Pub Date : 2025-12-26DOI: 10.1016/j.ultramic.2025.114305
Dana O. Byrne , Stephanie M. Ribet , Demie Kepaptsoglou , Quentin M. Ramasse , Colin Ophus , Frances I. Allen
Tetravacancies in monolayer hexagonal boron nitride (hBN) with consistent edge termination (boron or nitrogen) form triangular nanopores with electrostatic potentials that can be leveraged for applications such as selective ion transport and neuromorphic computing. In order to quantitatively predict the properties of these structures, an atomic-level understanding of their local electronic and chemical environments is required. Moreover, robust methods for their precision manufacture are needed. Here we use electron irradiation in a scanning transmission electron microscope (STEM) at a high dose rate to drive the formation of boron-terminated tetravacancies in monolayer hBN. Characterization of the defects is achieved using aberration-corrected STEM, monochromated electron energy-loss spectroscopy (EELS), and electron ptychography. Z-contrast in STEM and chemical fingerprinting by core-loss EELS enable identification of the edge terminations, while electron ptychography gives insight into structural relaxation of the tetravacancies and provides evidence of enhanced electron density around the defect perimeters indicative of bonding effects.
{"title":"Fabrication and characterization of boron-terminated tetravacancies in monolayer hBN using STEM, EELS and electron ptychography","authors":"Dana O. Byrne , Stephanie M. Ribet , Demie Kepaptsoglou , Quentin M. Ramasse , Colin Ophus , Frances I. Allen","doi":"10.1016/j.ultramic.2025.114305","DOIUrl":"10.1016/j.ultramic.2025.114305","url":null,"abstract":"<div><div>Tetravacancies in monolayer hexagonal boron nitride (hBN) with consistent edge termination (boron or nitrogen) form triangular nanopores with electrostatic potentials that can be leveraged for applications such as selective ion transport and neuromorphic computing. In order to quantitatively predict the properties of these structures, an atomic-level understanding of their local electronic and chemical environments is required. Moreover, robust methods for their precision manufacture are needed. Here we use electron irradiation in a scanning transmission electron microscope (STEM) at a high dose rate to drive the formation of boron-terminated tetravacancies in monolayer hBN. Characterization of the defects is achieved using aberration-corrected STEM, monochromated electron energy-loss spectroscopy (EELS), and electron ptychography. Z-contrast in STEM and chemical fingerprinting by core-loss EELS enable identification of the edge terminations, while electron ptychography gives insight into structural relaxation of the tetravacancies and provides evidence of enhanced electron density around the defect perimeters indicative of bonding effects.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114305"},"PeriodicalIF":2.0,"publicationDate":"2025-12-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897877","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Scanning tunneling microscopy (STM) has significantly influenced the fields of nanoscience and nanotechnology. However, the tip effect and thermal drift cause loss and distortion of data in the STM images. Here, we propose a physics-guided optimization model for extracting STM imaging parameters, including tip shape, thermal drift, depth of field, current, and height. The model uses partial charge densities from density functional theory (DFT) simulation and works based on the mass comparison of experimental and simulated images using a two-dimensional Pearson correlation. Testing the model on Si(111)-7 × 7 reconstruction images provided higher than 96 % correlations for both biases. The fitting showed the highest correlation for only two bands in each image instead of the integration of all bands. Gaussian functions were used in the model to simulate the tip effect, which could recover 1.5-6 % of the lost data due to the blurring effect. Additionally, thermal drift was detected and corrected in the negative bias image, which could linearly distort the data by about 19 %. An important advantage of using this model is increasing the microscopy speed because there is no need to slow down the scanning process in microscopy experiments to evade thermal drift.
{"title":"A correlation-based optimization model to recover lost and distorted data from scanning tunneling microscopy images based on density functional theory","authors":"Ehsan Moradpur-Tari , Andreas Kyritsakis , Mohadeseh Karimkhah , Veronika Zadin","doi":"10.1016/j.ultramic.2025.114306","DOIUrl":"10.1016/j.ultramic.2025.114306","url":null,"abstract":"<div><div>Scanning tunneling microscopy (STM) has significantly influenced the fields of nanoscience and nanotechnology. However, the tip effect and thermal drift cause loss and distortion of data in the STM images. Here, we propose a physics-guided optimization model for extracting STM imaging parameters, including tip shape, thermal drift, depth of field, current, and height. The model uses partial charge densities from density functional theory (DFT) simulation and works based on the mass comparison of experimental and simulated images using a two-dimensional Pearson correlation. Testing the model on Si(111)-7 × 7 reconstruction images provided higher than 96 % correlations for both biases. The fitting showed the highest correlation for only two bands in each image instead of the integration of all bands. Gaussian functions were used in the model to simulate the tip effect, which could recover 1.5-6 % of the lost data due to the blurring effect. Additionally, thermal drift was detected and corrected in the negative bias image, which could linearly distort the data by about 19 %. An important advantage of using this model is increasing the microscopy speed because there is no need to slow down the scanning process in microscopy experiments to evade thermal drift.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114306"},"PeriodicalIF":2.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pixelated differential phase contrast (DPC) is a four-dimensional scanning transmission electron microscopy (4D-STEM) technique in which the position of the transmitted beam is tracked to reconstruct the electromagnetic fields of a sample. Although it can provide (semi-) quantitative information for a range of different applications, the measurements are greatly affected by the microscope’s optical and acquisition settings in terms of sensitivity, accuracy, and spatial resolution, particularly when measuring weak electric fields. Herein, we focus on the nano-beam 4D-STEM configuration and systematically study the way in which all the parameters typically selected by users for pixelated-DPC experiments influence the lowest achievable electric field sensitivity. First, we define the metric by which the sensitivity is assessed, discussing the optimal ranges for parameters including convergence semi-angle, electron dose, and camera length in absence of external field, while also evaluating the effect of the scanning system. Next, the sensitivity and its error are assessed under field-bound conditions, realized by a coplanar capacitor that allows the position of the transmitted beam to be shifted controllably using an external bias. Comparison of the experimental results with finite element method calculations yields quantitative information about the accuracy that can be attained for these measurements, while the effects of microscope drift and sample charging are also discussed. Our findings provide a platform for the quantitative assessment of weak electric fields as calculated by pixelated-DPC experiments, while highlighting the challenges associated with these measurements.
{"title":"Assessing the electric field sensitivity measured by pixelated differential phase contrast imaging in vacuum both in the absence of external fields and under field-bound conditions","authors":"Pierpaolo Ranieri , Reinis Ignatans , Victor Boureau , Vasiliki Tileli","doi":"10.1016/j.ultramic.2025.114307","DOIUrl":"10.1016/j.ultramic.2025.114307","url":null,"abstract":"<div><div>Pixelated differential phase contrast (DPC) is a four-dimensional scanning transmission electron microscopy (4D-STEM) technique in which the position of the transmitted beam is tracked to reconstruct the electromagnetic fields of a sample. Although it can provide (semi-) quantitative information for a range of different applications, the measurements are greatly affected by the microscope’s optical and acquisition settings in terms of sensitivity, accuracy, and spatial resolution, particularly when measuring weak electric fields. Herein, we focus on the nano-beam 4D-STEM configuration and systematically study the way in which all the parameters typically selected by users for pixelated-DPC experiments influence the lowest achievable electric field sensitivity. First, we define the metric by which the sensitivity is assessed, discussing the optimal ranges for parameters including convergence semi-angle, electron dose, and camera length in absence of external field, while also evaluating the effect of the scanning system. Next, the sensitivity and its error are assessed under field-bound conditions, realized by a coplanar capacitor that allows the position of the transmitted beam to be shifted controllably using an external bias. Comparison of the experimental results with finite element method calculations yields quantitative information about the accuracy that can be attained for these measurements, while the effects of microscope drift and sample charging are also discussed. Our findings provide a platform for the quantitative assessment of weak electric fields as calculated by pixelated-DPC experiments, while highlighting the challenges associated with these measurements.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114307"},"PeriodicalIF":2.0,"publicationDate":"2025-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-21DOI: 10.1016/j.ultramic.2025.114304
T. Ben Britton, Tianbi Zhang
We present a simple ‘shift and add’ based improvement in the angular resolution of single electron backscatter diffraction (EBSD) patterns. Sub-pixel image registration is used to measure the (sub-pixel) difference in projection parameters for patterns collected within a map, and then the pattern is shifted and added together. The resultant EBSD-pattern is shown to contain more angular information than a long-exposure single pattern, via 2D Fast Fourier Transform (FFT)-based analysis. In particular, this method has the potential to enhance the scope of small compact direct electron detectors (DEDs).
{"title":"Angular resolution enhancement of electron backscatter diffraction patterns","authors":"T. Ben Britton, Tianbi Zhang","doi":"10.1016/j.ultramic.2025.114304","DOIUrl":"10.1016/j.ultramic.2025.114304","url":null,"abstract":"<div><div>We present a simple ‘shift and add’ based improvement in the angular resolution of single electron backscatter diffraction (EBSD) patterns. Sub-pixel image registration is used to measure the (sub-pixel) difference in projection parameters for patterns collected within a map, and then the pattern is shifted and added together. The resultant EBSD-pattern is shown to contain more angular information than a long-exposure single pattern, via 2D Fast Fourier Transform (FFT)-based analysis. In particular, this method has the potential to enhance the scope of small compact direct electron detectors (DEDs).</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114304"},"PeriodicalIF":2.0,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145834867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-21DOI: 10.1016/j.ultramic.2025.114303
Francisco Fernandez-Canizares , Javier Rodriguez-Vazquez , Rafael V. Ferreira , Isabel Tenreiro , Alberto Rivera-Calzada , Amalia Fernando-Saavedra , Miguel A. Sanchez-Garcia , Yong Xie , Andres Castellanos-Gomez , Maria Varela , Gabriel Sánchez-Santolino
Automated atomic column detection and identification constitutes an active open front in advanced scanning transmission electron microscopy techniques. In this work we use clustering algorithms in combination with dimensionality reduction techniques to identify specific columns in a series of very different cutting-edge materials, ranging from ultrathin 2D materials to bulk semiconductors or complex oxides, which include different types of columns (heavy and light), and thus pose a challenge towards automated detection. By implementing a three-stage cascaded clustering pipeline, we are able to automatically identify all atomic column sites of our test materials and resolve them from the background interatomic space. This approach could enable new data-driven in-depth analysis of materials, allowing the automatic detection of chemical and structural characteristics of materials.
{"title":"Automated atomic site determination by four-dimensional scanning transmission electron microscopy data analytics","authors":"Francisco Fernandez-Canizares , Javier Rodriguez-Vazquez , Rafael V. Ferreira , Isabel Tenreiro , Alberto Rivera-Calzada , Amalia Fernando-Saavedra , Miguel A. Sanchez-Garcia , Yong Xie , Andres Castellanos-Gomez , Maria Varela , Gabriel Sánchez-Santolino","doi":"10.1016/j.ultramic.2025.114303","DOIUrl":"10.1016/j.ultramic.2025.114303","url":null,"abstract":"<div><div>Automated atomic column detection and identification constitutes an active open front in advanced scanning transmission electron microscopy techniques. In this work we use clustering algorithms in combination with dimensionality reduction techniques to identify specific columns in a series of very different cutting-edge materials, ranging from ultrathin 2D materials to bulk semiconductors or complex oxides, which include different types of columns (heavy and light), and thus pose a challenge towards automated detection. By implementing a three-stage cascaded clustering pipeline, we are able to automatically identify all atomic column sites of our test materials and resolve them from the background interatomic space. This approach could enable new data-driven in-depth analysis of materials, allowing the automatic detection of chemical and structural characteristics of materials.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114303"},"PeriodicalIF":2.0,"publicationDate":"2025-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145884241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-19DOI: 10.1016/j.ultramic.2025.114291
Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier
This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.
{"title":"Morphologies of caustics studied by catastrophe charged-particle optics","authors":"Tom Fraysse, Robin Cours, Hugo Lourenço-Martins, Florent Houdellier","doi":"10.1016/j.ultramic.2025.114291","DOIUrl":"10.1016/j.ultramic.2025.114291","url":null,"abstract":"<div><div>This paper explores the topologies of caustics observed in instruments that employ charged particles, such as electron and ion microscopes. These geometrical figures are studied here using catastrophe theory. The application of this geometrical theory to our optical situation has enabled us to analytically reproduce the behaviours of various caustics. The interest lies mainly in the universal nature of these results since our treatment requires no prior knowledge of the optical configuration, but only a smart definition of the control space. This universal approach has finally made it possible to extract mathematical relationships between the aberration coefficients of any optical system, which were hidden by the complexity of optical trajectories but revealed by the set of catastrophes in the control space. These results provide a glimpse for future applications of caustics in the development of new corrected optical systems, especially for ions-based devices.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"282 ","pages":"Article 114291"},"PeriodicalIF":2.0,"publicationDate":"2025-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145928659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-18DOI: 10.1016/j.ultramic.2025.114301
Nicolò M. Della Ventura , Kalani Moore , McLean P. Echlin , Matthew R. Begley , Tresa M. Pollock , Marc De Graef , Daniel S. Gianola
Accurate quantification of the energy distribution of backscattered electrons (BSEs) contributing to electron backscatter diffraction (EBSD) patterns remains as an active challenge. This study introduces an energy-resolved EBSD methodology based on a monolithic active pixel sensor direct electron detector and an electron-counting algorithm to enable the energy quantification of individual BSEs, providing direct measurements of electron energy spectra within diffraction patterns. Following detector calibration of the detector signal as a function of primary beam energy, measurements using a 12 keV primary beam on Si(100) reveal a broad BSE energy distribution across the diffraction pattern, extending down to 3 keV. Furthermore, an angular dependence in the weighted average BSE energy is observed, closely matching predictions from Monte Carlo simulations. Pixel-resolved energy maps reveal subtle modulations at Kikuchi band edges, offering insights into the backscattering process. By applying energy filtering within spectral windows as narrow as 2 keV centered on the primary beam energy, significant enhancement in pattern clarity and high-frequency detail is observed. Notably, BSEs in the 9–10 keV range dominate Kikuchi pattern formation, while BSEs in the 2–8 keV range, despite having undergone substantial energy loss, still produce Kikuchi patterns. By enabling energy determination at the single-electron level, this approach introduces a versatile tool-set for expanding the quantitative capabilities of EBSD, thereby offering the potential to deepen the understanding of diffraction contrast mechanisms and to advance the precision of crystallographic measurements.
{"title":"Energy-resolved EBSD using a monolithic direct electron detector","authors":"Nicolò M. Della Ventura , Kalani Moore , McLean P. Echlin , Matthew R. Begley , Tresa M. Pollock , Marc De Graef , Daniel S. Gianola","doi":"10.1016/j.ultramic.2025.114301","DOIUrl":"10.1016/j.ultramic.2025.114301","url":null,"abstract":"<div><div>Accurate quantification of the energy distribution of backscattered electrons (BSEs) contributing to electron backscatter diffraction (EBSD) patterns remains as an active challenge. This study introduces an energy-resolved EBSD methodology based on a monolithic active pixel sensor direct electron detector and an electron-counting algorithm to enable the energy quantification of individual BSEs, providing direct measurements of electron energy spectra within diffraction patterns. Following detector calibration of the detector signal as a function of primary beam energy, measurements using a 12 keV primary beam on Si(100) reveal a broad BSE energy distribution across the diffraction pattern, extending down to 3 keV. Furthermore, an angular dependence in the weighted average BSE energy is observed, closely matching predictions from Monte Carlo simulations. Pixel-resolved energy maps reveal subtle modulations at Kikuchi band edges, offering insights into the backscattering process. By applying energy filtering within spectral windows as narrow as 2 keV centered on the primary beam energy, significant enhancement in pattern clarity and high-frequency detail is observed. Notably, BSEs in the 9–10 keV range dominate Kikuchi pattern formation, while BSEs in the 2–8 keV range, despite having undergone substantial energy loss, still produce Kikuchi patterns. By enabling energy determination at the single-electron level, this approach introduces a versatile tool-set for expanding the quantitative capabilities of EBSD, thereby offering the potential to deepen the understanding of diffraction contrast mechanisms and to advance the precision of crystallographic measurements.</div></div>","PeriodicalId":23439,"journal":{"name":"Ultramicroscopy","volume":"281 ","pages":"Article 114301"},"PeriodicalIF":2.0,"publicationDate":"2025-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145791018","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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