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Detection of defects in atomic-resolution images of materials using cycle analysis Adv. Struct. Chem. Imag. Pub Date : 2020-03-30 Oleg S. Ovchinnikov, Andrew O’Hara, Stephen Jesse, Bethany M. Hudak, Shi‐Ze Yang, Andrew R. Lupini, Matthew F. Chisholm, Wu Zhou, Sergei V. Kalinin, Albina Y. Borisevich, Sokrates T. Pantelides
The automated detection of defects in high-angle annular dark-field Z-contrast (HAADF) scanning-transmission-electron microscopy (STEM) images has been a major challenge. Here, we report an approach for the automated detection and categorization of structural defects based on changes in the material’s local atomic geometry. The approach applies geometric graph theory to the already-found positions
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Imaging of polymer:fullerene bulk-heterojunctions in a scanning electron microscope: methodology aspects and nanomorphology by correlative SEM and STEM Adv. Struct. Chem. Imag. Pub Date : 2020-03-04 Yonghe Li, Erich Müller, Christian Sprau, Alexander Colsmann, Dagmar Gerthsen
Scanning transmission electron microscopy (STEM) at low energies (≤ 30 keV) in a scanning electron microscope is well suited to distinguish weakly scattering materials with similar materials properties and analyze their microstructure. The capabilities of the technique are illustrated in this work to resolve material domains in PTB7:PC71BM bulk-heterojunctions, which are commonly implemented for light-harvesting
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mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks Adv. Struct. Chem. Imag. Pub Date : 2020-01-27 Debangshu Mukherjee, Leixin Miao, Greg Stone, Nasim Alem
The standard technique for sub-pixel estimation of atom positions from atomic resolution scanning transmission electron microscopy images relies on fitting intensity maxima or minima with a two-dimensional Gaussian function. While this is a widespread method of measurement, it can be error prone in images with non-zero aberrations, strong intensity differences between adjacent atoms or in situations
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Investigation of hole-free phase plate performance in transmission electron microscopy under different operation conditions by experiments and simulations Adv. Struct. Chem. Imag. Pub Date : 2019-10-01 Rebecca Pretzsch, Manuel Dries, Simon Hettler, Martin Spiecker, Martin Obermair, Dagmar Gerthsen
Hole-free phase plates (HFPPs), also known as Volta phase plates, were already demonstrated to be well suited for in-focus transmission electron microscopy imaging of organic objects. However, the underlying physical processes have not been fully understood yet. To further elucidate the imaging properties of HFPPs, phase shift measurements were carried out under different experimental conditions. Both
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Optimal principal component analysis of STEM XEDS spectrum images. Adv. Struct. Chem. Imag. Pub Date : 2019-04-09 Pavel Potapov,Axel Lubk
STEM XEDS spectrum images can be drastically denoised by application of the principal component analysis (PCA). This paper looks inside the PCA workflow step by step on an example of a complex semiconductor structure consisting of a number of different phases. Typical problems distorting the principal components decomposition are highlighted and solutions for the successful PCA are described. Particular
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Unsupervised machine learning applied to scanning precession electron diffraction data Adv. Struct. Chem. Imag. Pub Date : 2019-03-15 Ben H. Martineau, Duncan N. Johnstone, Antonius T. J. van Helvoort, Paul A. Midgley, Alexander S. Eggeman
Scanning precession electron diffraction involves the acquisition of a two-dimensional precession electron diffraction pattern at every probe position in a two-dimensional scan. The data typically comprise many more diffraction patterns than the number of distinct microstructural volume elements (e.g. crystals) in the region sampled. A dimensionality reduction, ideally to one representative diffraction
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Fast approximate STEM image simulations from a machine learning model Adv. Struct. Chem. Imag. Pub Date : 2019-03-12 Aidan H. Combs, Jason J. Maldonis, Jie Feng, Zhongnan Xu, Paul M. Voyles, Dane Morgan
Accurate quantum mechanical scanning transmission electron microscopy image simulation methods such as the multislice method require computation times that are too large to use in applications in high-resolution materials imaging that require very large numbers of simulated images. However, higher-speed simulation methods based on linear imaging models, such as the convolution method, are often not
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Analysis of crystal defects by scanning transmission electron microscopy (STEM) in a modern scanning electron microscope Adv. Struct. Chem. Imag. Pub Date : 2019-03-09 Cheng Sun, Erich Müller, Matthias Meffert, Dagmar Gerthsen
Dislocations and stacking faults are important crystal defects, because they strongly influence material properties. As of now, transmission electron microscopy (TEM) is the most frequently used technique to study the properties of single dislocations and stacking faults. Specifically, the Burgers vector b of dislocations or displacement vector R of stacking faults can be determined on the basis of
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Protein structural biology using cell-free platform from wheat germ. Adv. Struct. Chem. Imag. Pub Date : 2018-11-10 Irina V Novikova,Noopur Sharma,Trevor Moser,Ryan Sontag,Yan Liu,Michael J Collazo,Duilio Cascio,Tolou Shokuhfar,Hanjo Hellmann,Michael Knoblauch,James E Evans
One of the biggest bottlenecks for structural analysis of proteins remains the creation of high-yield and high-purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes, while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited
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Multiscale higher-order TV operators for L1 regularization. Adv. Struct. Chem. Imag. Pub Date : 2018-10-23 Toby Sanders,Rodrigo B Platte
In the realm of signal and image denoising and reconstruction, $$\ell _1$$ regularization techniques have generated a great deal of attention with a multitude of variants. In this work, we demonstrate that the $$\ell _1$$ formulation can sometimes result in undesirable artifacts that are inconsistent with desired sparsity promoting $$\ell _0$$ properties that the $$\ell _1$$ formulation is intended
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An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data. Adv. Struct. Chem. Imag. Pub Date : 2018-09-22 Laurent P René de Cotret,Martin R Otto,Mark J Stern,Bradley J Siwick
This paper details a software ecosystem comprising three free and open-source Python packages for processing raw ultrafast electron scattering (UES) data and interactively exploring the processed data. The first package, iris, is graphical user-interface program and library for interactive exploration of UES data. Under the hood, iris makes use of npstreams, an extensions of numpy to streaming array-processing
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Sub-Ångstrom electric field measurements on a universal detector in a scanning transmission electron microscope. Adv. Struct. Chem. Imag. Pub Date : 2018-08-24 Jordan A Hachtel,Juan Carlos Idrobo,Miaofang Chi
Scanning transmission electron microscopy (STEM) excels in accessing atomic-scale structure and chemistry. Enhancing our ability to directly image the functionalities of local features in materials has become one of the most important topics in the future development of STEM. Recently, differential phase contrast (DPC) imaging has been utilized to map the internal electric and magnetic fields in materials
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Multi-slice frozen phonon simulations of high-angle annular dark field scanning transmission electron microscopy images of the structurally and compositionally complex Mo-V-Nb-Te oxide catalyst. Adv. Struct. Chem. Imag. Pub Date : 2018-07-31 Douglas A Blom,Thomas Vogt
We report frozen phonon multi-slice image simulations for the complex oxidation catalyst M1. Quantitative analysis of the simulations suggests that the detailed order of the cations along the electron propagation direction in a [001] zone axis orientation can lead to different high-angle annular dark field signals from atomic columns with identical composition. The annular dark field signal varies
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Micro-Extinction Spectroscopy (MExS): a versatile optical characterization technique Adv. Struct. Chem. Imag. Pub Date : 2018-07-12 Anjli Kumar, Eduardo Villarreal, Xiang Zhang, Emilie Ringe
Micro-Extinction Spectroscopy (MExS), a flexible, optical, and spatial-scanning hyperspectral technique, has been developed and is described with examples. Software and hardware capabilities are described in detail, including transmission, reflectance, and scattering measurements. Each capability is demonstrated through a case study of nanomaterial characterization, i.e., transmission of transition
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Maximising the resolving power of the scanning tunneling microscope. Adv. Struct. Chem. Imag. Pub Date : 2018-06-07 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
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Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform. Adv. Struct. Chem. Imag. Pub Date : 2018-04-30 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
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Accurate lattice parameters from 2D-periodic images for subsequent Bravais lattice type assignments. Adv. Struct. Chem. Imag. Pub Date : 2018-03-28 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
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ASCI: providing a forum for imaging scientists. Adv. Struct. Chem. Imag. Pub Date : 2018-03-10 Nigel D Browning
Images are an essential part of the scientific discovery process in many research fields with the idiom “an image is worth a thousand words” holding true now more than ever. However, in many cases, these individual fields have developed their own methods for both acquiring and interpreting images based on new hardware and computational approaches, leading to a rapid divergence in what is considered
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Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging. Adv. Struct. Chem. Imag. Pub Date : 2018-03-01 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
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Differentiating the structure of PtNi octahedral nanoparticles through combined ADF-EDX simulations. Adv. Struct. Chem. Imag. Pub Date : 2018-02-20 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
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A non-rigid registration method for the analysis of local deformations in the wood cell wall. Adv. Struct. Chem. Imag. Pub Date : 2018-01-22 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
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Correction to: Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles. Adv. Struct. Chem. Imag. Pub Date : 2017-11-07 Jacob Madsen,Pei Liu,Jakob B Wagner,Thomas W Hansen,Jakob Schiøtz
Unfortunately, after publication of this article [1], it was noticed that the name of the fifth author was incorrectly displayed as Jakob Schiøz. The correct name is Jakob Schiøtz and can be seen in the corrected author list above. The original article has also been updated to correct this error.
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Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles. Adv. Struct. Chem. Imag. Pub Date : 2017-10-25 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
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A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy. Adv. Struct. Chem. Imag. Pub Date : 2017-10-25 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
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A fast image simulation algorithm for scanning transmission electron microscopy. Adv. Struct. Chem. Imag. Pub Date : 2017-05-10 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
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An environmental transfer hub for multimodal atom probe tomography. Adv. Struct. Chem. Imag. Pub Date : 2017-05-02 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
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Dynamic X-ray diffraction imaging of the ferroelectric response in bismuth ferrite. Adv. Struct. Chem. Imag. Pub Date : 2017-03-21 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
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Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography. Adv. Struct. Chem. Imag. Pub Date : 2017-02-22 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
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Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting. Adv. Struct. Chem. Imag. Pub Date : 2017-02-13 Magnus Nord,Per Erik Vullum,Ian MacLaren,Thomas Tybell,Randi Holmestad
Scanning transmission electron microscopy (STEM) data with atomic resolution can contain a large amount of information about the structure of a crystalline material. Often, this information is hard to extract, due to the large number of atomic columns and large differences in intensity from sublattices consisting of different elements. In this work, we present a free and open source software tool for
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Prospects for atomic resolution in-line holography for a 3D determination of atomic structures from single projections. Adv. Struct. Chem. Imag. Pub Date : 2017-02-06 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
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Nanosurveyor: a framework for real-time data processing. Adv. Struct. Chem. Imag. Pub Date : 2017-01-31 Benedikt J Daurer,Hari Krishnan,Talita Perciano,Filipe R N C Maia,David A Shapiro,James A Sethian,Stefano Marchesini
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. 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
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Trace: a high-throughput tomographic reconstruction engine for large-scale datasets. Adv. Struct. Chem. Imag. Pub Date : 2017-01-28 Tekin Bicer,Doğa Gürsoy,Vincent De Andrade,Rajkumar Kettimuthu,William Scullin,Francesco De Carlo,Ian T Foster
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
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SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows. Adv. Struct. Chem. Imag. Pub Date : 2017-01-19 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
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Efficient implementation of a local tomography reconstruction algorithm. Adv. Struct. Chem. Imag. Pub Date : 2017-01-19 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
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Data systems for the Linac coherent light source. Adv. Struct. Chem. Imag. Pub Date : 2017-01-14 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
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Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT. Adv. Struct. Chem. Imag. Pub Date : 2017-01-03 Federica Marone,Alain Studer,Heiner Billich,Leonardo Sala,Marco Stampanoni
Sub-second full-field tomographic microscopy at third-generation synchrotron sources is a reality, opening up new possibilities for the study of dynamic systems in different fields. Sustained elevated data rates of multiple GB/s in tomographic experiments will become even more common at diffraction-limited storage rings, coming in operation soon. The computational tools necessary for the post-processing
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Applying shot boundary detection for automated crystal growth analysis during in situ transmission electron microscope experiments. Adv. Struct. Chem. Imag. Pub Date : 2017-01-03 W A Moeglein,R Griswold,B L Mehdi,N D Browning,J Teuton
In situ scanning transmission electron microscopy is being developed for numerous applications in the study of nucleation and growth under electrochemical driving forces. For this type of experiment, one of the key parameters is to identify when nucleation initiates. Typically, the process of identifying the moment that crystals begin to form is a manual process requiring the user to perform an observation
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Analyzing microtomography data with Python and the scikit-image library. Adv. Struct. Chem. Imag. Pub Date : 2016-12-07 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
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A distributed ASTRA toolbox. Adv. Struct. Chem. Imag. Pub Date : 2016-12-07 Willem Jan Palenstijn,Jeroen Bédorf,Jan Sijbers,K Joost Batenburg
While iterative reconstruction algorithms for tomography have several advantages compared to standard backprojection methods, the adoption of such algorithms in large-scale imaging facilities is still limited, one of the key obstacles being their high computational load. Although GPU-enabled computing clusters are, in principle, powerful enough to carry out iterative reconstructions on large datasets
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Improved tomographic reconstruction of large-scale real-world data by filter optimization. Adv. Struct. Chem. Imag. Pub Date : 2016-12-03 Daniël M Pelt,Vincent De Andrade
In advanced tomographic experiments, large detector sizes and large numbers of acquired datasets can make it difficult to process the data in a reasonable time. At the same time, the acquired projections are often limited in some way, for example having a low number of projections or a low signal-to-noise ratio. Direct analytical reconstruction methods are able to produce reconstructions in very little
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The MAX IV imaging concept. Adv. Struct. Chem. Imag. Pub Date : 2016-12-01 Zdeněk Matěj,Rajmund Mokso,Krister Larsson,Vincent Hardion,Darren Spruce
The MAX IV Laboratory is currently the synchrotron X-ray source with the beam of highest brilliance. Four imaging beamlines are in construction or in the project phase. Their common characteristic will be the high acquisition rates of phase-enhanced images. This high data flow will be managed at the local computing cluster jointly with the Swedish National Computing Infrastructure. A common image reconstruction
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Automatic software correction of residual aberrations in reconstructed HRTEM exit waves of crystalline samples. Adv. Struct. Chem. Imag. Pub Date : 2016-11-30 Colin Ophus,Haider I Rasool,Martin Linck,Alex Zettl,Jim Ciston
We develop an automatic and objective method to measure and correct residual aberrations in atomic-resolution HRTEM complex exit waves for crystalline samples aligned along a low-index zone axis. Our method uses the approximate rotational point symmetry of a column of atoms or single atom to iteratively calculate a best-fit numerical phase plate for this symmetry condition, and does not require information
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Identifying local structural states in atomic imaging by computer vision. Adv. Struct. Chem. Imag. Pub Date : 2016-11-02 Nouamane Laanait,Maxim Ziatdinov,Qian He,Albina Borisevich
The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic
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Detecting structural variances of Co3O4 catalysts by controlling beam-induced sample alterations in the vacuum of a transmission electron microscope. Adv. Struct. Chem. Imag. Pub Date : 2016-11-02 C Kisielowski,H Frei,P Specht,I D Sharp,J A Haber,S Helveg
This article summarizes core aspects of beam-sample interactions in research that aims at exploiting the ability to detect single atoms at atomic resolution by mid-voltage transmission electron microscopy. Investigating the atomic structure of catalytic Co3O4 nanocrystals underscores how indispensable it is to rigorously control electron dose rates and total doses to understand native material properties
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Structural damage reduction in protected gold clusters by electron diffraction methods. Adv. Struct. Chem. Imag. Pub Date : 2016-09-26 Eduardo Ortega,Arturo Ponce,Ulises Santiago,Diego Alducin,Alfredo Benitez-Lara,Germán Plascencia-Villa,Miguel José-Yacamán
The present work explores electron diffraction methods for studying the structure of metallic clusters stabilized with thiol groups, which are susceptible to structural damage caused by electron beam irradiation. There is a compromise between the electron dose used and the size of the clusters since they have small interaction volume with electrons and as a consequence weak reflections in the diffraction
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Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images. Adv. Struct. Chem. Imag. Pub Date : 2016-09-15 James C Bouwer,Thomas J Deerinck,Eric Bushong,Vadim Astakhov,Ranjan Ramachandra,Steven T Peltier,Mark H Ellisman
Serial block-face scanning electron microscopy (SBEM) is quickly becoming an important imaging tool to explore three-dimensional biological structure across spatial scales. At probe-beam-electron energies of 2.0 keV or lower, the axial resolution should improve, because there is less primary electron penetration into the block face. More specifically, at these lower energies, the interaction volume
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HRTEM low dose: the unfold of the morphed graphene, from amorphous carbon to morphed graphenes. Adv. Struct. Chem. Imag. Pub Date : 2016-08-22 H A Calderon,A Okonkwo,I Estrada-Guel,V G Hadjiev,F Alvarez-Ramírez,F C Robles Hernández
We present experimental evidence under low-dose conditions transmission electron microscopy for the unfolding of the evolving changes in carbon soot during mechanical milling. The milled soot shows evolving changes as a function of the milling severity or time. Those changes are responsible for the transformation from amorphous carbon to graphenes, graphitic carbon, and highly ordered structures such
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Growth of dendritic nanostructures by liquid-cell transmission electron microscopy: a reflection of the electron-irradiation history Adv. Struct. Chem. Imag. Pub Date : 2016-06-30 Nabeel Ahmad, Yann Le Bouar, Christian Ricolleau, Damien Alloyeau
Studying dynamical processes by transmission electron microscopy (TEM) requires considering the electron-irradiation history, including the instantaneous dose rate and the cumulative dose delivered to the sample. Here, we have exploited liquid-cell TEM to study the effects of the electron-irradiation history on the radiochemical growth of dendritic Au nanostructures. Besides the well-established direct
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3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography. Adv. Struct. Chem. Imag. Pub Date : 2016-06-28 Sébastien Phan,Daniela Boassa,Phuong Nguyen,Xiaohua Wan,Jason Lanman,Albert Lawrence,Mark H Ellisman
Transmission electron microscopy allows the collection of multiple views of specimens and their computerized three-dimensional reconstruction and analysis with electron tomography. Here we describe development of methods for automated multi-tilt data acquisition, tilt-series processing, and alignment which allow assembly of electron tomographic data from a greater number of tilt series, yielding enhanced
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Electron beam induced dehydrogenation of MgH2 studied by VEELS Adv. Struct. Chem. Imag. Pub Date : 2016-06-23 Alexander Surrey, Ludwig Schultz, Bernd Rellinghaus
Nanosized or nanoconfined hydrides are promising materials for solid-state hydrogen storage. Most of these hydrides, however, degrade fast during the structural characterization utilizing transmission electron microscopy (TEM) upon the irradiation with the imaging electron beam due to radiolysis. We use ball-milled MgH2 as a reference material for in-situ TEM experiments under low-dose conditions to
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Dynamic scan control in STEM: spiral scans Adv. Struct. Chem. Imag. Pub Date : 2016-06-13 Xiahan Sang, Andrew R. Lupini, Raymond R. Unocic, Miaofang Chi, Albina Y. Borisevich, Sergei V. Kalinin, Eirik Endeve, Richard K. Archibald, Stephen Jesse
Scanning transmission electron microscopy (STEM) has emerged as one of the foremost techniques to analyze materials at atomic resolution. However, two practical difficulties inherent to STEM imaging are: radiation damage imparted by the electron beam, which can potentially damage or otherwise modify the specimen and slow-scan image acquisition, which limits the ability to capture dynamic changes at
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Detecting magnetic ordering with atomic size electron probes Adv. Struct. Chem. Imag. Pub Date : 2016-05-27 Juan Carlos Idrobo, Ján Rusz, Jakob Spiegelberg, Michael A. McGuire, Christopher T. Symons, Ranga Raju Vatsavai, Claudia Cantoni, Andrew R. Lupini
Although magnetism originates at the atomic scale, the existing spectroscopic techniques sensitive to magnetic signals only produce spectra with spatial resolution on a larger scale. However, recently, it has been theoretically argued that atomic size electron probes with customized phase distributions can detect magnetic circular dichroism. Here, we report a direct experimental real-space detection
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On the role of the gas environment, electron-dose-rate, and sample on the image resolution in transmission electron microscopy Adv. Struct. Chem. Imag. Pub Date : 2016-05-04 Martin Ek, Sebastian P. F. Jespersen, Christian D. Damsgaard, Stig Helveg
The introduction of gaseous atmospheres in transmission electron microscopy offers the possibility of studying materials in situ under chemically relevant environments. The presence of a gas environment can degrade the resolution. Surprisingly, this phenomenon has been shown to depend on the electron-dose-rate. In this article, we demonstrate that both the total and areal electron-dose-rates work as
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Recovering low spatial frequencies in wavefront sensing based on intensity measurements Adv. Struct. Chem. Imag. Pub Date : 2016-03-22 Amin Parvizi, Wouter Van den Broek, Christoph T. Koch
The transport of intensity equation (TIE) offers a convenient method to retrieve the phase of a wave function from maps of the irradiance (images) recorded at different planes along the optic axis of an optical system. However, being a second-order partial differential equation, even for noise-free data a unique solution of the TIE requires boundary conditions to be specified which are generally not
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Automated analysis of evolving interfaces during in situ electron microscopy Adv. Struct. Chem. Imag. Pub Date : 2016-02-26 Nicholas M. Schneider, Jeung Hun Park, Michael M. Norton, Frances M. Ross, Haim H. Bau
In situ electron microscopy allows one to monitor dynamical processes at high spatial and temporal resolution. This produces large quantities of data, and hence automated image processing algorithms are needed to extract useful quantitative measures of the observed phenomena. In this work, we outline an image processing workflow for the analysis of evolving interfaces imaged during liquid cell electron
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Assessment of off-axis and in-line electron holography for measurement of potential variations in Cu(In,Ga)Se2 thin-film solar cells Adv. Struct. Chem. Imag. Pub Date : 2016-01-13 Debora Keller, Stephan Buecheler, Patrick Reinhard, Fabian Pianezzi, Etienne Snoeck, Christophe Gatel, Marta D. Rossell, Rolf Erni, Ayodhya N. Tiwari
Electron holography is employed to study variations of the electrostatic crystal potential in Cu(In,Ga)Se2 (CIGS) thin-film solar cells at different length scales: Long-range potential variations across the layer structure of the solar cell as well as inhomogeneities within the layers are analyzed by off-axis holography. In-line holography is applied to examine the local potential variation across