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| Author | De wael, A.; De Backer, A.; Van Aert, S. | ||||
| Title | Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations | Type | A1 Journal article | ||
| Year | 2020 | Publication | Ultramicroscopy | Abbreviated Journal  |
Ultramicroscopy |
| Volume | 219 | Issue | Pages | 113131 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments. | ||||
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| Language | Wos | 000594770500003 | Publication Date | 2020-10-03 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. | Approved | Most recent IF: 2.2; 2020 IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:172449 | Serial | 6417 | ||
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| Author | De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S. | ||||
| Title | Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt | Type | A1 Journal article | ||
| Year | 2021 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | Issue | Pages | 113391 | ||
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt. | ||||
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| Language | Wos | 000704334200001 | Publication Date | 2021-09-24 | |
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.843 | Times cited | Open Access | OpenAccess | |
| Notes | This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp.; esteem3JRA; esteem3reported | Approved | Most recent IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:181462 | Serial | 6810 | ||
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| Author | Robert, Hl.; Lobato, I.; Lyu, Fj.; Chen, Q.; Van Aert, S.; Van Dyck, D.; Müller-Caspary, K. | ||||
| Title | Dynamical diffraction of high-energy electrons investigated by focal series momentum-resolved scanning transmission electron microscopy at atomic resolution | Type | A1 Journal article | ||
| Year | 2022 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | 233 | Issue | Pages | 113425 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab | ||||
| Abstract | We report a study of scattering dynamics in crystals employing momentum-resolved scanning transmission electron microscopy under varying illumination conditions. As we perform successive changes of the probe focus, multiple real-space signals are obtained in dependence of the shape of the incident electron wave. With support from extensive simulations, each signal is shown to be characterised by an optimum focus for which the contrast is maximum and which differs among different signals. For instance, a systematic focus mismatch is found between images formed by high-angle scattering, being sensitive to thickness and chemical composition, and the first moment in diffraction space, being sensitive to electric fields. It follows that a single recording at one specific probe focus is usually insufficient to characterise materials comprehensively. Most importantly, we demonstrate in experiment and simulation that the second moment ( |
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| Language | Wos | 000734396800009 | Publication Date | 2021-11-13 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | We thank Dr. Florian Winkler for valuable discussions and experimental work at the early stages of this study. This work was supported by the Initiative and Network Fund of the Helmholtz Association (Germany) under contracts VH-NG-1317 and ZT-I-0025. This project furthermore received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 770887). | Approved | Most recent IF: 2.2 | ||
| Call Number | EMAT @ emat @c:irua:184833 | Serial | 6898 | ||
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| Author | Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. | ||||
| Title | Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors | Type | A1 Journal article | ||
| Year | 2022 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | 242 | Issue | Pages | 113626 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
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| Language | Wos | 000873778100001 | Publication Date | 0000-00-00 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra | Approved | Most recent IF: 2.2 | ||
| Call Number | EMAT @ emat @c:irua:190925 | Serial | 7118 | ||
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| Author | Lobato, I.; De Backer, A.; Van Aert, S. | ||||
| Title | Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network | Type | A1 Journal article | ||
| Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | 251 | Issue | Pages | 113769 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag, Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS values for a wide range of input parameters that are commonly used for aberration-corrected transmission electron microscopes. |
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| Language | Wos | 001011617200001 | Publication Date | 2023-06-01 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. | Approved | Most recent IF: 2.2; 2023 IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:197275 | Serial | 8812 | ||
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| Author | Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S. | ||||
| Title | Atom counting from a combination of two ADF STEM images | Type | A1 Journal article | ||
| Year | 2024 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | 255 | Issue | Pages | 113859 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures. | ||||
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| Language | Wos | 001089064200001 | Publication Date | 2023-09-23 | |
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). | Approved | Most recent IF: 2.2; 2024 IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:201008 | Serial | 8964 | ||
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| Author | Şentürk, D.G.; De Backer, A.; Van Aert, S. | ||||
| Title | Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination | Type | A1 Journal Article | ||
| Year | 2024 | Publication | Ultramicroscopy | Abbreviated Journal |
Ultramicroscopy |
| Volume | 259 | Issue | Pages | 113941 | |
| Keywords | A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; | ||||
| Abstract | In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy. | ||||
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| Language | Wos | Publication Date | 2024-02-19 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). | Approved | Most recent IF: 2.2; 2024 IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:204353 | Serial | 8996 | ||
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| Author | Klingstedt, M.; Sundberg, M.; Eriksson, L.; Haigh, S.; Kirkland, A.; Grüner, D.; de Backer, A.; Van Aert, S.; Tarasaki, O. | ||||
| Title | Exit wave reconstruction from focal series of HRTEM images, single crystal XRD and total energy studies on SbxWO3+y (x\sim0.11) | Type | A1 Journal article | ||
| Year | 2012 | Publication | Zeitschrift für Kristallographie | Abbreviated Journal |
Z Krist-Cryst Mater |
| Volume | 227 | Issue | 6 | Pages | 341-349 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | A new tungsten bronze in the SbWO system has been prepared in a solid state reaction from Sb2O3, WO3 and W metal powder. The average structure was determined by single crystal X-ray diffraction. SbxWO3+y (x ∼ 0.11) crystallizes in the orthorhombic space group Pm21n (no. 31), a = 27.8135(9) Å, b = 7.3659(2) Å and c = 3.8672(1) Å. The structure belongs to the (n)-ITB class of intergrowth tungsten bronzes. It contains slabs of hexagonal channels formed by six WO6 octahedra. These slabs are separated by three layers of WO6 octahedra that are arranged in a WO3-type fashion. The WO6 octahedra share all vertices to build up a three-dimensional framework. The hexagonal channels are filled with Sb atoms to ∼80% and additional O atoms. The atoms are shifted out of the center of the channels. Exit-wave reconstruction of focal series of high resolution-transmission-electron-microscope (HRTEM) images combined with statistical paramäeter estimation techniques allowed to study local ordering in the channels. Sb atoms in neighbouring channels tend to be displaced in the same direction, which is in agreement with total energy calculations on ordered structure models, but the ratio of the occupation of the two possible Sb sites varies from channel to channel. The structure of SbxWO3+y exhibits pronounced local modulations. | ||||
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| Publisher | Place of Publication | München | Editor | ||
| Language | Wos | 000307314200003 | Publication Date | 2012-06-06 | |
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| ISSN | 2194-4946; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 3.179 | Times cited | 4 | Open Access | |
| Notes | Fwo; Esteem 026019 | Approved | Most recent IF: 3.179; 2012 IF: NA | ||
| Call Number | UA @ lucian @ c:irua:101218 | Serial | 1131 | ||
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