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Advanced Structural and Chemical Imaging

Lewys Jones, Shuqiu Wang, Xiao Hu, Shams Ur Rahman, Martin R Castell
The usual way to present images from a scanning tunneling microscope (STM) is to take multiple images of the same area, to then manually select the one that appears to be of the highest quality, and then to discard the other almost identical images. This is in contrast to most other disciplines where the signal to noise ratio (SNR) of a data set is improved by taking repeated measurements and averaging them. Data averaging can be routinely performed for 1D spectra, where their alignment is straightforward. However, for serial-acquired 2D STM images the nature and variety of image distortions can severely complicate accurate registration...
2018: Advanced Structural and Chemical Imaging
R Kannan, A V Ievlev, N Laanait, M A Ziatdinov, R K Vasudevan, S Jesse, S V Kalinin
Many spectral responses in materials science, physics, and chemistry experiments can be characterized as resulting from the superposition of a number of more basic individual spectra. In this context, unmixing is defined as the problem of determining the individual spectra, given measurements of multiple spectra that are spatially resolved across samples, as well as the determination of the corresponding abundance maps indicating the local weighting of each individual spectrum. Matrix factorization is a popular linear unmixing technique that considers that the mixture model between the individual spectra and the spatial maps is linear...
2018: Advanced Structural and Chemical Imaging
P Moeck, P DeStefano
Three different algorithms, as implemented in three different computer programs, were put to the task of extracting direct space lattice parameters from four sets of synthetic images that were per design more or less periodic in two dimensions (2D). One of the test images in each set was per design free of noise and, therefore, genuinely 2D periodic so that it adhered perfectly to the constraints of a Bravais lattice type, Laue class, and plane symmetry group. Gaussian noise with a mean of zero and standard deviations of 10 and 50% of the maximal pixel intensity was added to the individual pixels of the noise-free images individually to create two more images and thereby complete the sets...
2018: Advanced Structural and Chemical Imaging
Nigel D Browning
No abstract text is available yet for this article.
2018: Advanced Structural and Chemical Imaging
Suhas Somnath, Christopher R Smith, Sergei V Kalinin, Miaofang Chi, Albina Borisevich, Nicholas Cross, Gerd Duscher, Stephen Jesse
We develop an algorithm for feature extraction based on structural similarity and demonstrate its application for atom and pattern finding in high-resolution electron and scanning probe microscopy images. The use of the combined local identifiers formed from an image subset and appended Fourier, or other transform, allows tuning selectivity to specific patterns based on the nature of the recognition task. The proposed algorithm is implemented in Pycroscopy, a community-driven scientific data analysis package, and is accessible through an interactive Jupyter notebook available on GitHub...
2018: Advanced Structural and Chemical Imaging
Katherine E MacArthur, Marc Heggen, Rafal E Dunin-Borkowski
Advances in catalysis rely on the synthesis and characterisation of nanoparticles that have tailored structures and compositions. Although energy-dispersive X-ray (EDX) spectroscopy can be used to study local variations in the compositions of individual supported nanoparticles on the atomic-scale in the scanning transmission electron microscope, electron beam induced damage and contamination can preclude the use of long exposure times and tomographic approaches. Here, we perform simulations of EDX maps of seven different octahedral PtNi nanoparticles for a selection of crystallographic orientations and tilts, to evaluate which of them can be distinguished from elemental mapping performed in only one orientation...
2018: Advanced Structural and Chemical Imaging
Alessandra Patera, Stephan Carl, Marco Stampanoni, Dominique Derome, Jan Carmeliet
This paper concerns the problem of wood cellular structure image registration. Given the large variability of wood geometry and the important changes in the cellular organization due to moisture sorption, an affine-based image registration technique is not exhaustive to describe the overall hygro-mechanical behaviour of wood at micrometre scales. Additionally, free tools currently available for non-rigid image registration are not suitable for quantifying the structural deformations of complex hierarchical materials such as wood, leading to errors due to misalignment...
2018: Advanced Structural and Chemical Imaging
Emmanuelle Gouillart, Juan Nunez-Iglesias, Stéfan van der Walt
The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements...
2017: Advanced Structural and Chemical Imaging
Alan Pryor, Colin Ophus, Jianwei Miao
Simulation of atomic-resolution image formation in scanning transmission electron microscopy can require significant computation times using traditional methods. A recently developed method, termed plane-wave reciprocal-space interpolated scattering matrix (PRISM), demonstrates potential for significant acceleration of such simulations with negligible loss of accuracy. Here, we present a software package called Prismatic for parallelized simulation of image formation in scanning transmission electron microscopy (STEM) using both the PRISM and multislice methods...
2017: Advanced Structural and Chemical Imaging
Jacob Madsen, Pei Liu, Jakob B Wagner, Thomas W Hansen, Jakob Schiøz
Strain analysis from high-resolution transmission electron microscopy (HRTEM) images offers a convenient tool for measuring strain in materials at the atomic scale. In this paper we present a theoretical study of the precision and accuracy of surface strain measurements directly from aberration-corrected HRTEM images. We examine the influence of defocus, crystal tilt and noise, and find that absolute errors of at least 1-2% strain should be expected. The model structures include surface relaxations determined using molecular dynamics, and we show that this is important for correctly evaluating the errors introduced by image aberrations...
2017: Advanced Structural and Chemical Imaging
Nouamane Laanait, Wittawat Saenrang, Hua Zhou, Chang-Beom Eom, Zhan Zhang
X-ray diffraction imaging is rapidly emerging as a powerful technique by which one can capture the local structure of crystalline materials at the nano- and meso-scale. Here, we present investigations of the dynamic structure of epitaxial monodomain BiFeO3 thin-films using a novel full-field Bragg diffraction imaging modality. By taking advantage of the depth penetration of hard X-rays and their exquisite sensitivity to the atomic structure, we imaged in situ and in operando, the electric field-driven structural responses of buried BiFeO3 epitaxial thin-films in micro-capacitor devices, with sub-100 nm lateral resolution...
2017: Advanced Structural and Chemical Imaging
Colin Ophus
Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, namely the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor f that has typical values of 4-20 for atomic resolution simulations. We show that in many cases PRISM can provide a speedup that scales with f(4) compared to multislice simulations, with a negligible loss of accuracy...
2017: Advanced Structural and Chemical Imaging
Daniel E Perea, Stephan S A Gerstl, Jackson Chin, Blake Hirschi, James E Evans
Environmental control during transfer between instruments is required for samples sensitive to air or thermal exposure to prevent morphological or chemical changes prior to analysis. Atom probe tomography is a rapidly expanding technique for three-dimensional structural and chemical analysis, but commercial instruments remain limited to loading specimens under ambient conditions. In this study, we describe a multifunctional environmental transfer hub allowing controlled cryogenic or room-temperature transfer of specimens under atmospheric or vacuum pressure conditions between an atom probe and other instruments or reaction chambers...
2017: Advanced Structural and Chemical Imaging
R Prakash Kolli
Residual hydrogen (H2) gas in the analysis chamber of an atom probe instrument limits the ability to measure H concentration in metals and alloys. Measuring H concentration would permit quantification of important physical phenomena, such as hydrogen embrittlement, corrosion, hydrogen trapping, and grain boundary segregation. Increased insight into the behavior of residual H2 gas on the specimen tip surface in atom probe instruments could help reduce these limitations. The influence of user-selected experimental parameters on the field adsorption and desorption of residual H2 gas on nominally pure copper (Cu) was studied during ultraviolet pulsed laser atom probe tomography...
2017: Advanced Structural and Chemical Imaging
F-R Chen, C Kisielowski, D Van Dyck
It is now established that the 3D structure of homogeneous nanocrystals can be recovered from in-line hologram of single projections. The method builds on a quantitative contrast interpretation of electron exit wave functions. Since simulated exit wave functions of single and bilayers of graphene reveal the atomic structure of carbon-based materials with sufficient resolution, we explore theoretically how the approach can be expanded beyond periodic carbon-based materials to include non-periodic molecular structures...
2017: Advanced Structural and Chemical Imaging
Benedikt J Daurer, Hari Krishnan, Talita Perciano, Filipe R N C Maia, David A Shapiro, James A Sethian, Stefano Marchesini
BACKGROUND: The ever improving brightness of accelerator based sources is enabling novel observations and discoveries with faster frame rates, larger fields of view, higher resolution, and higher dimensionality. RESULTS: Here we present an integrated software/algorithmic framework designed to capitalize on high-throughput experiments through efficient kernels, load-balanced workflows, which are scalable in design. We describe the streamlined processing pipeline of ptychography data analysis...
2017: Advanced Structural and Chemical Imaging
Tekin Bicer, Doğa Gürsoy, Vincent De Andrade, Rajkumar Kettimuthu, William Scullin, Francesco De Carlo, Ian T Foster
BACKGROUND: Modern synchrotron light sources and detectors produce data at such scale and complexity that large-scale computation is required to unleash their full power. One of the widely used imaging techniques that generates data at tens of gigabytes per second is computed tomography (CT). Although CT experiments result in rapid data generation, the analysis and reconstruction of the collected data may require hours or even days of computation time with a medium-sized workstation, which hinders the scientific progress that relies on the results of analysis...
2017: Advanced Structural and Chemical Imaging
Pierre Paleo, Alessandro Mirone
We propose an efficient implementation of an interior tomography reconstruction method based on a known subregion. This method iteratively refines a reconstruction, aiming at reducing the local tomography artifacts. To cope with the ever increasing data volumes, this method is highly optimized on two aspects: firstly, the problem is reformulated to reduce the number of variables, and secondly, the operators involved in the optimization algorithms are efficiently implemented. Results show that [Formula: see text] slices can be processed in tens of seconds, while being beyond the reach of equivalent exact local tomography method...
2017: Advanced Structural and Chemical Imaging
Francesco Brun, Lorenzo Massimi, Michela Fratini, Diego Dreossi, Fulvio Billé, Agostino Accardo, Roberto Pugliese, Alessia Cedola
When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images...
2017: Advanced Structural and Chemical Imaging
J Thayer, D Damiani, C Ford, M Dubrovin, I Gaponenko, C P O'Grady, W Kroeger, J Pines, T J Lane, A Salnikov, D Schneider, T Tookey, M Weaver, C H Yoon, A Perazzo
The data systems for X-ray free-electron laser (FEL) experiments at the Linac coherent light source (LCLS) are described. These systems are designed to acquire and to reliably transport shot-by-shot data at a peak throughput of 5 GB/s to the offline data storage where experimental data and the relevant metadata are archived and made available for user analysis. The analysis and monitoring implementation (AMI) and Photon Science ANAlysis (psana) software packages are described. Psana is open source and freely available...
2017: Advanced Structural and Chemical Imaging
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