The morphology, composition, and distribution of elements within nanocrystals are critical parameters which dictate the material's properties and performance in a diverse array of emerging applications. The (scanning) transmission electron microscope ((S)TEM) represents a powerful tool for probing the structure and chemistry of materials on the nanoscale. Understanding of the mechanisms by which nanocrystals grow, transform, and degrade is vital if we are to develop rational synthesis routes and hence control the properties of the resulting materials. Electron microscopy represents a key tool in developing such an understanding. In situ techniques, where the material of interest is subjected to stimuli such as heat or a chemically reactive environment in the microscope, allow direct observation of dynamic transformations. Ex situ approaches, where multiple samples are prepared in the lab with the reaction parameters systematically altered, can also give important mechanistic insights. This thesis explores the use of both in situ and ex situ (S)TEM to gain insights into the growth and transformation of nanocrystals. Ex situ TEM is used to assess the structure of PbS nanocrystals in a polymer matrix, revealing new methods of morphological control through reaction temperature, precursor structures (appendix 4), and the processing of the polymer matrix (appendix 5). In situ techniques are used to observe the solution phase growth and shelling of nanocrystals (appendix 1) as well as the transformations of nanocrystals during heating in vacuum (appendices 2 and 3). The subjects of my in situ investigations are systems with heterogeneous distributions of elements. Historically, in situ electron microscope has been largely limited to imaging. However, to understand many dynamic transformations knowledge of changing elemental distributions is vital. For this reason, I have focused on the use of energy dispersive X-ray (EDX) spectroscopy to reveal changes in composition and elemental distributions during in situ experiments (appendices 1-3). This type of in situ elemental mapping is especially challenging for liquid-cell experiments, and my results represent the first report of EDX spectrum imaging for nanomaterials in liquid (appendix 1).

Magnetic resonance imaging (MRI) has transformed the world of non-invasive imaging for diagnostic purposes. Modern techniques such as diffusion weighted imaging (DWI), diffusion tensor imaging (DTI), and diffusion spectrum imaging (DSI) have been used to reconstruct fiber pathways of the brain - providing a graphical picture of the so-called "connectome." However, there exists controversy in the literature as to the accuracy of the diffusion tractography reconstruction. Although various attempts at histological validation been attempted, there is still no 3D histological pathway validation of the fiber bundle trajectories seen in diffusion MRI. Such a validation is necessary in order to show the viability of current DSI tractography techniques in the ultimate goal for clinical diagnostic application. This project developed methods to provide this 3D histological validation using the rhesus monkey motor pathway as a model system. By injecting biotinylated dextran amine (BDA) tract tracer into the hand area of primary motor cortex, brain section images were reconstructed to create 3D fiber pathways labeled at the axonal level. Using serial coronal brain sections, the BDA label was digitized with a high resolution digital camera to create image montages of the fiber pathway with individual sections spaced at 1200 micron intervals through the brain. An MRI analysis system, OSIRX, was then used to reconstruct these sections into a 3D volume. This is an important technical step toward merging the BDA fiber tract histology with diffusion MRI tractography of the same brain, enabling identification of the valid and inaccurate aspects of diffusion fiber reconstruction. This will ultimately facilitate the use of diffusion MRI to quantify tractography, non-invasively and in vivo, in the human brain.

Code written in the DigitalMicrograph® scripting language enables a new experimental design for acquiring the magnetic dichroism in EELS. Called the q-E STEM setup, it provides simultaneous acquisition of the dichroic pairs of spectra (eliminating major error sources) while preserving the real-space resolution of STEM. This gives the setup great potential for real-space maps of magnetic momenta which can be instrumental in furthering the understanding of e.g. interfacial magnetic effects. The report includes a thorough presentation of the created acquisition routine, a detailed outline of future work and a fast introduction to the DMscript language.

abstract: In this dissertation research, conventional and aberration-corrected (AC) transmission electron microscopy (TEM) techniques were used to evaluate the structural and compositional properties of thin-film semiconductor compounds/alloys grown by molecular beam epitaxy for infrared photo-detection. Imaging, diffraction and spectroscopy techniques were applied to TEM specimens in cross-section geometry to extract information about extended structural defects, chemical homogeneity and interface abruptness. The materials investigated included InAs1-xBix alloys grown on GaSb (001) substrates, InAs/InAs1-xSbx type-II superlattices grown on GaSb (001) substrates, and CdTe-based thin-film structures grown on InSb (001) substrates. The InAsBi dilute-bismide epitaxial films were grown on GaSb (001) substrates at relatively low growth temperatures. The films were mostly free of extended defects, as observed in diffraction-contrast images, but the incorporation of bismuth was not homogeneous, as manifested by the lateral Bi-composition modulation and Bi-rich surface droplets. Successful Bi incorporation into the InAs matrix was confirmed using lattice expansion measurements obtained from misfit strain analysis of high-resolution TEM (HREM) images. Analysis of averaged intensity line profiles in HREM and scanning TEM (STEM) images of the Ga-free InAs/InAs1-xSbx type-II strained superlattices indicated slight variations in layer thickness across the superlattice stack. The interface abruptness was evaluated using misfit strain analysis of AC-STEM images, electron energy-loss spectroscopy and 002 dark-field imaging. The compositional profiles of antimony across the superlattices were fitted to a segregation model and revealed a strong antimony segregation probability. The CdTe/MgxCd1-xTe double-heterostructures were grown with Cd overflux in a dual-chamber molecular beam epitaxy with an ultra-high vacuum transfer loadlock. Diffraction-contrast images showed that the growth temperature had a strong impact on the structural quality of the epilayers. Very abrupt CdTe/InSb interfaces were obtained for epilayers grown at the optimum temperature of 265 °C, and high-resolution imaging using AC-STEM revealed an interfacial transition region with a width of a few monolayers and smaller lattice spacing than either CdTe or InSb. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2017

Cette thèse est consacrée à l'élaboration de nouvelles méthodes d'acquisition et de traitement de données en IRM de diffusion (IRMd) afin de caractériser la diffusion des molécules d'eau dans les fibres de matière blanche à l'échelle d'un voxel. Plus particulièrement, nous travaillons sur un moyen de reconstruction précis de l'Ensemble Average Propagator (EAP), qui représente la fonction de probabilité de diffusion des molécules d'eau. Plusieurs modèles de diffusion tels que le tenseur de diffusion ou la fonction de distribution d'orientation sont très utilisés dans la communauté de l'IRMd afin de quantifier la diffusion des molécules d'eau dans le cerveau. Ces modèles sont des représentations partielles de l'EAP et ont été développés en raison du petit nombre de mesures nécessaires à leurs estimations. Cependant, il est important de pouvoir reconstruire précisément l'EAP afin d'acquérir une meilleure compréhension des mécanismes du cerveau et d'améliorer le diagnostique des troubles neurologiques. Une estimation correcte de l'EAP nécessite l'acquisition de nombreuses images de diffusion sensibilisées à des orientations différentes dans le q-space. Ceci rend son estimation trop longue pour être utilisée dans la plupart des scanners cliniques. Dans cette thèse, nous utilisons des techniques de reconstruction parcimonieuses et en particulier la technique connue sous le nom de Compressive Sensing (CS) afin d’accélérer le calcul de l'EAP. Les multiples aspects de la théorie du CS et de son application à l'IRMd sont présentés dans cette thèse. / This thesis is dedicated to the development of new acquisition and processing methods in diffusion MRI (dMRI) to characterize the diffusion of water molecules in white matter fiber bundles at the scale of a voxel. In particular, we focus our attention on the accurate recovery of the Ensemble Average Propagator (EAP), which represents the full 3D displacement of water molecule diffusion. Diffusion models such that the Diffusion Tensor or the Orientation Distribution Function (ODF) are largely used in the dMRI community in order to quantify water molecule diffusion. These models are partial EAP representations and have been developed due to the small number of measurement required for their estimations. It is thus of utmost importance to be able to accurately compute the EAP and order to acquire a better understanding of the brain mechanisms and to improve the diagnosis of neurological disorders. Estimating the full 3D EAP requires the acquisition of many diffusion images sensitized todifferent orientations in the q-space, which render the estimation of the EAP impossible in most of the clinical dMRI scanner. A surge of interest has been seen in order to decrease this time for acquisition. Some works focus on the development of new and efficient acquisition sequences. In this thesis, we use sparse coding techniques, and in particular Compressive Sensing (CS) to accelerate the computation of the EAP. Multiple aspects of the CS theory and its application to dMRI are presented in this thesis.