A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations

Pelz, Philipp; Rakowski, Alexander; DaCosta, Luis Rangel; Savitzky, Benjamin H.; Scott, Mary; Ophus, Colin

doi:10.1017/s1431927621012083

Cited by 14 publications

(9 citation statements)

References 54 publications

(61 reference statements)

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“…STEM image simulations were performed by using the PRISM algorithm implemented in MATLAB with interpolation factor 4. − The probe was set to zero defocus at the entrance surface of the simulation cell. The projected potentials were calculated using a 3D lookup table method using the parameterized atomic potentials given in Kirkland .…”

Section: Methodsmentioning

confidence: 99%

Scanning Transmission Electron Microscopy in a Scanning Electron Microscope for the High-Throughput Imaging of Biological Assemblies

et al. 2022

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Electron microscopy of soft and biological materials, or "soft electron microscopy", is essential to the characterization of macromolecules. Soft microscopy is governed by enhancing contrast while maintaining low electron doses, and sample preparation and imaging methodologies are driven by the length scale of features of interest. While cryo-electron microscopy offers the highest resolution, larger structures can be characterized efficiently and with high contrast using low-voltage electron microscopy by performing scanning transmission electron microscopy in a scanning electron microscope (STEM-in-SEM). Here, STEM-in-SEM is demonstrated for a four-lobed protein assembly where the arrangement of the proteins in the construct must be examined. STEM image simulations show the theoretical contrast enhancement at SEM-level voltages for unstained structures, and experimental images with multiple STEM modes exhibit the resolution possible for negative-stained proteins. This technique can be extended to complex protein assemblies, larger structures such as cell sections, and hybrid materials, making STEM-in-SEM a valuable high-throughput imaging method.

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Section: Methodsmentioning

confidence: 99%

Scanning Transmission Electron Microscopy in a Scanning Electron Microscope for the High-Throughput Imaging of Biological Assemblies

et al. 2022

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“…This is particularly attractive in case of a large field of view. The accelerated speed is at the cost of accuracy [57,59,62]. However, when facing the ordering possibilities for each column multiplied by the number of columns that are potentially mixed, the PRISM algorithm can also be time consuming.…”

Section: Computational Complexity and Accuracymentioning

confidence: 99%

“…From these histograms it follows that most of the prediction errors are less than the scattering cross-section of single atoms. We do not compare the PRISM accuracy further in this paper as it has been discussed in several studies [57,59,62], which is highly dependent on the interpolation scheme. The interpolation factor of 20 used here corresponds to ∼10% error in PRISM as shown in [57].…”

Section: Computational Complexity and Accuracymentioning

confidence: 99%

Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions

Zhang¹,

Lobato²,

Backer³

et al. 2022

Preprint

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Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simu-1

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“…Some available packages are Hyperspy, py4DSTEM, LiberTEM, Pycroscopy, pixSTEM, and the Cornell Spectrum Imager plugin for ImageJ. 4D-STEM simulation software ( Pelz et al, 2021 ) is also critical component of analysis of 4D datasets.…”

Section: Linking Real and Reciprocal-space Information With 4d-stemmentioning

confidence: 99%

Probing Multiscale Disorder in Pyrochlore and Related Complex Oxides in the Transmission Electron Microscope: A Review

et al. 2021

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Transmission electron microscopy (TEM), and its counterpart, scanning TEM (STEM), are powerful materials characterization tools capable of probing crystal structure, composition, charge distribution, electronic structure, and bonding down to the atomic scale. Recent (S)TEM instrumentation developments such as electron beam aberration-correction as well as faster and more efficient signal detection systems have given rise to new and more powerful experimental methods, some of which (e.g., 4D-STEM, spectrum-imaging, in situ/operando (S)TEM)) facilitate the capture of high-dimensional datasets that contain spatially-resolved structural, spectroscopic, time- and/or stimulus-dependent information across the sub-angstrom to several micrometer length scale. Thus, through the variety of analysis methods available in the modern (S)TEM and its continual development towards high-dimensional data capture, it is well-suited to the challenge of characterizing isometric mixed-metal oxides such as pyrochlores, fluorites, and other complex oxides that reside on a continuum of chemical and spatial ordering. In this review, we present a suite of imaging and diffraction (S)TEM techniques that are uniquely suited to probe the many types, length-scales, and degrees of disorder in complex oxides, with a focus on disorder common to pyrochlores, fluorites and the expansive library of intermediate structures they may adopt. The application of these techniques to various complex oxides will be reviewed to demonstrate their capabilities and limitations in resolving the continuum of structural and chemical ordering in these systems.

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A Fast Algorithm for Scanning Transmission Electron Microscopy Imaging and 4D-STEM Diffraction Simulations

Abstract: Abstract

Cited by 14 publications

References 54 publications

Scanning Transmission Electron Microscopy in a Scanning Electron Microscope for the High-Throughput Imaging of Biological Assemblies

Scanning Transmission Electron Microscopy in a Scanning Electron Microscope for the High-Throughput Imaging of Biological Assemblies

Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions

Probing Multiscale Disorder in Pyrochlore and Related Complex Oxides in the Transmission Electron Microscope: A Review

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