Articles

mpfit: a robust method for fitting atomic resolution images with multiple Gaussian peaks

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 Gau...

Authors: Debangshu Mukherjee, Leixin Miao, Greg Stone and Nasim Alem

Investigation of hole-free phase plate performance in transmission electron microscopy under different operation conditions by experiments and simulations

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 p...

Authors: Rebecca Pretzsch, Manuel Dries, Simon Hettler, Martin Spiecker, Martin Obermair and Dagmar Gerthsen

Optimal principal component analysis of STEM XEDS spectrum images

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 st...

Authors: Pavel Potapov and Axel Lubk

Unsupervised machine learning applied to scanning precession electron diffraction data

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 man...

Authors: Ben H. Martineau, Duncan N. Johnstone, Antonius T. J. van Helvoort, Paul A. Midgley and Alexander S. Eggeman

Fast approximate STEM image simulations from a machine learning model

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-resoluti...

Authors: Aidan H. Combs, Jason J. Maldonis, Jie Feng, Zhongnan Xu, Paul M. Voyles and Dane Morgan

Analysis of crystal defects by scanning transmission electron microscopy (STEM) in a modern scanning electron microscope

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 s...

Authors: Cheng Sun, Erich Müller, Matthias Meffert and Dagmar Gerthsen

Protein structural biology using cell-free platform from wheat germ

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 cu...

Authors: Irina V. Novikova, Noopur Sharma, Trevor Moser, Ryan Sontag, Yan Liu, Michael J. Collazo, Duilio Cascio, Tolou Shokuhfar, Hanjo Hellmann, Michael Knoblauch and James E. Evans

Multiscale higher-order TV operators for L1 regularization

Authors: Toby Sanders and Rodrigo B. Platte

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data

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 fir...

Authors: Laurent P. René de Cotret, Martin R. Otto, Mark J. Stern and Bradley J. Siwick

Sub-Ångstrom electric field measurements on a universal detector in a scanning transmission electron microscope

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 ...

Authors: Jordan A. Hachtel, Juan Carlos Idrobo and Miaofang Chi

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

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 propagat...

Authors: Douglas A. Blom and Thomas Vogt

Micro-Extinction Spectroscopy (MExS): a versatile optical characterization technique

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 d...

Authors: Anjli Kumar, Eduardo Villarreal, Xiang Zhang and Emilie Ringe

Maximising the resolving power of the scanning tunneling microscope

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 di...

Authors: Lewys Jones, Shuqiu Wang, Xiao Hu, Shams ur Rahman and Martin R. Castell

Deep data analysis via physically constrained linear unmixing: universal framework, domain examples, and a community-wide platform

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...

Authors: R. Kannan, A. V. Ievlev, N. Laanait, M. A. Ziatdinov, R. K. Vasudevan, S. Jesse and S. V. Kalinin

Accurate lattice parameters from 2D-periodic images for subsequent Bravais lattice type assignments

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 ...

Authors: P. Moeck and P. DeStefano

ASCI: providing a forum for imaging scientists

Authors: Nigel D. Browning

Feature extraction via similarity search: application to atom finding and denoising in electron and scanning probe microscopy imaging

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 ...

Authors: Suhas Somnath, Christopher R. Smith, Sergei V. Kalinin, Miaofang Chi, Albina Borisevich, Nicholas Cross, Gerd Duscher and Stephen Jesse

Differentiating the structure of PtNi octahedral nanoparticles through combined ADF–EDX simulations

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 ...

Authors: Katherine E. MacArthur, Marc Heggen and Rafal E. Dunin-Borkowski

A non-rigid registration method for the analysis of local deformations in the wood cell wall

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 a...

Authors: Alessandra Patera, Stephan Carl, Marco Stampanoni, Dominique Derome and Jan Carmeliet

Correction to: Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles

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...

Authors: Jacob Madsen, Pei Liu, Jakob B. Wagner, Thomas W. Hansen and Jakob Schiøtz

A streaming multi-GPU implementation of image simulation algorithms for scanning transmission electron microscopy

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 ...

Authors: Alan Pryor Jr., Colin Ophus and Jianwei Miao

Accuracy of surface strain measurements from transmission electron microscopy images of nanoparticles

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...

Authors: Jacob Madsen, Pei Liu, Jakob B. Wagner, Thomas W. Hansen and Jakob Schiøtz

A fast image simulation algorithm for scanning transmission electron microscopy

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 prese...

Authors: Colin Ophus

An environmental transfer hub for multimodal atom probe tomography

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...

Authors: Daniel E. Perea, Stephan S. A. Gerstl, Jackson Chin, Blake Hirschi and James. E. Evans

Dynamic X-ray diffraction imaging of the ferroelectric response in bismuth ferrite

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 d...

Authors: Nouamane Laanait, Wittawat Saenrang, Hua Zhou, Chang-Beom Eom and Zhan Zhang

Controlling residual hydrogen gas in mass spectra during pulsed laser atom probe tomography

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 importan...

Authors: R. Prakash Kolli

Atomap: a new software tool for the automated analysis of atomic resolution images using two-dimensional Gaussian fitting

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,...

Authors: Magnus Nord, Per Erik Vullum, Ian MacLaren, Thomas Tybell and Randi Holmestad

Prospects for atomic resolution in-line holography for a 3D determination of atomic structures from single projections

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 exi...

Authors: F. -R. Chen, C. Kisielowski and D. Van Dyck

Nanosurveyor: a framework for real-time data processing

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.

Authors: Benedikt J. Daurer, Hari Krishnan, Talita Perciano, Filipe R. N. C. Maia, David A. Shapiro, James A. Sethian and Stefano Marchesini

Trace: a high-throughput tomographic reconstruction engine for large-scale datasets

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 gen...

Authors: Tekin Bicer, Doğa Gürsoy, Vincent De Andrade, Rajkumar Kettimuthu, William Scullin, Francesco De Carlo and Ian T. Foster

Efficient implementation of a local tomography reconstruction algorithm

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 arti...

Authors: Pierre Paleo and Alessandro Mirone

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows

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 ...

Authors: Francesco Brun, Lorenzo Massimi, Michela Fratini, Diego Dreossi, Fulvio Billé, Agostino Accardo, Roberto Pugliese and Alessia Cedola

Data systems for the Linac coherent light source

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 ...

Authors: 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 and A. Perazzo

Applying shot boundary detection for automated crystal growth analysis during in situ transmission electron microscope experiments

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 th...

Authors: W. A. Moeglein, R. Griswold, B. L. Mehdi, N. D. Browning and J. Teuton

Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT

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 rat...

Authors: Federica Marone, Alain Studer, Heiner Billich, Leonardo Sala and Marco Stampanoni

A distributed ASTRA toolbox

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...

Authors: Willem Jan Palenstijn, Jeroen Bédorf, Jan Sijbers and K. Joost Batenburg

Analyzing microtomography data with Python and the scikit-image library

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 ...

Authors: Emmanuelle Gouillart, Juan Nunez-Iglesias and Stéfan van der Walt

Improved tomographic reconstruction of large-scale real-world data by filter optimization

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 o...

Authors: Daniël M. Pelt and Vincent De Andrade

The MAX IV imaging concept

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 ...

Authors: Zdeněk Matěj, Rajmund Mokso, Krister Larsson, Vincent Hardion and Darren Spruce

Automatic software correction of residual aberrations in reconstructed HRTEM exit waves of crystalline samples

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 us...

Authors: Colin Ophus, Haider I Rasool, Martin Linck, Alex Zettl and Jim Ciston

Identifying local structural states in atomic imaging by computer vision

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 ...

Authors: Nouamane Laanait, Maxim Ziatdinov, Qian He and Albina Borisevich

Detecting structural variances of Co₃O₄ catalysts by controlling beam-induced sample alterations in the vacuum of a transmission electron microscope

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. Inv...

Authors: C. Kisielowski, H. Frei, P. Specht, I. D. Sharp, J. A. Haber and S. Helveg

Structural damage reduction in protected gold clusters by electron diffraction methods

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 irradiati...

Authors: Eduardo Ortega, Arturo Ponce, Ulises Santiago, Diego Alducin, Alfredo Benitez-Lara, Germán Plascencia-Villa and Miguel José-Yacamán

Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images

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...

Authors: James C. Bouwer, Thomas J. Deerinck, Eric Bushong, Vadim Astakhov, Ranjan Ramachandra, Steven T. Peltier and Mark H. Ellisman

HRTEM low dose: the unfold of the morphed graphene, from amorphous carbon to morphed graphenes

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 c...

Authors: H. A. Calderon, A. Okonkwo, I. Estrada-Guel, V. G. Hadjiev, F. Alvarez-Ramírez and F. C. Robles Hernández

Growth of dendritic nanostructures by liquid-cell transmission electron microscopy: a reflection of the electron-irradiation history

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 samp...

Authors: Nabeel Ahmad, Yann Le Bouar, Christian Ricolleau and Damien Alloyeau

3D reconstruction of biological structures: automated procedures for alignment and reconstruction of multiple tilt series in electron tomography

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...

Authors: Sébastien Phan, Daniela Boassa, Phuong Nguyen, Xiaohua Wan, Jason Lanman, Albert Lawrence and Mark H. Ellisman

Electron beam induced dehydrogenation of MgH₂ studied by VEELS

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...

Authors: Alexander Surrey, Ludwig Schultz and Bernd Rellinghaus

Dynamic scan control in STEM: spiral scans

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: radia...

Authors: Xiahan Sang, Andrew R. Lupini, Raymond R. Unocic, Miaofang Chi, Albina Y. Borisevich, Sergei V. Kalinin, Eirik Endeve, Richard K. Archibald and Stephen Jesse

Detecting magnetic ordering with atomic size electron probes

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 ...

Authors: Juan Carlos Idrobo, Ján Rusz, Jakob Spiegelberg, Michael A. McGuire, Christopher T. Symons, Ranga Raju Vatsavai, Claudia Cantoni and Andrew R. Lupini