomal escape, the latter being a key step in the process of gene transfer. The unambiguous identification of lipoplexes throughout their intracellular trafficking has been made possible thanks to the labelling of DNA by core-shell silica nanoparticles with an electron dense maghemite core (Fe2O3). The labeling strategy has also been applied to study the mechanism of action of a nonionic block copolymer (P188 or Lutrol). Interestingly, these synthetic vectors have an in vivo transfection efficiency in mice lung and muscle tissue while they are totally inefficient in vitro. We have shown that Lutrol induces an increase of DNA internalization into cells and fails to trigger endosomal escape, which would explain the lack of in vitro efficacy. These findings suggest that the in vivo mechanism of action of Lutrol would involve other internalization pathways

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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 iteration
Tomographische 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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11

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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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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13

Ihiawakrim, Dris. "Etude par les techniques avancées de microscopie électronique en transmission de matériaux fragiles." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAE005/document.

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Le travail présenté dans ce manuscrit a montré l’importance du développement méthodologique et technique pour identifier et débloquer les verrous empêchant l’analyse de matériaux hybrides et complexes qui se dégradent sous irradiation par un faisceau d’électrons. Nous avons mis en évidence que des dégâts sur l’échantillon produits par les électrons n’apparaissent qu’au-dessus d'un certain seuil de densité de courant électronique qui dépend de la nature du matériau et de ses caractéristiques morphologiques et structurales. Ces développements couplés à la Cryo-EM, nous ont permis de mettre en évidence l’architecture des matériaux hybrides à base de carbone, la variation de la distance lamellaire dans une pérovskite en fonction de la molécule insérée et le positionnement du métal, d’identifier les interactions à l’interface entre deux cristaux moléculaires et la quantification 3D de la fonctionnalisation d’un MOF. Dans la dernière partie, nous avons mis en évidence les processus de nucléation et de croissance d’oxyde de fer par MET in-situ en phase liquide
The present manuscript shows the importance of methodological and technical development to identify and to unblock locks preventing the analysis of hybrid and complex materials that undergo degradation under electron beam irradiation. We have shown that beam-induced damage to the sample only appears above some specific threshold of current density. Such a threshold depends on the nature of the material and on its morphological and structural characteristics. These developments in synergy with the use of Cryo-EM, allowed us to expose the architecture of carbon-based hybrid materials, measure the variation of the lamellar distance in a perovskite according to the molecular spacer and to the positioning of the metal, identify the interactions at the interface between two molecular crystals, and the 3D quantification of the functionalization within a MOF. Lastly, we brought to light the processes of nucleation and growth of iron oxide by in-situ liquid phase TEM

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14

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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15

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 future
This 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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16

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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17

Limage, Stéphanie. "Relations entre propriétés et structures dans les émulsions stabilisées par un mélange de tensioactifs et de nanoparticules." Thesis, Aix-Marseille 3, 2011. http://www.theses.fr/2011AIX30053.

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Ce travail de thèse s’inscrit dans le cadre du projet ISS/FSL/FASES dont l’objectif est de comprendre les mécanismes de vieillissement des émulsions en microgravité. Ce manuscrit est dédié à l’étude au sol des émulsions de ce projet et notamment de celles stabilisées par des mélanges tensioactifs/nanoparticules. Ces émulsions sont diluées et constituées d’une phase continue d’huile de paraffine et d’une phase dispersée aqueuse contenant un tensioactif et des nanoparticules. Leur étude et leur caractérisation est réalisée par microscopie tomographique optique et cryo-microscopie électronique à balayage. Une étude préalable de la phase dispersée permet de démontrer que les proportions respectives en tensioactif et nanoparticules modifient les propriétés rhéologiques et microscopiques de ces mélanges. Ces modifications permettent de caractériser le couplage entre les molécules tensioactives et les nanoparticules. Lorsque cette phase dispersée est émulsifiée dans l’huile de paraffine, une transition dans la morphologie des gouttes peut être mise en évidence. Les gouttes de phase dispersée présentent une topologie dépendante du ratio des concentrations en tensioactif et nanoparticules : de sphérique (pour les grandes valeurs de ce ratio) elles deviennent polymorphes (pour les petites valeurs). L’observation de ces émulsions en cryo-microscopie électronique à balayage permet de visualiser des microstructures de nanoparticules et d’expliquer l’origine de la déformation des gouttes
This thesis is part of the ISS/FSL/FASES project which aims at understanding emulsion ageing mechanisms in microgravity. This manuscript is dedicated to the ground study of these emulsions, and particularly to those stabilized by surfactant/nanoparticles mixtures. These emulsions are diluted and composed of a paraffin oil continuous phase and an aqueous dispersed phase composed of the surfactant/particle mixtures. Emulsion characterization is performed with optical tomographic microscopy and cryo-scanning electron microscopy. A preliminary investigation of the dispersed phase shows that the proportion of surfactant and nanoparticles changes the rheological and microscopic properties of these mixtures. These changes allow the characterization of the coupling between surfactant molecules and nanoparticles. When these mixtures are emulsified in paraffin oil, a transition in the droplets morphology is evidenced. Indeed, dispersed phase droplets exhibit different shapes depending on the ratio of surfactant and nanoparticle concentrations: from spherical (for high ratios) they become polymorphous (for small ratios). Observations of these emulsions with cryo-scanning electron microscopy show the existence of nanoparticles microstructures that helps the understanding of the origin of droplets deformation

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18

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 réel
In 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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19

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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20

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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21

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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22

Limage, Stéphanie. "Relations entre propriétés et structures dans les émulsions stabilisées par un mélange de tensioactifs et de nanoparticules." Electronic Thesis or Diss., Aix-Marseille 3, 2011. http://www.theses.fr/2011AIX30053.

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Анотація:

Ce travail de thèse s’inscrit dans le cadre du projet ISS/FSL/FASES dont l’objectif est de comprendre les mécanismes de vieillissement des émulsions en microgravité. Ce manuscrit est dédié à l’étude au sol des émulsions de ce projet et notamment de celles stabilisées par des mélanges tensioactifs/nanoparticules. Ces émulsions sont diluées et constituées d’une phase continue d’huile de paraffine et d’une phase dispersée aqueuse contenant un tensioactif et des nanoparticules. Leur étude et leur caractérisation est réalisée par microscopie tomographique optique et cryo-microscopie électronique à balayage. Une étude préalable de la phase dispersée permet de démontrer que les proportions respectives en tensioactif et nanoparticules modifient les propriétés rhéologiques et microscopiques de ces mélanges. Ces modifications permettent de caractériser le couplage entre les molécules tensioactives et les nanoparticules. Lorsque cette phase dispersée est émulsifiée dans l’huile de paraffine, une transition dans la morphologie des gouttes peut être mise en évidence. Les gouttes de phase dispersée présentent une topologie dépendante du ratio des concentrations en tensioactif et nanoparticules : de sphérique (pour les grandes valeurs de ce ratio) elles deviennent polymorphes (pour les petites valeurs). L’observation de ces émulsions en cryo-microscopie électronique à balayage permet de visualiser des microstructures de nanoparticules et d’expliquer l’origine de la déformation des gouttes
This thesis is part of the ISS/FSL/FASES project which aims at understanding emulsion ageing mechanisms in microgravity. This manuscript is dedicated to the ground study of these emulsions, and particularly to those stabilized by surfactant/nanoparticles mixtures. These emulsions are diluted and composed of a paraffin oil continuous phase and an aqueous dispersed phase composed of the surfactant/particle mixtures. Emulsion characterization is performed with optical tomographic microscopy and cryo-scanning electron microscopy. A preliminary investigation of the dispersed phase shows that the proportion of surfactant and nanoparticles changes the rheological and microscopic properties of these mixtures. These changes allow the characterization of the coupling between surfactant molecules and nanoparticles. When these mixtures are emulsified in paraffin oil, a transition in the droplets morphology is evidenced. Indeed, dispersed phase droplets exhibit different shapes depending on the ratio of surfactant and nanoparticle concentrations: from spherical (for high ratios) they become polymorphous (for small ratios). Observations of these emulsions with cryo-scanning electron microscopy show the existence of nanoparticles microstructures that helps the understanding of the origin of droplets deformation

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23

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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24

Melinte, Georgian. "Advanced 3D and in-situ TEM approaches applied to carbon-based and zeolitic nanomaterials." Thesis, Strasbourg, 2015. http://www.theses.fr/2015STRAE009/document.

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Dans le cadre de cette thèse, des techniques avancées de Microscopie électronique à transmission (MET)ont été utilisées dans le but de caractériser et de fabriquer de nouveaux nanomatériaux pour des applications dans les domaines de la nanoélectronique et de la catalyse. Trois types de matériaux fonctionnalisés sont étudiés: le graphène multifeuillets (FLG– Few-Layer Graphene) avec des nanomotifs,des nanotubes de carbone (CNTs - Carbon Nanotubes en anglais) et des zéolithes mésoporeux. La formation de nanomotifs de tranchées et de tunnels sur des flocons de FLG à l’aide de nanoparticules(NPs) de fer est étudiée dans une approche qui combine la tomographie électronique et la MET environnementale. Le rôle des facettes de la nanoparticule et des paramètres topographiques de FLG a été déterminé du point de vue quantitatif, ce qui a mené à la mise en évidence du mécanisme de formation des nanomotifs de tranchées et de tunnels. Le transfert de nanoparticules à base de métal entre deux nanostructures de carbone a été également étudié, en temps réel, en employant un porte-échantillon MET couplé avec un dispositif STM (Scanning Tunneling Microscope en anglais). Le protocole de contrôle du transfert des nanoparticules, les transformations chimiques et structurales subies par celles-ci, le mécanisme de croissance de nouvelles nanoparticules et d’autres phénomènes liés à ces effets ont été étudiés avec attention. La dernière partie de la thèse est centrée sur l’étude de la tomographie électronique à faible dose de la porosité induite dans deux classes de zéolithes, ZSM-5 et zéolithe Y, en utilisant un traitement chimique novateur à base de fluor
In this thesis, advanced Transmission Electron Microscopy (TEM) techniques are used to characterize and fabricate new nanomaterials with applications in nanoelectronics and catalysis. Three types of functionalized materials are investigated: nanopatterned few-layer graphene (FLG), carbon nanotubes(CNTs) and mesoporous zeolites. The nanopatterning process of FLG flakes by iron nanoparticles (NPs) is studied using an approach combining electron tomography (ET) and environmental TEM. The role of the nanoparticle faceting and of the FLG topographic parameters has been quantitatively determined leading to the first determination of the operating mechanism of the patterning process. The mass transfer of metallic-based NPs between two carbon nanostructures was studied as well in real-time by using a TEMSTMholder. The protocol of controlling the mass transfer, the chemical and structural transformations of the NPs, the growth mechanism of the new NPs and other related phenomena were carefully investigated.The last part deals with the low-dose ET investigation of the porosity induced in two classes of zeolites,ZSM-5 and zeolite Y, by an innovative fluoride-based chemical treatment

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25

Trépout, Sylvain. "Etude de l'assemblage du système d'efflux membranaire MexAB-OprM impliqué dans la résistance aux antibiotiques chez Pseudomonas aeruginosa : caractérisation combinée par Microbalance à cristal de quartz avec mesure de dissipation et cryo-tomographie électronique." Thesis, Bordeaux 1, 2008. http://www.theses.fr/2008BOR13710/document.

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Pseudomonas aeruginosa est une bactérie Gram-négative qui présente une grande résistance aux antibiotiques, lui permettant de sévir dans le milieu hospitalier en infectant plus particulièrement les patients immunodéprimés. Cette résistance est principalement due au système d’efflux membranaire MexAB-OprM, capable d’exporter les antibiotiques en dehors de la cellule. Cette pompe à efflux est composée de trois protéines, MexA, MexB et OprM, incorporées dans les membranes internes et externes de la paroi bactérienne. Les structures de MexA, OprM et AcrB -une protéine présente chez E. coli, homologue de MexB- ont été déterminées individuellement par cristallographie des rayons X. Cependant, la structure du complexe entier, regroupant les trois protéines en interaction, ainsi que le mécanisme de cette pompe font toujours défaut. Le renforcement de nos connaissances structurales et fonctionnelles est donc capital pour lutter plus efficacement contre ces bactéries, par de nouvelles stratégies médicamenteuses. Ce travail porte sur l’étude de la structure et de la stœchiométrie de l’assemblage des protéines OprM et MexA au sein d’une membrane lipidique. La caractérisation du complexe OprM/MexA a été réalisée à l’aide de nouvelles techniques de caractérisation physico-chimique des surfaces, telle que la Microbalance à Cristal de Quartz avec Mesure de Dissipation (QCM-D), et par des méthodes d’imagerie, telles que la Cryo-Microscopie Electronique en Transmission (CryoMET) et la Cryo-Tomographie Electronique (CryoTE). En QCM-D, les mesures d’interaction entre OprM et MexA ont été réalisées sur support solide en contrôlant l’orientation d’OprM placée dans un environnement lipidique. Après ajout de la protéine MexA, la formation de complexes OprM/MexA a été mise évidence. Pour comprendre l’organisation de ce complexe, nous avons procédé à une étude comparative de l’organisation des protéines OprM, MexA et du complexe OprM/MexA incorporés dans une membrane lipidique, par CryoMET. Trois types d’organisation, respectivement spécifiques d’OprM, de MexA et du complexe OprM/MexA, ont été mis en évidence. Une analyse structurale de ces trois différents assemblages, pris en sandwich entre deux membranes lipidiques, a été menée par CryoTE. La reconstitution de la protéine OprM conduit à la formation de protéoliposomes, dû à des interactions intervenant entre les protéines OprM au niveau de leurs hélices périplasmiques. La protéine MexA s’organise sous forme d’une structure annulaire de 13 nm de hauteur au sein des membranes lipidiques, et d’une structure plus complexe de 26 nm de hauteur, résultant de l’empilement tête-bêche de deux structures annulaires de 13 nm. Ce travail révèle les dimensions exactes de l’assemblage formé par MexA, et permet de localiser à proximité des membranes les domaines non résolus dans la structure cristallographique. La reconstitution du complexe OprM/MexA révèle une disposition régulière des deux protéines dans les membranes lipidiques. Au sein des complexes, les protéines OprM sont présentes sous forme de trimères. Dans la membrane opposée, à l’aplomb d’une molécule d’OprM, MexA ne forme pas une structure annulaire similaire à celle décrite précédemment, indiquant un état d’oligomérisation différent de celui observé dans les assemblages MexA. Les densités de MexA sont compatibles avec la présence de quelques molécules de MexA. Cependant des structures annulaires de MexA, positionnées à l’aplomb de trois trimères d’OprM sont visibles. Notre étude montre que MexA adopte des structures oligomériques spécifiques en fonction de ses interactions avec les membranes lipidiques ou avec son partenaire OprM
The structure determination of membrane protein in lipid environment can be carried out using cryo electron microscopy combined with the recent development of data collection and image processing. We describe a protocol to study assemblies or stacks of membrane protein reconstitued into a lipid membrane using both cryo electron tomography and single particle analysis which is an alternative approach to electron crystallography for solving 3D structure. We show the organization of the successive layers of OprM molecules revealing the protein-protein interactions between OprM molecules of two successive lipid bilayers

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Zschiesche, Hannes. "Formation and segregation in cobalt silicide and manganese germanide thin films : correlative study by electron microscopy and atom probe tomography." Electronic Thesis or Diss., Aix-Marseille, 2019. http://www.theses.fr/2019AIXM0219.

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Dans cette thèse, des formations des germaniures de manganèse et des disiliciures de cobalt en couche minces ont été étudié comme la structure et chimie. Dans le système Mn-Ge, deux nouvelles relations entre des grains du Mn5Ge3 et (111)Ge ont été identifiées. De plus, il a été montré que la pureté du Mn5Ge3 dans les couches déposées par pulvérisation cathodique magnétron dépend du mécanisme de croissance. Une diffusion réactive donne du Mn5Ge3 presque pure tandis qu’une réaction non-diffusive donne du Mn5Ge3 qui contient la plupart des impuretés de la pulvérisation cathodique magnétron. Dans CoSi2 qui a été formé d’une configuration Co/Ti/Si, une ségrégation du Ti a été détectée dans les joints de grains du CoSi2. En outre, la distribution du Ti ségrégé a été caractérisée d’être inhomogènes. Pour étudier la ségrégation dans les joints de grains systématiquement, une méthode a été développé qui permet de corréler des investigations structurelle et chimie à l’échelle atomique sur un et le même échantillon dans les joints de grains sélectionnes. Finalement, une méthode a été proposée pour quantifier une ségrégation dans les points triple
Germanide and silicide thin films have application in different field such as thermoelectricity, magnetism and/or microelectronics. This PhD thesis study the formation, structure and chemistry of Mn5Ge3 thin films, which is interesting due to its ferromagnetic property for possible spintronic devices, and of CoSi2 thin films, which are used as contact materials. Two new epitaxial relationships between Mn5Ge3 grains and (111)Ge have been identified. The chemical purity of Mn5Ge3 has been related to the deposition by magnetron sputtering: Mn5Ge3 thin films grown by reactive-diffusion are relatively pure while the significant incorporation of impurities in Mn5Ge3 grown by non-diffusive reaction is beneficial for the ferromagnetic property. Ti segregation to CoSi2 grain boundaries has been quantified in CoSi2 grown from a Co/Ti/Si thin film. Additionally, an inhomogeneous distribution of Ti at CoSi2 grain boundary has been related to the defect density. A method has been developed for correlative structural and chemical investigations at the atomic scale on selected interfaces. Finally, a method to quantify the triple junction segregation has been proposed

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27

Weber, Juliane Verfasser], Dirk [Akademischer Betreuer] Bosbach, and Georg [Akademischer Betreuer] [Roth. "Fundamental insights into the radium uptake into barite by atom probe tomography and electron microscopy / Juliane Weber ; Dirk Bosbach, Georg Roth." Aachen : Universitätsbibliothek der RWTH Aachen, 2017. http://d-nb.info/1157122507/34.

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Weber, Juliane [Verfasser], Dirk Akademischer Betreuer] Bosbach, and Georg [Akademischer Betreuer] [Roth. "Fundamental insights into the radium uptake into barite by atom probe tomography and electron microscopy / Juliane Weber ; Dirk Bosbach, Georg Roth." Aachen : Universitätsbibliothek der RWTH Aachen, 2017. http://d-nb.info/1157122507/34.

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KC, Prabhat. "3D Reconstruction of the Magnetic Vector Potential of Magnetic Nanoparticles Using Model Based Vector Field Electron Tomography." Research Showcase @ CMU, 2017. http://repository.cmu.edu/dissertations/935.

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Lorentz TEM observations of magnetic nanoparticles contain information on the magnetic and electrostatic potentials of the sample. These potentials can be extracted from the electron wave phase shift by separating electrostatic and magnetic phase shifts, followed by 3D tomographic reconstructions. In past, Vector Field Electron Tomography (VFET) was utilized to perform the reconstruction. However, VFET is based on a conventional tomography method called filtered back-projection (FBP). Consequently, the VFET approach tends to produce inconsistencies that are prominent along the edges of the sample. We propose a model-based iterative reconstruction (MBIR) approach to improve the reconstruction of magnetic vector potential, A(r). In the case of scalar tomography, the MBIR method is known to yield better reconstructions than the conventional FBP approach, due to the fact that MBIR can incorporate prior knowledge about the system to be reconstructed. For the same reason, we seek to use the MBIR approach to optimize vector field tomographic reconstructions via incorporation of prior knowledge. We combine a forward model for image formation in TEM experiments with a prior model to formulate the tomographic problem as a maximum a posteriori probability estimation problem (MAP). The MAP cost function is minimized iteratively to deduce the vector potential. A detailed study of reconstructions from simulated as well as experimental data sets is provided to establish the superiority of the MBIR approach over the VFET approach.

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Hwang, Junyeon Kaufman M. J. "Characterization and mechanical properties of nanoscale precipitates in modified Al-Si-Cu alloys using transmission electron microscopy and 3D atom probe tomography." [Denton, Tex.] : University of North Texas, 2007. http://digital.library.unt.edu/permalink/meta-dc-3661.

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Hwang, Junyeon. "Characterization and Mechanical Properties of Nanoscale Precipitates in Modified Al-Si-Cu Alloys Using Transmission Electron Microscopy and 3D Atom Probe Tomography." Thesis, University of North Texas, 2007. https://digital.library.unt.edu/ark:/67531/metadc3661/.

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Among the commercial aluminum alloys, aluminum 319 (Al-7wt%Si-4wt%Cu) type alloys are popularly used in automobile engine parts. These alloys have good casting characteristics and excellent mechanical properties resulting from a suitable heat treatment. To get a high strength in the 319 type alloys, grain refining, reducing the porosity, solid solution hardening, and precipitation hardening are preferred. All experimental variables such as solidification condition, composition, and heat treatment are influence on the precipitation behavior; however, precipitation hardening is the most significant because excess alloying elements from supersaturated solid solution form fine particles which act as obstacles to dislocation movement. The challenges of the 319 type alloys arise due to small size of precipitate and complex aging response caused by multi components. It is important to determine the chemical composition, crystal structure, and orientation relationship as well as precipitate morphology in order to understand the precipitation behavior and strengthening mechanism. In this study, the mechanical properties and microstructure were investigated using transmission electron microscopy and three dimensional atom probe tomography. The Mn and Mg effects on the microstructure and mechanical properties are discussed with crystallographic study on the iron intermetallic phases. The microstructural evolution and nucleation study on the precipitates in the low-Si 319 type aluminum alloys are also presented with sample preparation and analysis condition of TEM and 3DAP tomography.

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Phan, Minh-Son. "Contribution à l'estimation de la similarité dans un ensemble de projections tomographiques non-orientées." Thesis, Strasbourg, 2016. http://www.theses.fr/2016STRAD041/document.

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La cryo-microscopie électronique est une technique tomographique permettant de reconstituer la structure 3D d’un objet complexe en biologie à partir d’un jeu d’acquisitions. Ces images de l’objet complexe sont appelées les projections et sont acquises sous orientations inconnues. Un des avantages de la cryo-microscopie électronique est l’obtention d’un modèle 3D de très haute résolution de l’objet dans un état naturel. La procédure de reconstruction comporte plusieurs étapes telles que l’alignement, la classification des projections, l’estimation de leurs orientations et le raffinement des projections. Lors de ces étapes, la distance entre deux projections est fréquemment mesurée. Le travail réalisé au cours de cette thèse s’organise autour de la recherche théorique d’une distance entre des projections non-orientées avec comme objectif l’amélioration de la procédure de reconstruction tomographique en cryo-microscopie électronique. La contribution de ce travail de thèse est une méthode permettant d’estimer la différence angulaire entre deux projections dans les cas 2D et 3D. Notre méthode est basée sur la construction d’un graphe de voisinage dont les sommets sont les projections, dont les arêtes relient des projections voisines et sont pondérées par une approximation locale de la différence angulaire. Le calcul de ces poids repose sur les propriétés des moments de projection. Notre méthode est testée sur des images simulées de différentes résolutions et de différents niveaux du bruit. La comparaison avec des autres méthodes d’estimation de la différence angulaire est aussi réalisée
Cryo-electron microscopy is a tomographic technique allowing to reconstruct a 3D model of complex structure in biology from a set of acquired images. These images are known as the tomographic projections and are taken at unknown directions. The advantage of the cryo-electron microscopy is the 3D reconstruction at very high resolution. The reconstruction procedure consists of many steps such as projection alignment, projection classification, orientation estimation and projection refinement. During these steps, the distance between two projections is frequently measured. The work in this thesis aims at studying the distances mesured between two unknown-direction projections with the objective of improving the reconstruction result in the cryo-electron microscopy. The contribution of this thesis is the developement of a method for estimating the angular difference between two projections in 2D and 3D. Our method is based on the construction of a neighborhood graph whose vertices are the projections, whose edges link the projection neighbors and are weighted by a local approximation of the angular difference. The calculation of the weights relies on the projection moment properties. The proposed method has been tested on simulated images with different resolutions and at different noise levels. The comparison with others estimation methods of angular difference has been realised

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Briggs, John A. G. "Cryo-electron microscopy of retroviruses." Thesis, University of Oxford, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.408819.

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34

Ramos, Cruz Ana Raquel. "Characterization of the surface of segmented filamentous bacteria from the unicellular to filamentous stage." Electronic Thesis or Diss., Université Paris Cité, 2024. http://www.theses.fr/2024UNIP5192.

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35

Burk, Robin [Verfasser], and Hans-Georg [Akademischer Betreuer] Kräusslich. "Visualization of the HIV-1 Nuclear Preintegration Complex Structure by High Precision Correlative Light - and Electron Microscopy and - Tomography / Robin Burk ; Betreuer: Hans-Georg Kräusslich." Heidelberg : Universitätsbibliothek Heidelberg, 2020. http://d-nb.info/1225625653/34.

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Yedra, Cardona Lluís. "Towards a new dimension in analytical TEM: EELS, Tomography and the Spectrum Volume." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/145317.

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The main goal of this thesis is to combine electron tomography and electron energy loss spectroscopy (EELS) in the TEM, in order to obtain chemical and electronic information in 3D in the nanoscale. Tomography in the TEM has been discussed and the advantages and disadvantages of HAADF STEM tomography have been analyzed. - A Fe3O4 nanocube sample has been considered to illustrate the acquisition, alignment, tilt axis assessment, reconstruction and visualization processes. - HAADF STEM tomography has been used to reconstruct the shape of a series of Cu2O nanoparticles. For one of the samples, the facets of the Cu2O nanoparticles, octahedral in shape, have been found to correspond to {111} planes. The physics and the data analysis methods of core-loss EELS have been briefly summarized. Two relevant contributions have been made: - The effects of beam precession on EELS have been investigated. A signal enhancement due to electron beam precession in the TEM when in zone axis conditions has been discovered for the first time. - A homemade software, Oxide Wizard, for valence state determination of transition metals has been developed and applied to map the Mn oxidation state of a MnOx/FeOy nanoparticle. EELS spectrum imaging and electron tomography have been combined to recover chemical information in 3D for FexCo(3-x)O4@Co3O4 mesoporous nanoparticles. - The samples have been first characterized by HAADF STEM tomography and EELS. - EELS chemical information is, of course, limited to 2D maps, while only structural information is be recovered in 3D form HAADF tomography. . An EELS-SI tilt series has been acquired at 80 kV and low acquisition times, resulting in a very noisy dataset. - Principal component analysis (PCA) has been used to separate the noise from the signal. - Quantifications of the O, Fe and Co signals have been reconstructed, and the shape of the particle recovered. - From the noise clean dataset, components with physical meaning (iron oxide, cobalt oxide and thickness) have been extracted using independent component analysis (ICA), and reconstructed in 3D. - A new kind of signal with chemical and thickness information has been obtained by combining the thickness component with the quantification results. This signal is able to properly reconstruct the chemical structure of the sample in 3D, detecting a higher presence of iron in the surface, and an even distribution of Fe inside of the particle. . Another EELS-SI tilt series has been acquired at 80 kV and low acquisition times with enough spatial resolution to resolve the porous structure. - The noise has been reduced using PCA. - Four signals extracted from the spectrum have been reconstructed: the integrated edge intensities for oxygen, iron and cobalt, and the integrated background prior to the oxygen edge. EELS-SI tomography has been applied to reconstruct CoFe2O4 (CFO) nanocolumns embedded in a BiFeO3 (BFO) matrix grown on LaNiO3 buffered LaAlO3 substrate (BFO-CFO//LNO/LAO). - The nanocomposite sample has been prepared in a nanoneedle shape by means of focused ion beam (FIB). This preparation has the advantage of keeping the thickness of the sample constant throughout the tilting experiment. The nanoneedle contains an island of CFO in a matrix of BFO, as well as the LNO/LAO substrate. - The noise has been discarded using PCA. - The oxygen, iron and lanthanum edges intensities have been extracted and reconstructed. A new kind of data hypercube, the Spectrum Volume, has been proposed. Just as a Spectrum Image contains a spectrum per pixel, a Spectrum Volume is to contain a spectrum per voxel. EELS-SI tomography has been applied to successfully acquire a spectrum volume (SV) of the (BFO-CFO//LNO/LAO) system. - PCA has been used to discard the noise and Bayesian linear unmixing (BLU) has been used to extract independent components (eigenspectra). - Each eigenspectrum has a 2D weighting map for each tilt; weighting maps have been reconstructed into 3D weighting volumes. - Full single spectra for any point in the reconstructed space can now be recovered as a weighed sum of eigenspectra, using the 3D weighting distributions. This approach is used to extract single spectra, spectrum lines and spectrum images from the inside of the sample. In the context of this thesis, tomography and EELS-SI have been combined to successfully recover chemical information in 3D at the nanoscale, and a new kind of data hypercube, the Spectrum Volume, has been proposed and experimentally recovered.
En el microscopi electrònic de transmissió (TEM), es poden obtenir imatges d’una mostra des de diferents angles i posteriorment reconstruir aquestes imatges en tres dimensions (3D). Per altra banda, les interaccions dels electrons del feix amb els electrons de la mostra poden ser analitzades mitjançant l’espectroscòpia de pèrdues d’energia dels electrons (EELS), obtenint així informació química de la mostra. L’objectiu d’aquesta tesi és la combinació de l’espectroscòpia EELS amb la tomografia electrònica per obtenir informació química en 3 dimensions a la nanoescala. S’han explicat les bases de la tomografia electrònica i el procediment de la reconstrucció ha estat il•lustrat amb una mostra de nanocubs d’òxid de ferro. Posteriorment, s’ha aplicat a una sèrie de nanopartícules de Cu2O per tal de descriure’n la forma. També s’ha explicat la física en què es basa l’EELS, fent especial atenció als llindars d’altes pèrdues d’energia. A continuació, s’ha mostrat l’augment del senyal obtingut amb precessió electrònica al TEM quan la mostra es troba en condicions d’eix de zona. Seguint amb les aplicacions d’EELS, s’ha explotat la possibilitat de caracteritzar els estats d’oxidació dels metalls de transició mitjançant un programa propi, escrit per a Digital Micrograph i anomenat Oxide Wizard. Una vegada la tomografia electrònica i l’espectroscòpia de pèrdues d’energia dels electrons han estat explicades, s’ha procedit a reconstruir informació extreta d’EELS en 3D. S’han realitzat una sèrie d’experiments amb partícules mesoporoses que han demostrat la utilitat d’aplicar l’anàlisi multivariable per tal de reduir el soroll de les dades i extreure’n els components. Finalment, s’ha dissenyat un experiment en el qual ha estat possible recuperar l’espectre corresponent a cada unitat d’espai com la combinació d’espectres propis en una mostra preparada en forma de nanoagulla. Els espectres recuperats corresponen a la contribució de cada unitat de volum als espectres projectats. Aquest nou tipus de dades permet extreure espectres de l’interior d’una mostra. Finalment, doncs, s’ha pogut combinar amb èxit la tomografia electrònica i EELS per obtenir informació química en tres dimensions a la nanoescala.

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Mühlbacher, Marlene. "High-resolution characterization of TiN diffusion barrier layers." Licentiate thesis, Linköpings universitet, Tunnfilmsfysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-120394.

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Titanium nitride (TiN) films are widely applied as diffusion barrier layers in microelectronic devices. The continued miniaturization of such devices not only poses new challenges to material systems design, but also puts high demands on characterization techniques. To gain understanding of diffusion processes that can eventually lead to failure of the barrier layer and thus of the whole device, it is essential to develop routines to chemically and structurally investigate these layers down to the atomic scale. In the present study, model TiN diffusion barriers with a Cu overlayer acting as the diffusion source were grown by reactive magnetron sputtering on MgO(001) and thermally oxidized Si(001) substrates. Cross-sectional transmission electron microscopy (XTEM) of the pristine samples revealed epitaxial, single-crystalline growth of TiN on MgO(001), while the polycrystalline TiN grown on Si(001) exhibited a [001]-oriented columnar microstructure. Various annealing treatments were carried out to induce diffusion of Cu into the TiN layer. Subsequently, XTEM images were recorded with a high-angle annular dark field detector, which provides strong elemental contrast, to illuminate the correlation between the structure and the barrier efficiency of the single- and polycrystalline TiN layers. Particular regions of interest were investigated more closely by energy dispersive X-ray (EDX) mapping. These investigations are completed by atom probe tomography (APT) studies, which provide a three-dimensional insight into the elemental distribution at the near-interface region with atomic chemical resolution and high sensitivity. In case of the single-crystalline barrier, a uniform Cu-enriched diffusion layer of 12 nm could be detected at the interface after an annealing treatment at 1000 °C for 12 h. This excellent barrier performance can be attributed to the lack of fast diffusion paths such as grain boundaries. Moreover, density-functional theory calculations predict a stoichiometry-dependent atomic diffusion mechanism of Cu in bulk TiN, with Cu diffusing on the N-sublattice for the experimental N/Ti ratio. In comparison, the polycrystalline TiN layers exhibited grain boundaries reaching from the Cu-TiN interface to the substrate, thus providing direct diffusion paths for Cu. However, the microstructure of these columnar layers was still dense without open porosity or voids, so that the onset of grain boundary diffusion could only be found after annealing at 900 °C for 1 h. The present study shows how to combine two high resolution state-of-the-art methods, TEM and APT, to characterize model TiN diffusion barriers. It is shown how to correlate the microstructure with the performance of the barrier layer by two-dimensional EDX mapping and three-dimensional APT. Highly effective Cu-diffusion barrier function is thus demonstrated for single-crystal TiN(001) (up to 1000 °C) and dense polycrystalline TiN (900 °C).

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38

Toropova, Katerina. "Cryo-electron microscopy of bacteriophage MS2." Thesis, University of Leeds, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.503345.

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39

Wang, Danqi. "LOW-TEMPERATURE GAS-PHASE CARBURIZING AND NITRIDING OF 17-7 PH STAINLESS STEEL." Case Western Reserve University School of Graduate Studies / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=case1386165240.

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40

Wang, Qing. "Protein labels for cellular electron cryo-tomography." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609234.

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41

Grant, Timothy R. "Advances in single particle cryo electron microscopy." Thesis, Imperial College London, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.542950.

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42

Narasimha, Rajesh. "Application of Information Theory and Learning to Network and Biological Tomography." Diss., Georgia Institute of Technology, 2007. http://hdl.handle.net/1853/19889.

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Studying the internal characteristics of a network using measurements obtained from endhosts is known as network tomography. The foremost challenge in measurement-based approaches is the large size of a network, where only a subset of measurements can be obtained because of the inaccessibility of the entire network. As the network becomes larger, a question arises as to how rapidly the monitoring resources (number of measurements or number of samples) must grow to obtain a desired monitoring accuracy. Our work studies the scalability of the measurements with respect to the size of the network. We investigate the issues of scalability and performance evaluation in IP networks, specifically focusing on fault and congestion diagnosis. We formulate network monitoring as a machine learning problem using probabilistic graphical models that infer network states using path-based measurements. We consider the theoretical and practical management resources needed to reliably diagnose congested/faulty network elements and provide fundamental limits on the relationships between the number of probe packets, the size of the network, and the ability to accurately diagnose such network elements. We derive lower bounds on the average number of probes per edge using the variational inference technique proposed in the context of graphical models under noisy probe measurements, and then propose an entropy lower (EL) bound by drawing similarities between the coding problem over a binary symmetric channel and the diagnosis problem. Our investigation is supported by simulation results. For the congestion diagnosis case, we propose a solution based on decoding linear error control codes on a binary symmetric channel for various probing experiments. To identify the congested nodes, we construct a graphical model, and infer congestion using the belief propagation algorithm. In the second part of the work, we focus on the development of methods to automatically analyze the information contained in electron tomograms, which is a major challenge since tomograms are extremely noisy. Advances in automated data acquisition in electron tomography have led to an explosion in the amount of data that can be obtained about the spatial architecture of a variety of biologically and medically relevant objects with sizes in the range of 10-1000 nm A fundamental step in the statistical inference of large amounts of data is to segment relevant 3D features in cellular tomograms. Procedures for segmentation must work robustly and rapidly in spite of the low signal-to-noise ratios inherent in biological electron microscopy. This work evaluates various denoising techniques and then extracts relevant features of biological interest in tomograms of HIV-1 in infected human macrophages and Bdellovibrio bacterial tomograms recorded at room and cryogenic temperatures. Our approach represents an important step in automating the efficient extraction of useful information from large datasets in biological tomography and in speeding up the process of reducing gigabyte-sized tomograms to relevant byte-sized data. Next, we investigate automatic techniques for segmentation and quantitative analysis of mitochondria in MNT-1 cells imaged using ion-abrasion scanning electron microscope, and tomograms of Liposomal Doxorubicin formulations (Doxil), an anticancer nanodrug, imaged at cryogenic temperatures. A machine learning approach is formulated that exploits texture features, and joint image block-wise classification and segmentation is performed by histogram matching using a nearest neighbor classifier and chi-squared statistic as a distance measure.

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Verguet, Amandine. "Développements méthodologiques et informatiques pour la microscopie électronique en transmission appliqués à des échantillons biologiques Alignment of Tilt Series (Chapter 7 of the Book: Cellular Imaging: Electron Tomography and Related Techniques, Hanssen Eric) An ImageJ tool for simplified post-treatment of TEM phase contrast images (SPCI) Comparison of methods based on feature tracking for fiducial-less image alignment in electron tomography." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS487.

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La microscopie électronique en transmission est une technique pertinente pour les études structurales en biologie. Certaines méthodes d’acquisition et d’analyse doivent être améliorées pour permettre l’observation d’échantillons sensibles aux doses d’électrons dans de bonnes conditions de contraste et de rapport signal sur bruit. Au cours de cette thèse, j’ai exploré différentes approches méthodologiques et informatiques dans le but d’améliorer la qualité des images. J’ai ainsi évalué la pertinence de la combinaison de l’imagerie en énergie filtrée avec le mode STEM. Je montre que cette combinaison est prometteuse puisqu’elle permet d’améliorer le rapport signal sur bruit des images. Par ailleurs, j’ai collaboré à des développements algorithmiques et logiciels pour la reconstitution d’images de contraste de phase. Ceci permet l’amélioration du contraste par rapport à une acquisition classique. Je montre aussi qu’à cette fin, la phase plate tout comme les séries focales sont des outils efficaces. En étudiant une approche logicielle pour l’exploitation des séries focales, nous avons déterminé qu’il est possible d’obtenir, en plus de données quantitatives, un résultat qualitatif à partir d’une seule image. J’ai ainsi développé le plugin SPCI pour le logiciel ImageJ, qui permet de traiter de une à trois images focales. Je m’intéresse également à l’optimisation du processus de reconstruction tomographique, tant à l’alignement qu’à la reconstruction proprement dite. L’approche évaluée pour l’alignement utilise des points caractéristiques associés à des descripteurs locaux. Elle s’est montrée performante et permet de traiter des images sans marqueurs fiduciaires. Enfin, je propose une nouvelle méthode unifiée de reconstruction tridimensionnelle de séries tomographiques parcimonieuses. Il en découle une approche innovante mélangeant reconstruction et alignement dont l’ébauche servira de base à des travaux futurs pour le traitement de séries tomographiques parcimonieuses. L’ensemble des méthodes évoquées ici, leur validation, ainsi que les perspectives d’évolution associées sont décrites dans ce manuscrit
Transmission Electron Microscopy is a major tool for performing structural studies in biology. Some methods used for image sampling and analysis need to be improved in order to observe electron dose sensitive samples with good contrast and good signal to noise ratio. During this thesis, various methodological and computational approaches have been studied which aim to improve image quality. First, I evaluated the relevance of combining energy filtered imaging with the STEM mode. I show that this allows an improvement of the signal to noise ratio of images. Then, I devised an algorithm that generates an image from phase data. This approach allows improving the image contrast over direct imaging. The use of a phase plate and focal tilt series are both efficient tools to achieve this goal. While working on the software approach for processing of tilt series, we found that a qualitative result can be obtained from a single image. I developped the SPCI plugin for the ImageJ software. It allows processing between one and three focal images. My work involves optimization of the tomographic reconstruction process, including working with both alignment algorithms and reconstruction algorithms. I expose my studies on image alignment methods used on tilt series. These methods do rely on the use of key points and associated local descriptors. They have proved to be efficient to process images lacking fiducial markers. Finally, I propose a new unified algorithmic approach for 3D reconstruction of tomographic tilt series acquired with sparse sampling. I then derived another novel method that integrates the image alignment step in the process. Studies and developments will continue on both methods in futur work

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Lottin, Delphine. "Dimensions fractales, morphologie et caractéristiques dimensionnelles 2D et 3D d'agrégats de nanoparticules de suie aéronautique : Etude par microscopie électronique en transmission et tomographie électronique." Thesis, Aix-Marseille, 2013. http://www.theses.fr/2013AIXM4012/document.

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Les agrégats de suie émis par les processus de combustion dans les turbines aéronautiques contribuent à modifier le bilan radiatif de l'atmosphère et la qualité de l'air. La connaissance de leurs caractéristiques physiques et chimiques est indispensable pour évaluer leur rôle dans les processus physico-chimiques atmosphériques et leur impact sur l'environnement et la santé publique. Dans ce contexte, notre étude vise à déterminer la taille et la morphologie d'agrégats de suie aéronautique à partir de mesures expérimentales menées en microscopie électronique en transmission (MET) et en tomographie électronique.Nous avons réalisé des clichés MET d'agrégats de suie émis par des turboréacteurs aéronautiques. Nous avons établi une méthode pour caractériser la morphologie des agrégats en déterminant leur allongement, leur compacité et la tortuosité de leur contour en analysant leur projection. Nous avons également développé un logiciel de traitement et d'analyse des images MET qui permet de reconstruire en 3D un agrégat à partir de ses projections et l'analyse de ses caractéristiques dimensionnelles et morphologiques à partir de sa reconstruction. Les résultats obtenus nous ont permis d'étudier la validité des relations liant les caractéristiques microphysiques 2D et 3D proposées dans la littérature et d'en proposer de nouvelles pour les agrégats étudiés.Ces résultats constituent la première caractérisation morphologique 3D d'agrégats de suie aéronautique à partir d'analyses par MET et tomographie électronique. Ils montrent que les propriétés morphologiques de ces agrégats ne permettent pas d'utiliser la méthode d'ensemble pour déterminer la dimension fractale massique
Soot aggregates emitted by aircraft engines' combustion processes are involved in the modification of the global radiative budget and the air quality. The knowledge of their physical and chemical characteristics is a prerequisite to any evaluation of the way they may act in the atmospheric physical and chemical processes and their impact on the environment and public health. In this context, our study aims at determining the size and morphological characteristics of aircraft soot aggregates on the basis of experimental measurements by transmission electron microscopy (TEM) and electron tomography.We have acquired TEM pictures of soot aggregates emitted by aircraft engines. We have established a method to characterize the morphology of these aggregates by determining their elongation, their compacity and the tortuosity of their edge. This method is based on the analysis of their TEM projection. Besides, we have developed a software to process and analyse TEM pictures. It allows to reconstruct aggregates from their projections and to determine their size and morphological characteristics. Our results have lead us to study the validity of the relationships linking the 2D and 3D microphysical characteristics presented in the literature and to suggest new ones for the studied aggregates.These results constitute the first 3D morphological and size characterizations of aircraft soot aggregates using TEM and electron tomography. They highlight the fact that the morphological properties of these aggregates do not fulfil the hypotheses required for the use of the collective method to determine the mass fractal dimension

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Palmer, Colin Michael. "A cylindrical specimen holder for electron cryo-tomography." Thesis, University of Cambridge, 2013. https://www.repository.cam.ac.uk/handle/1810/244503.

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The ‘missing wedge’ is a long-standing problem in electron tomography, caused by the use of slab-like flat specimens, which increase in thickness when tilted to high angles. Attempts have been made to reduce the undesirable effects caused by the missing wedge, but the problem remains, particularly for the radiation-sensitive frozen-hydrated specimens used for high resolution imaging. Specimens with cylindrical symmetry offer a way to overcome this problem, since the thickness remains constant at all viewing angles. However, while this has been suggested before, it has never been demonstrated for frozen-hydrated specimens. In this work, I present a way to make cylindrical specimens for electron cryo-tomography, using thin-walled carbon tubes as specimen holders. The tubes are made in a multi-step process, involving carbon deposition on glass micropipette templates and subsequent removal of the glass. Tube diameters are typically a few hundred nanometres, with a wall thickness of 10–20 nm. To make frozen-hydrated specimens, the tubes are filled with an aqueous sample and then plunge-frozen in liquid ethane. Electron images acquired from the tubes have equal quality at all viewing angles, with a tilt range restricted only by the physical limits of the microscope. Tomograms from specimens such as gold particles and liposomes show that the effects of the missing wedge are substantially reduced, with much improved resolution along the electron beam axis. Structural features oriented in all directions are visible in the reconstructions, in marked contrast to tomograms acquired over a more restricted angular range. These results are promising, however some technical challenges remain before this method can be used routinely.

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Shrestha, Sachin. "Characterising the effect of Niobium-rich clusters on the microstructure-property relationships in CASTRIP® steels." Thesis, The University of Sydney, 2013. http://hdl.handle.net/2123/10297.

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Many properties of steels, especially those that are important for engineering purposes, are determined by their microstructures. Therefore the key driver to controlling properties of these materials lies within the characterisation and manipulation of their microstructure down to their atomic-scale structure. For industrial product development, strength and ductility are considered to be the most important properties and are highly ‘microstructure sensitive’. This thesis investigates the effect of niobium microalloying and clustering on the microstructure-property relationship of ultra-thin strip cast steels produced by the CASTRIP® steel manufacturing process using mechanical testing and advanced microanalysis techniques. The CASTRIP® process is a revolutionary new method of steel strip casting that requires significantly less energy, time, equipment, and floor space compared to conventional strip casting methods. New and improved microanalysis characterisation techniques were also developed as a part of this project in order to better characterise these steels. The work presented in this thesis will have industrial and scientific significance that is both of benefit to the CASTRIP® steel making process and its products and more generally for the microstructural characterisation of ferrous alloys, one of the most important classes of engineering materials.

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47

Cheng, Kimberley. "Single-particle cryo-electron microscopy of macromolecular assemblies." Doctoral thesis, Stockholm : Skolan för teknik och hälsa, Kungliga Tekniska högskolan, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-11769.

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Leong, Peter Anthony Jensen Grant J. Fraser Scott E. "Computational challenges in high-resolution cryo-electron microscopy /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-08072008-171049.

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Lacerda, Mariane Floriano Lopes Santos. "Limpeza e modelagem de canais ovais após preparo químico-mecânico utilizando três sistemas de instrumentação e irrigação com hipoclorito de sódio: estudo correlativo usando microtomografia computadorizada e histologia." Universidade Estácio de Sá, 2017. https://repositorio.ufjf.br/jspui/handle/ufjf/6179.

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PROQUALI (UFJF)
Objetivos: O presente estudo se propôs a avaliar a limpeza e modelagem de canais ovais após preparo com 3 sistemas de instrumentação usando correlação entre método analíticos. Materiais e métodos: Raízes distais de molares inferiores com canais ovais e vitalidade pulpar foram inicialmente escaneadas por microtomografia computadorizada (micro-CT) para seleção e distribuição das amostras em três grupos experimentais de acordo com o instrumento a ser avaliado: selfadjusting files (SAF), TRUShape e XP-endo Shaper. Em todos os grupos, hipoclorito de sódio a 5,25% aquecido a 37°C foi o irrigante. Após novo escaneamento em micro-CT, as áreas não tocadas das paredes do canal foram calculadas e, em seguida, avaliadas histologicamente quanto à quantidade de remanescente pulpar nos terços radiculares. Resultados: A 4mm do ápice, SAF apresentou valor significativamente menor de paredes não tocadas em relação ao XP-endo Shaper (P<0,049). Não foi possível verificar diferença estatística a 10 mm do ápice (P>0,05). A quantidade de remanescentes pulpares não apresentou diferença significativa entre os instrumentos, em nenhum dos terços avaliados. Não houve correlação significativa entre área não tocada e remanescente pulpar para os instrumentos testados. Conclusão: Não houve diferença no percentual de paredes não tocadas entre os 3 grupos, exceto entre SAF e XP-endo Shaper na avaliação dos 4 mm apicais. Também não houve diferença significativa na limpeza das paredes não tocadas. A não correlação entre paredes não tocadas e a quantidade de remanescentes pulpares indica a eficácia do preparo químico-mecânico com hipoclorito de sódio como irrigante na eliminação de matéria orgânica sobre as paredes.
Purpose: The present study evaluated the cleaning and shaping ability of three instrumentation systems in oval canals of vital teeth using a correlative analytical approach. Materials and methods: Distal roots of oval canals with pulp vitality were scanned by computed microtomography (micro-CT) for sample selection and distribution into three experimental groups according to the instrument to be evaluated: self-adjusting files (SAF), TRUShape and XP-endo Shaper. In all groups, the irrigant was sodium hypochlorite (5.25%) heated at 37°C. After rescanning by micro-CT, the untouched walls were measured and then histologically evaluated for the amount of pulp remaining in the root thirds. Results: SAF was more effective in touching the walls at 4 mm from the apex, presenting a significantly lower value of untouched walls when compared to XPendo Shaper (P <0.049). However, it was not possible to verify significant differences in the full canal length between groups. The amount of pulp remnants also did not differ between instruments in the canal thirds. There was no significant correlation between untouched areas and pulp remnants for any instrument. Conclusion: There was no significant difference in the amount of untouched walls between instruments, except between SAF and XP-endo Shaper in the apical 4 mm. There was no significant difference in the cleaning ability either. The non-correlation between untouched walls and pulp remnants indicates the effectiveness of different instruments and sodium hypochlorite irrigation in the elimination of soft tissue from unprepared walls.

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Channagiri, Samartha A. "Multiscale characterization of aging mechanisms in commercial LiFePO4 battery cathodes." The Ohio State University, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=osu1468233768.

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Дисертації з теми "Cryo-electron microscopy and tomography"

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