Measuring Interatomic Bonding and Charge Redistributions in Defects by Combining 4D-STEM and STEM Multislice Simulations

Heimes, Damien; Belz, Jürgen; Beyer, Andreas; Volz, Kerstin

doi:10.1017/s1431927620014713

Cited by 2 publications

(2 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…All of the listed codes currently use the IAM to calculate the electrostatic potential, apart from the recently released abTEM code, which was built to directly support simulations with ab initio potentials through integration with the gpaw code. Heimes and co-workers also recently reported on the latter's upcoming integration with the STEMsalabim code [63].…”

Section: Simulation Of Electron Scatteringmentioning

confidence: 97%

$\textit{ab initio}$ description of bonding for transmission electron microscopy

Madsen,

Pennycook,

Susi

2020

Preprint

View full text Add to dashboard Cite

The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but model-based reconstructions in TEM are widely used across the physical and biological sciences. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and accurate, especially for annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We

show abstract

Section: Simulation Of Electron Scatteringmentioning

confidence: 97%

$\textit{ab initio}$ description of bonding for transmission electron microscopy

Madsen,

Pennycook,

Susi

2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Furthermore, 4D-STEM can be more dose-efficient than conventional STEM methods, and therefore can be used to study beam-sensitive targets (e.g., biological samples) (Pennycook et al, 2015(Pennycook et al, , 2019Yang et al, 2015aYang et al, , 2015bYang et al, , 2016Pelz et al, 2017;Zhou et al, 2020). Among various 4D-STEM techniques, atom-resolved in-focus 4D-STEM (Nguyen et al, 2016;Müller-Caspary et al, 2019;Heimes et al, 2020) has been particularly popular, since having a Z-contrast STEM signal simultaneously available usually helps to effectively extract information from the 4D-STEM dataset (Yang et al, 2016;Wen et al, 2019). Successful implementation of a 4D-STEM experiment requires establishing an accurate geometrical relationship (e.g., scaling, rotation, shearing) between the scanning positions on the sample plane and the diffraction patterns collected on the camera.…”

Section: Introductionmentioning

confidence: 99%

Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets

Ning

et al. 2022

Microsc Microanal

View full text Add to dashboard Cite

Accurate geometrical calibration between the scan coordinates and the camera coordinates is critical in four-dimensional scanning transmission electron microscopy (4D-STEM) for both quantitative imaging and ptychographic reconstructions. For atomic-resolved, in-focus 4D-STEM datasets, we propose a hybrid method incorporating two sub-routines, namely a J-matrix method and a Fourier method, which can calibrate the uniform affine transformation between the scan-camera coordinates using raw data, without a priori knowledge of the crystal structure of the specimen. The hybrid method is found robust against scan distortions and residual probe aberrations. It is also effective even when defects are present in the specimen, or the specimen becomes relatively thick. We will demonstrate that a successful geometrical calibration with the hybrid method will lead to a more reliable recovery of both the specimen and the electron probe in a ptychographic reconstruction. We will also show that, although the elimination of local scan position errors still requires an iterative approach, the rate of convergence can be improved, and the residual errors can be further reduced if the hybrid method can be firstly applied for initial calibration. The code is made available as a simple-to-use tool to correct affine transformations of the scan-camera coordinates in 4D-STEM experiments.

show abstract

Measuring Interatomic Bonding and Charge Redistributions in Defects by Combining 4D-STEM and STEM Multislice Simulations

Abstract: This is an Accepted Manuscript for the Microscopy and Microanalysis 2020 Proceedings. This version may be subject to change during the production process.

Cited by 2 publications

References 9 publications

$\textit{ab initio}$ description of bonding for transmission electron microscopy

$\textit{ab initio}$ description of bonding for transmission electron microscopy

Accurate and Robust Calibration of the Uniform Affine Transformation Between Scan-Camera Coordinates for Atom-Resolved In-Focus 4D-STEM Datasets

Contact Info

Product

Resources

About