Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Scanning precession electron tomography for three-dimensional nanoscale orientation imaging and crystallographic analysis.

ABSTRACT: Three-dimensional (3D) reconstructions from electron tomography provide important morphological, compositional, optical and electro-magnetic information across a wide range of materials and devices. Precession electron diffraction, in combination with scanning transmission electron microscopy, can be used to elucidate the local orientation of crystalline materials. Here we show, using the example of a Ni-base superalloy, that combining these techniques and extending them to three dimensions, to produce scanning precession electron tomography, enables the 3D orientation of nanoscale sub-volumes to be determined and provides a one-to-one correspondence between 3D real space and 3D reciprocal space for almost any polycrystalline or multi-phase material.

SUBMITTER: Eggeman AS

PROVIDER: S-EPMC4458861 | biostudies-literature | 2015 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Scanning precession electron tomography for three-dimensional nanoscale orientation imaging and crystallographic analysis.

Eggeman Alexander S AS Krakow Robert R Midgley Paul A PA

Nature communications 20150601

Three-dimensional (3D) reconstructions from electron tomography provide important morphological, compositional, optical and electro-magnetic information across a wide range of materials and devices. Precession electron diffraction, in combination with scanning transmission electron microscopy, can be used to elucidate the local orientation of crystalline materials. Here we show, using the example of a Ni-base superalloy, that combining these techniques and extending them to three dimensions, to ...[more]

PMID: 26028514

Similar Datasets

Nanoscale 3D cellular imaging by axial scanning transmission electron tomography.

Project description:Electron tomography provides three-dimensional structural information about supramolecular assemblies and organelles in a cellular context, but image degradation, caused by scattering of transmitted electrons, limits applicability in specimens thicker than 300 nm. We found that scanning transmission electron tomography of 1,000-nm-thick samples using axial detection provided resolution comparable to that of conventional electron tomography. We demonstrated the method by reconstructing a human erythrocyte infected with the malaria parasite Plasmodium falciparum.

| S-EPMC2755602 | biostudies-literature

Nanoscale Three-Dimensional Charge Density and Electric Field Mapping by Electron Holographic Tomography.

Project description:The operation of nanoscale electronic devices is related intimately to the three-dimensional (3D) charge density distributions within them. Here, we demonstrate the quantitative 3D mapping of the charge density and long-range electric field associated with an electrically biased carbon fiber nanotip with a spatial resolution of approximately 5 nm using electron holographic tomography in the transmission electron microscope combined with model-based iterative reconstruction. The approach presented here can be applied to a wide range of other nanoscale materials and devices.

| S-EPMC9912371 | biostudies-literature

Four dimensional-scanning transmission electron microscopy study on relationship between crystallographic orientation and spontaneous polarization in epitaxial BiFeO<sub>3</sub>.

Project description:Spontaneous polarization and crystallographic orientations within ferroelectric domains are investigated using an epitaxially grown BiFeO3 thin film under bi-axial tensile strain. Four dimensional-scanning transmission electron microscopy (4D-STEM) and atomic resolution STEM techniques revealed that the tensile strain applied is not enough to cause breakdown of equilibrium BiFeO3 symmetry (rhombohedral with space group: R3c). 4D-STEM data exhibit two types of BiFeO3 ferroelectric domains: one with projected polarization vector possessing out-of-plane component only, and the other with that consisting of both in-plane and out-of-plane components. For domains with only out-of-plane polarization, convergent beam electron diffraction (CBED) patterns exhibit "extra" Bragg's reflections (compared to CBED of cubic-perovskite) that indicate rhombohedral symmetry. In addition, beam damage effects on ferroelectric property measurements were investigated by systematically changing electron energy from 60 to 300 keV.

| S-EPMC11226628 | biostudies-literature

Three-dimensional scanning transmission electron microscopy of biological specimens.

Project description:A three-dimensional (3D) reconstruction of the cytoskeleton and a clathrin-coated pit in mammalian cells has been achieved from a focal-series of images recorded in an aberration-corrected scanning transmission electron microscope (STEM). The specimen was a metallic replica of the biological structure comprising Pt nanoparticles 2-3 nm in diameter, with a high stability under electron beam radiation. The 3D dataset was processed by an automated deconvolution procedure. The lateral resolution was 1.1 nm, set by pixel size. Particles differing by only 10 nm in vertical position were identified as separate objects with greater than 20% dip in contrast between them. We refer to this value as the axial resolution of the deconvolution or reconstruction, the ability to recognize two objects, which were unresolved in the original dataset. The resolution of the reconstruction is comparable to that achieved by tilt-series transmission electron microscopy. However, the focal-series method does not require mechanical tilting and is therefore much faster. 3D STEM images were also recorded of the Golgi ribbon in conventional thin sections containing 3T3 cells with a comparable axial resolution in the deconvolved dataset.

| S-EPMC2917646 | biostudies-literature

Three-Dimensional Imaging of Dislocations in a Ti-35mass%Nb Alloy by Electron Tomography.

Project description:We have studied three-dimensional (3D) configurations of dislocations in the β phase of a Ti-35mass%Nb alloy by means of single-axis tilt tomography using bright-field scanning transmission electron microscopy (BF-STEM). To visualize dislocations, the hh0 systematic reflections were excited throughout tilt-series acquisition with the maximum tilt angle of 70°. Dislocations in the β grains were clearly reconstructed by the weighted back-projection algorithm. The slip planes of the dislocations were deduced by rotating the reconstructed volumes with the aid of selected area electron diffraction patterns. It was found that BF-STEM images with relatively low contrasts, taken along low-order zone axes, are capable to reproduce and preserve the quality of reconstructed image of dislocations. We also found that tilt angles as low as 40° are practically acceptable to visualize 3D configurations of dislocations, while there exists limitation in resolution due to the existence of a large missing wedge.

| S-EPMC5507017 | biostudies-literature

Nanoscale three-dimensional imaging of the human myocyte.

Project description:The ventricular human myocyte is spatially organized for optimal ATP and Ca(2+) delivery to sarcomeric myosin and ionic pumps during every excitation-contraction cycle. Comprehension of three-dimensional geometry of the tightly packed ultrastructure has been derived from discontinuous two-dimensional images, but has never been precisely reconstructed or analyzed in human myocardium. Using a focused ion beam scanning electron microscope, we created nanoscale resolution serial images to quantify the three-dimensional ultrastructure of a human left ventricular myocyte. Transverse tubules (t-tubule), lipid droplets, A-bands, and mitochondria occupy 1.8, 1.9, 10.8, and 27.9% of the myocyte volume, respectively. The complex t-tubule system has a small tortuosity (1.04±0.01), and is composed of long transverse segments with diameters of 317±24nm and short branches. Our data indicates that lipid droplets located well beneath the sarcolemma are proximal to t-tubules, where 59% (13 of 22) of lipid droplet centroids are within 0.50μm of a t-tubule. This spatial association could have an important implication in the development and treatment of heart failure because it connects two independently known pathophysiological alterations, a substrate switch from fatty acids to glucose and t-tubular derangement.

| S-EPMC4295200 | biostudies-literature

Three-dimensional ultrastructural analysis of cells in the periodontal ligament using focused ion beam/scanning electron microscope tomography.

Project description:The accurate comprehension of normal tissue provides essential data to analyse abnormalities such as disease and regenerative processes. In addition, understanding the proper structure of the target tissue and its microenvironment may facilitate successful novel treatment strategies. Many studies have examined the nature and structure of periodontal ligaments (PDLs); however, the three-dimensional (3D) structure of cells in normal PDLs remains poorly understood. In this study, we used focused ion beam/scanning electron microscope tomography to investigate the whole 3D ultrastructure of PDL cells along with quantitatively analysing their structural properties and ascertaining their orientation to the direction of the collagen fibre. PDL cells were shown to be in contact with each other, forming a widespread mesh-like network between the cementum and the alveolar bone. The volume of the cells in the horizontal fibre area was significantly larger than in other areas, whereas the anisotropy of these cells was lower than in other areas. Furthermore, the orientation of cells to the PDL fibres was not parallel to the PDL fibres in each area. As similar evaluations are recognized as being challenging using conventional two-dimensional methods, these novel 3D findings may contribute necessary knowledge for the comprehensive understanding and analysis of PDLs.

| S-EPMC5171660 | biostudies-literature

Attentional Ptycho-Tomography (APT) for three-dimensional nanoscale X-ray imaging with minimal data acquisition and computation time.

Project description:Noninvasive X-ray imaging of nanoscale three-dimensional objects, such as integrated circuits (ICs), generally requires two types of scanning: ptychographic, which is translational and returns estimates of the complex electromagnetic field through the IC; combined with a tomographic scan, which collects these complex field projections from multiple angles. Here, we present Attentional Ptycho-Tomography (APT), an approach to drastically reduce the amount of angular scanning, and thus the total acquisition time. APT is machine learning-based, utilizing axial self-Attention for Ptycho-Tomographic reconstruction. APT is trained to obtain accurate reconstructions of the ICs, despite the incompleteness of the measurements. The training process includes regularizing priors in the form of typical patterns found in IC interiors, and the physics of X-ray propagation through the IC. We show that APT with ×12 reduced angles achieves fidelity comparable to the gold standard Simultaneous Algebraic Reconstruction Technique (SART) with the original set of angles. When using the same set of reduced angles, then APT also outperforms Filtered Back Projection (FBP), Simultaneous Iterative Reconstruction Technique (SIRT) and SART. The time needed to compute the reconstruction is also reduced, because the trained neural network is a forward operation, unlike the iterative nature of these alternatives. Our experiments show that, without loss in quality, for a 4.48 × 93.2 × 3.92 µm3 IC (≃6 × 108 voxels), APT reduces the total data acquisition and computation time from 67.96 h to 38 min. We expect our physics-assisted and attention-utilizing machine learning framework to be applicable to other branches of nanoscale imaging, including materials science and biological imaging.

| S-EPMC10227032 | biostudies-literature

Three-dimensional imaging of the highly bent architecture of Bdellovibrio bacteriovorus by using cryo-electron tomography.

Project description:Bdellovibrio bacteriovorus cells are small deltaproteobacterial cells that feed on other gram-negative bacteria, including human pathogens. Using cryo-electron tomography, we demonstrated that B. bacteriovorus cells are capable of substantial flexibility and local deformation of the outer and inner membranes without loss of cell integrity. These shape changes can occur in less than 2 min, and analysis of the internal architecture of highly bent cells showed that the overall distribution of molecular machines and the nucleoid is similar to that in moderately bent cells. B. bacteriovorus cells appear to contain an extensive internal network of short and long filamentous structures. We propose that rearrangements of these structures, in combination with the unique properties of the cell envelope, may underlie the remarkable ability of B. bacteriovorus cells to find and enter bacterial prey.

| S-EPMC2293184 | biostudies-literature

Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography.

Project description:Battery function is determined by the efficiency and reversibility of the electrochemical phase transformations at solid electrodes. The microscopic tools available to study the chemical states of matter with the required spatial resolution and chemical specificity are intrinsically limited when studying complex architectures by their reliance on two-dimensional projections of thick material. Here, we report the development of soft X-ray ptychographic tomography, which resolves chemical states in three dimensions at 11 nm spatial resolution. We study an ensemble of nano-plates of lithium iron phosphate extracted from a battery electrode at 50% state of charge. Using a set of nanoscale tomograms, we quantify the electrochemical state and resolve phase boundaries throughout the volume of individual nanoparticles. These observations reveal multiple reaction points, intra-particle heterogeneity, and size effects that highlight the importance of multi-dimensional analytical tools in providing novel insight to the design of the next generation of high-performance devices.

| S-EPMC5834601 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data