Complementary 2D/3D Imaging of Functional Materials using X-ray & Electron Microscopy

Catalysts and other functional materials are generally hierarchically structured materials. Hence, the detailed characterization at different length scales, and especially under reaction conditions, are necessary to unravel their mechanisms and to improve their performance and catalytic activities. Besides, a combination of several techniques is required to acquire complementary information owing to the lack of a single technique able to cover all the length scales. With respect to length, the best way to investigate is by microscopy either in 2D or more preferably in 3D. The work began with an exploration of three different 3D imaging techniques, i.e. ptychographic X-ray computed tomography, electron tomography, and focused ion beam slice-and view. Using nanoporous gold as the model, this study aimed to exhibit the versatility of 3D microscopy as a method beyond imaging as well as to confirm the necessity of complementary nature between them, where electron offers better spatial resolution and X-ray provides larger field of view. The study then continued by utilizing ptychographic X-ray computed tomography for quasi in situ thermal treatment of the same materials under atmospheric pressure. This study highlighted its ease of use of implementing in situ studies, complemented by electron tomography to prove its powerful ability to resolve what ptychographic tomography cannot. The resulting 3D volumes were then used for air permeability and CO2 diffusion simulations, along with material’s electrical and thermal conductivity simulations in order to further expose another excellent benefit from 3D microscopy. Ultimately, the work proceeded into developing two cells in order to perform full in situ investigations under controlled temperatures and atmospheres, where one cell was built for 2D only (X-ray) ptychography experiments with simultaneous X-ray fluorescence mapping, and the other was constructed with an additional capability for 3D limited-angle ptychographic tomography experiments. The feasibility tests were conducted using several functional materials, i.e. nanoporous gold, zeolite, and cobalt-manganese-oxides hollow sphere, as the models for thermal annealing process under specific atmospheres. This work eventually attests the importance of in situ studies in precisely determining the onset annealing temperatures under particular environments, to visualize the morphology online either in 2D or 3D, and to simultaneously map elemental distributions live. Moreover, a complementary technique via transmission electron microscopy was also demonstrated on the same sample, adding up another advantage in using the cells. Despite the preliminary results from in situ limited-angle ptychographic tomography experiments for limitation in data reconstruction, a new tomographic reconstruction technique was recently developed as a solution to acquire 3D images with shortened acquisition times. In conclusions, the work here converges into the ideal case of performing all-around in situ 3D imaging of functional materials for quantitative analysis and simulation

X-ray and neutron μCT of biomedical samples: from image acquisition to quantification

Even though the validity of x-ray computed tomography in the analysis of biomedical samples is nowadays undisputed, the more recent imaging techniques and more advanced instruments (such as synchrotrons) are still relatively unknown to many medical doctors that could benefit from them.The doctoral work presented in this thesis joins a collective effort from the imaging community to demonstrate potential applications of advanced x-ray and neutron imaging methods to preclinical medical research, with the hope of contributing to reach a “critical mass” in the medical community and in the public opinion as well.Two main lines of work are detailed, one focused on the ex vivo evaluation of corrosion processes of magnesium-based biodegradable implants for osteosynthesis, the other dedicated to the assessment of neuropathy in human gastroenteric dysmotility. The aimed endpoint was to develop pipelines, from image acquisition all the way to data quantification, that could be used by other research groups with similar questions and may inspire future interdisciplinary collaborations between medicine, natural science and engineering.In the first line of work, we have attempted to employ synchrotron-radiation micro-computed tomography (µCT) coupled with in situ loading tests to assess the mechanical properties of the bone-implant interface (Paper I). We have revealed the crucial importance of the radiation dose deposited on the sample, and that the mechanical loading geometry should be accurately determined in the planning steps of the experiment. Moving away from the mechanical testing, we have also explored a novel three-dimensional analysis of the corrosion by-products of biodegradable implants by combining x-ray µCT, neutron µCT and x-ray fluorescence mapping (Papers IV and V). The second line of work has assessed the potential of x-ray phase-contrast µCT and nano-resolution holotomography as ways to perform virtual histology of unstained peripheral and autonomic neural tissue. In full-thickness biopsies of the myenteric nervous system, qualitative and potentially quantitative differences have been shown between controls and patients affected by gastrointestinal dysmotility (Paper II). In unstained skin biopsies, the methods have failed to visualise peripheral nerves, but we could identify structural changes in the connective tissue of some patients when compared to controls and other patients (Paper III)

Tomografia estendida : do básico até o mapeamento de cérebro de camundongos

Orientador: Mateus Borba CardosoTese (doutorado) - Universidade Estadual de Campinas, Instituto de Física Gleb WataghinResumo: Esta tese apresentará uma introdução a imagens de raios-x e como adquirir e processar imagens usando linhas de luz síncrotron. Apresentará os desafios matemáticos e técnicos para reconstruir amostras em três dimensões usando a reconstrução de Tomografia Computadorizada, uma técnica conhecida como CT. Esta técnica tem seu campo de visão limitado ao tamanho da câmera e ao tamanho da iluminação. Uma técnica para ampliar esse campo de visão vai ser apresentada e os desafios técnicos envolvidos para que isso aconteça. Um \textit{pipeline} é proposto e todos os algoritmos necessários foram empacotados em um pacote python chamado Tomosaic. A abordagem baseia-se em adquirir tomogramas parciais em posiçoes pré definidas e depois mesclar os dados em um novo conjunto de dados. Duas maneiras possíveis são apresentadas para essa mescla, uma no domínio das projeções e uma no domínio dos sinogramas. Experimentos iniciais serão então usadas para mostrar que o método proposto funciona com computadores normais. A técnica será aplicada mais tarde para pesquisar a anatomia de cérebros de camundongo completos. Um estudo será apresentado de como obter informação em diferentes escalas do cérebro completo do rato utilizando raios-xAbstract: This thesis will present an introduction to x-ray images and how to acquire and thread images using synchrotron beamlines. It will present the mathematical and technical challenges to reconstruct samples in three dimensions using Computed Tomography reconstruction, a technique known as CT. This technique has a field of view bounded to the camera size and the illumination size. A technique to extended this field of view is going to be presented and the technical challenges involved in order for that to happen will be described. A pipeline is proposed and all the necessary algorithms are contained into a python packaged called Tomosaic. The approach relies on acquired partial tomogram data in a defined grid and later merging the data into a new dataset. Two possible ways are presented in order to that: in the projection domain, and in the sinogram domain. Initial experiments will then be used to show that the pipeline works with normal computers. The technique will be later applied to survey the whole anatomy of whole mouse brains. A study will be shown of how to get the complete range of scales of the mouse brain using x-ray tomography at different resolutionsDoutoradoFísicaDoutor em Ciências163304/2013-01247445/2013, 1456912/2014CNPQCAPE

Constrained inverse volume rendering for planetary nebulae

Journal ArticleDetermining the three-dimensional structure of distant astronomical objects is a challenging task, given that terrestrial observations provide only one viewpoint. For this task, bipolar planetary nebulae are interesting objects of study because of their pronounced axial symmetry due to fundamental physical processes. Making use of this symmetry constraint, we present a technique to automatically recover the asymmetric structure of bipolar planetary nebulae from two-dimensional images. With GPU-based volume rendering driving a non-linear optimization, we estimate the nebula's local emission density as a function of its radial and axial coordinates, and we recover the orientation of the nebula relative to Earth. The optimization refines the nebula model and its orientation by minimizing the differences between the rendered image and the original astronomical image. The resulting model enables realistic 3D visualizations of planetary nebulae, e.g. for educational purposes in planetarium shows. In addition, the recovered spatial distribution of the emissive gas allows validating computer simulation results of the astrophysical formation processes of planetary nebulae

Fractal-like hierarchical organization of bone begins at the nanoscale

INTRODUCTION: The components of bone assemble hierarchically to provide stiffness and toughness. Deciphering the specific organization and relationship between bone’s principal components—mineral and collagen—requires answers to three main questions: whether the association of the mineral phase with collagen follows an intrafibrillar or extrafibrillar pattern, whether the morphology of the mineral building blocks is needle- or platelet-shaped, and how the mineral phase maintains continuity across an extensive network of cross-linked collagen fibrils. To address these questions, a nanoscale level of three-dimensional (3D) structural characterization is essential and has now been performed. RATIONALE: Because bone has multiple levels of 3D structural hierarchy, 2D imaging methods that do not detail the structural context of a sample are prone to interpretation bias. Site-specific focused ion beam preparation of lamellar bone with known orientation of the analyzed sample regions allowed us to obtain imaging data by 2D high-resolution transmission electron microscopy (HRTEM) and to identify individual crystal orientations. We studied higher-level bone mineral organization within the extracellular matrix by means of scanning TEM (STEM) tomography imaging and 3D reconstruction, as well as electron diffraction to determine crystal morphology and orientation patterns. Tomographic data allowed 3D visualization of the mineral phase as individual crystallites and/or aggregates that were correlated with atomic-resolution TEM images and corresponding diffraction patterns. Integration of STEM tomography with HRTEM and crystallographic data resulted in a model of 3D mineral morphology and its association with the organic matrix. RESULTS: To visualize and characterize the crystallites within the extracellular matrix, we recorded imaging data of the bone mineral in two orthogonal projections with respect to the arrays of mineralized collagen fibrils. Three motifs of mineral organization were observed: “filamentous” (longitudinal or in-plane) and “lacy” (out-of-plane) motifs, which have been reported previously, and a third “rosette” motif comprising hexagonal crystals. Tomographic reconstructions showed that these three motifs were projections of the same 3D assembly. Our data revealed that needle-shaped, curved nanocrystals merge laterally to form platelets, which further organize into stacks of roughly parallel platelets separated by gaps of approximately 2 nanometers. These stacks of platelets, single platelets, and single acicular crystals coalesce into larger polycrystalline aggregates exceeding the lateral dimensions of the collagen fibrils, and the aggregates span adjacent fibrils as continuous, cross-fibrillar mineralization. CONCLUSION: Our findings can be described by a model of mineral and collagen assembly in which the mineral organization is hierarchical at the nanoscale. First, the data reveal that mineral particles are neither exclusively needle- nor platelet-shaped, but indeed are a combination of both, because curved acicular elements merge laterally to form slightly twisted plates. This can only be detected when the organic extracellular matrix is preserved in the sample. Second, the mineral particles are neither exclusively intrafibrillar nor extrafibrillar, but rather form a continuous cross-fibrillar phase where curved and merging crystals splay beyond the typical dimensions of a single collagen fibril. Third, in the organization of the mineral phase of bone, a helical pattern can be identified. This 3D observation, integrated with previous studies of bone hierarchy and structure, illustrates that bone (as a material, as a tissue, and as an organ) follows a fractal-like organization that is self-affine. The assembly of bone components into nested, helix-like patterns helps to explain the paradoxical combination of enhanced stiffness and toughness of bone and results in an expansion of the previously known hierarchical structure of bone to at least 12 levels

A new method for discrete electron tomography

This thesis explores a novel tomographic reconstruction method that utilizes high angle annular dark field (HAADF) images to reconstruct the 3D structure of convex nanoparticles with homogenous composition and demonstrated the reconstruction of Au and Pt catalyst nanoparticles at a resolution of ~0.004nm³ Catalyst nanoparticles play a significant role in so many applications that a thorough understanding of structure-related catalytic performance is required. 2D analysis of such small structures appears to be inadequate and hence an efficient 3D characterization technique at atomic resolution is essential

Aging of a Pt/Al₂O₃ exhaust gas catalyst monitored by quasi in situ X-ray micro computed tomography

Catalyst aging effects were analyzed using X-ray absorption micro-computed tomography in combination with conventional characterization methods on various length scales ranging from nm to [small mu ]m to gain insight into deactivation mechanisms. For this purpose, a 4 wt% Pt/Al2O3 model exhaust gas catalyst was coated on a cordierite honeycomb and subjected to sequential thermal aging in static air at 950 [degree]C for 4, 8, 12 and 24 hours. The aging was followed on the one hand by traditional methods, i.e. CO-oxidation activity, scanning and transmission electron microscopy (SEM, TEM), and X-ray diffraction (XRD). On the other hand, all intermediate aging steps were captured by X-ray absorption micro-computed tomography ([small mu ]-CT) with 1.27 [small mu ]m voxel size using a quasi in situ approach as complementary tool. The [small mu ]-CT data allowed comparing exactly the same position after each treatment using a special alignment procedure during data analysis which took into account that the sample was remounted on the sample holder. A growth of the initially nanometer-sized Pt particles into larger crystals as well as its agglomeration was found, preferentially in voids between support grains. Sintering occurred especially around the larger particles, which is in line with the Ostwald ripening mechanism reported for this system on a nanometer scale. The distribution of chemical elements in an embedded and mechanically cross-sectioned honeycomb was additionally mapped by an electron probe micro analyzer (EPMA), which in agreement to the [small mu ]-CT results shows no diffusion of Pt into the cordierite. Together with studies on the nanometer scale, these results allow a more thorough multi-scale modeling of exhaust gas catalysts, especially also during aging

Structure-Property Relationships in Aluminum-Copper alloys using Transmission X-Ray Microscopy (TXM) and Micromechanical Testing

abstract: Aluminum alloys are ubiquitously used in almost all structural applications due to their high strength-to-weight ratio. Their superior mechanical performance can be attributed to complex dispersions of nanoscale intermetallic particles that precipitate out from the alloy’s solid solution and offer resistance to deformation. Although they have been extensively investigated in the last century, the traditional approaches employed in the past haven’t rendered an authoritative microstructural understanding in such materials. The effect of the precipitates’ inherent complex morphology and their three-dimensional (3D) spatial distribution on evolution and deformation behavior have often been precluded. In this study, for the first time, synchrotron-based hard X-ray nano-tomography has been implemented in Al-Cu alloys to measure growth kinetics of different nanoscale phases in 3D and reveal mechanistic insights behind some of the observed novel phase transformation reactions occurring at high temperatures. The experimental results were reconciled with coarsening models from the LSW theory to an unprecedented extent, thereby establishing a new paradigm for thermodynamic analysis of precipitate assemblies. By using a unique correlative approach, a non-destructive means of estimating precipitation-strengthening in such alloys has been introduced. Limitations of using existing mechanical strengthening models in such alloys have been discussed and a means to quantify individual contributions from different strengthening mechanisms has been established. The current rapid pace of technological progress necessitates the demand for more resilient and high-performance alloys. To achieve this, a thorough understanding of the relationships between material properties and its structure is indispensable. To establish this correlation and achieve desired properties from structural alloys, microstructural response to mechanical stimuli needs to be understood in three-dimensions (3D). To that effect, in situ tests were conducted at the synchrotron (Advanced Photon Source) using Transmission X-Ray Microscopy as well as in a scanning electron microscope (SEM) to study real-time damage evolution in such alloys. Findings of precipitate size-dependent transition in deformation behavior from these tests have inspired a novel resilient aluminum alloy design.Dissertation/ThesisDoctoral Dissertation Materials Science and Engineering 201

Three-dimensional segmentation of computed tomography data using Drishti Paint: new tools and developments

Computed tomography (CT) has become very widely used in scientific and medical research and industry for its non-destructive and high-resolution means of detecting internal structure. Three-dimensional segmentation of computed tomography data sheds light on internal features of target objects. Three-dimensional segmentation of CT data is supported by various well-established software programs, but the powerful functionalities and capabilities of open-source software have not been fully revealed. Here, we present a new release of the open-source volume exploration, rendering and three-dimensional segmentation software, Drishti v. 2.7. We introduce a new tool for thresholding volume data (i.e. gradient thresholding) and a protocol for performing three-dimensional segmentation using the 3D Freeform Painter tool. These new tools and workflow enable more accurate and precise digital reconstruction, three-dimensional modelling and three-dimensional printing results. We use scan data of a fossil fish as a case study, but our procedure is widely applicable in biological, medical and industrial research.This research was funded by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant no. XDB26000000) and the National Natural Science Foundation of China (grant no. 41872023). Y.H. was supported by a Postgraduate Research Scholarship at the Research School of Physics, Australian National University. The development of Drishti is supported by National Computational Infrastructure, Australian National University. CT scans and three-dimensional printing are supported by the Department of Applied Mathematics, Research School of Physics and ANU CT Lab, with funding support from Prof. T. Senden and Australian Research Council Discovery Grant DP160102460