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Author |
Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. |
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Title |
Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
170 |
Issue |
170 |
Pages |
128-138 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramer-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. |
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Address |
Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be |
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Language |
English |
Wos |
000386925500014 |
Publication Date |
2016-07-26 |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
6 |
Open Access |
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Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2 |
Approved |
Most recent IF: 2.843 |
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Call Number |
c:irua:135337 c:irua:135337 |
Serial |
4128 |
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Permanent link to this record |
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Author |
Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S. |
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Title |
Atom-counting in High Resolution Electron Microscopy: TEM or STEM – that's the question |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
174 |
Issue |
174 |
Pages |
112-120 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice. |
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Wos |
000403342200013 |
Publication Date |
2016-10-27 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
2 |
Open Access |
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Notes |
The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, G.0374.13N, and WO.010.16N) and a postdoctoral grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:137102 |
Serial |
4315 |
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Permanent link to this record |
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Author |
Gonnissen, J.; de Backer, A.; den Dekker, A.J.; Martinez, G.T.; Rosenauer, A.; Sijbers, J.; Van Aert, S. |
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Title |
Optimal experimental design for the detection of light atoms from high-resolution scanning transmission electron microscopy images |
Type |
A1 Journal article |
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Year |
2014 |
Publication |
Applied physics letters |
Abbreviated Journal |
Appl Phys Lett |
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Volume |
105 |
Issue |
6 |
Pages |
063116 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
We report an innovative method to explore the optimal experimental settings to detect light atoms from scanning transmission electron microscopy (STEM) images. Since light elements play a key role in many technologically important materials, such as lithium-battery devices or hydrogen storage applications, much effort has been made to optimize the STEM technique in order to detect light elements. Therefore, classical performance criteria, such as contrast or signal-to-noise ratio, are often discussed hereby aiming at improvements of the direct visual interpretability. However, when images are interpreted quantitatively, one needs an alternative criterion, which we derive based on statistical detection theory. Using realistic simulations of technologically important materials, we demonstrate the benefits of the proposed method and compare the results with existing approaches. |
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American Institute of Physics |
Place of Publication |
New York, N.Y. |
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Wos |
000341188700073 |
Publication Date |
2014-08-14 |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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ISSN |
0003-6951;1077-3118; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
3.411 |
Times cited |
12 |
Open Access |
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Notes |
FWO (G.0393.11; G.0064.10; and G.0374.13); European Union Seventh Framework Programme [FP7/2007-2013] under Grant Agreement No. 312483 (ESTEEM2); esteem2_jra2 |
Approved |
Most recent IF: 3.411; 2014 IF: 3.302 |
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Call Number |
UA @ lucian @ c:irua:118333 |
Serial |
2482 |
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Permanent link to this record |
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Author |
Gonnissen, J.; Batuk, D.; Nataf, G.F.; Jones, L.; Abakumov, A.M.; Van Aert, S.; Schryvers, D.; Salje, E.K.H. |
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Title |
Direct Observation of Ferroelectric Domain Walls in LiNbO3: Wall-Meanders, Kinks, and Local Electric Charges |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Advanced functional materials |
Abbreviated Journal |
Adv Funct Mater |
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Volume |
26 |
Issue |
26 |
Pages |
7599-7604 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
Direct observations of the ferroelectric domain boundaries in LiNbO3 are performed using high-resolution high-angle annular dark field scanning transmission electron microscopy imaging, revealing a very narrow width of the domain wall between the 180° domains. The domain walls demonstrate local side-way meandering, which results in inclinations even when the overall wall orientation follows the ferroelectric polarization. These local meanders contain kinks with “head-to-head” and “tail-to-tail” dipolar configurations and are therefore locally charged. The charged meanders are confined to a few cation layers along the polarization direction and are separated by longer stretches of straight domain walls. |
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Wos |
000388166700006 |
Publication Date |
2016-09-16 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1616-301X |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.124 |
Times cited |
23 |
Open Access |
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Notes |
J.G. acknowledges the support from the Research Foundation Flanders (FWO, Belgium) through various project fundings (G.0368.15N, G.0369.15N, and G.0374.13N), as well as the financial support from the European Union Seventh Framework Program (FP7/2007–2013) under Grant agreement no. 312483 (ESTEEM2). The authors thank J. Hadermann for useful suggestions on the interpretation of the HAADFSTEM images. E.K.H.S. thanks the EPSRC (EP/K009702/1) and the Leverhulme Trust (EM-2016-004) for support. G.F.N. thanks the National Research Fund, Luxembourg (FNR/P12/4853155/Kreisel) for support.; esteem2_jra2 |
Approved |
Most recent IF: 12.124 |
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Call Number |
c:irua:135336 c:irua:135336 |
Serial |
4129 |
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Permanent link to this record |
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Author |
Geuchies, J.J.; van Overbeek, C.; Evers, W.H.; Goris, B.; de Backer, A.; Gantapara, A.P.; Rabouw, F.T.; Hilhorst, J.; Peters, J.L.; Konovalov, O.; Petukhov, A.V.; Dijkstra, M.; Siebbeles, L.D.A.; van Aert, S.; Bals, S.; Vanmaekelbergh, D. |
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Title |
In situ study of the formation mechanism of two-dimensional superlattices from PbSe nanocrystals |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Nature materials |
Abbreviated Journal |
Nat Mater |
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Volume |
15 |
Issue |
15 |
Pages |
1248-1254 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Oriented attachment of PbSe nanocubes can result in the formation of two-dimensional (2D) superstructures with long-range nanoscale and atomic order. This questions the applicability of classic models in which the superlattice grows by first forming a nucleus, followed by sequential irreversible attachment of nanocrystals, as one misaligned attachment would disrupt the 2D order beyond repair. Here, we demonstrate the formation mechanism of 2D PbSe superstructures with square geometry by using in situ grazing-incidence X-ray scattering (small angle and wide angle), ex situ electron microscopy, and Monte Carlo simulations. We observed nanocrystal adsorption at the liquid/gas interface, followed by the formation of a hexagonal nanocrystal monolayer. The hexagonal geometry transforms gradually through a pseudo-hexagonal phase into a phase with square order, driven by attractive interactions between the {100} planes perpendicular to the liquid substrate, which maximize facet-to-facet overlap. The nanocrystals then attach atomically via a necking process, resulting in 2D square superlattices. |
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Address |
Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands |
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Language |
English |
Wos |
000389104400011 |
Publication Date |
2016-09-05 |
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Abbreviated Series Title |
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Series Issue |
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Edition |
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ISSN |
1476-1122 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
39.737 |
Times cited |
182 |
Open Access |
OpenAccess |
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Notes |
This research is part of the programme ‘Designing Dirac Carriers in semiconductor honeycomb superlattices (DDC13),’ which is supported by the Foundation for Fundamental Research on Matter (FOM), which is part of the Dutch Research Council (NWO). J.J.G. acknowledges funding from the Debye and ESRF Graduate Programs. The authors gratefully acknowledge funding from the Research Foundation Flanders (G.036915 G.037413 and funding of postdoctoral grants to B.G. and A.d.B). S.B. acknowledges the European Research Council, ERC grant No 335078—Colouratom. The authors gratefully acknowledge I. Swart and M. van Huis for fruitful discussions. We acknowledge funding from NWO-CW TOPPUNT ‘Superficial Superstructures’. The X-ray scattering measurements were performed at the ID10 beamline at ESRF under proposal numbers SC-4125 and SC-3786. The authors thank G. L. Destri and F. Zontone for their support during the experiments.; ECAS_Sara; (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); |
Approved |
Most recent IF: 39.737 |
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Call Number |
EMAT @ emat @ c:irua:136165 |
Serial |
4289 |
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Permanent link to this record |
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Author |
Gauquelin, N.; van den Bos, K.H.W.; Béché, A.; Krause, F.F.; Lobato, I.; Lazar, S.; Rosenauer, A.; Van Aert, S.; Verbeeck, J. |
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Title |
Determining oxygen relaxations at an interface: A comparative study between transmission electron microscopy techniques |
Type |
A1 Journal article |
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Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
181 |
Issue |
181 |
Pages |
178-190 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Nowadays, aberration corrected transmission electron microscopy (TEM) is a popular method to characterise nanomaterials at the atomic scale. Here, atomically resolved images of nanomaterials are acquired, where the contrast depends on the illumination, imaging and detector conditions of the microscope. Visualization of light elements is possible when using low angle annular dark field (LAADF) STEM, annular bright field (ABF) STEM, integrated differential phase contrast (iDPC) STEM, negative spherical aberration imaging (NCSI) and imaging STEM (ISTEM). In this work, images of a NdGaO3-La0.67Sr0.33MnO3 (NGO-LSMO) interface are quantitatively evaluated by using statistical parameter estimation theory. For imaging light elements, all techniques are providing reliable results, while the techniques based on interference contrast, NCSI and ISTEM, are less robust in terms of accuracy for extracting heavy column locations. In term of precision, sample drift and scan distortions mainly limits the STEM based techniques as compared to NCSI. Post processing techniques can, however, partially compensate for this. In order to provide an outlook to the future, simulated images of NGO, in which the unavoidable presence of Poisson noise is taken into account, are used to determine the ultimate precision. In this future counting noise limited scenario, NCSI and ISTEM imaging will provide more precise values as compared to the other techniques, which can be related to the mechanisms behind the image recording. |
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Wos |
000411170800022 |
Publication Date |
2017-06-03 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
34 |
Open Access |
OpenAccess |
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Notes |
The authors acknowledge financial support from Flanders (FWO, Belgium) through project fundings (G.0044.13N, G.0374.13N, G.0368.15N, G.0369.15N), and by a Ph.D. grant to K.H.W.v.d.B. The Qu-Ant-EM microscope used for this study was partly funded by the Hercules fund from the Flemish Government. A.B. and N.G. acknowledge the EUROTAPES project (FP7-NMP.2011.2.2-1 Grant no.280432) which partly funded this study. N.G., A.B. and J.V. acknowledge funding from the European Research Council under the 7th Framework Program (FP7), ERC Starting Grant 278510 VORTEX. The research leading to these results has received funding from the Deutsche Forschungsgemeinschaft under Contract No. RO 2057/4-2 and the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2. We thank Prof. G. Koster from the University of Twente for kindly providing us with the LSMO-NGO test sample. |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:144435UA @ admin @ c:irua:144435 |
Serial |
4620 |
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Permanent link to this record |
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Author |
Friedrich, T.; Yu, C.-P.; Verbeek, J.; Pennycook, T.; Van Aert, S. |
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Title |
Phase retrieval from 4-dimensional electron diffraction datasets |
Type |
P1 Proceeding |
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Year |
2021 |
Publication |
Proceedings
T2 – IEEE International Conference on Image Processing (ICIP), SEP 19-22, 2021, Electr. network |
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Volume |
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Issue |
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Pages |
3453-3457 |
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Keywords |
P1 Proceeding; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
We present a computational imaging mode for large scale electron microscopy data, which retrieves a complex wave from noisy/sparse intensity recordings using a deep learning approach and subsequently reconstructs an image of the specimen from the Convolutional Neural Network (CNN) predicted exit waves. We demonstrate that an appropriate forward model in combination with open data frameworks can be used to generate large synthetic datasets for training. In combination with augmenting the data with Poisson noise corresponding to varying dose-values, we effectively eliminate overfitting issues. The U-NET[1] based architecture of the CNN is adapted to the task at hand and performs well while maintaining a relatively small size and fast performance. The validity of the approach is confirmed by comparing the reconstruction to well-established methods using simulated, as well as real electron microscopy data. The proposed method is shown to be effective particularly in the low dose range, evident by strong suppression of noise, good spatial resolution, and sensitivity to different atom types, enabling the simultaneous visualisation of light and heavy elements and making different atomic species distinguishable. Since the method acts on a very local scale and is comparatively fast it bears the potential to be used for near-real-time reconstruction during data acquisition. |
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Wos |
000819455103114 |
Publication Date |
2021-08-23 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
978-1-6654-4115-5 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
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Times cited |
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Open Access |
OpenAccess |
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Notes |
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Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:189462 |
Serial |
7089 |
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Permanent link to this record |
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Author |
Friedrich, T.; Yu, C.-P.; Verbeeck, J.; Van Aert, S. |
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Title |
Phase object reconstruction for 4D-STEM using deep learning |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
Microscopy and microanalysis |
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Volume |
29 |
Issue |
1 |
Pages |
395-407 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
In this study, we explore the possibility to use deep learning for the reconstruction of phase images from 4D scanning transmission electron microscopy (4D-STEM) data. The process can be divided into two main steps. First, the complex electron wave function is recovered for a convergent beam electron diffraction pattern (CBED) using a convolutional neural network (CNN). Subsequently, a corresponding patch of the phase object is recovered using the phase object approximation. Repeating this for each scan position in a 4D-STEM dataset and combining the patches by complex summation yields the full-phase object. Each patch is recovered from a kernel of 3x3 adjacent CBEDs only, which eliminates common, large memory requirements and enables live processing during an experiment. The machine learning pipeline, data generation, and the reconstruction algorithm are presented. We demonstrate that the CNN can retrieve phase information beyond the aperture angle, enabling super-resolution imaging. The image contrast formation is evaluated showing a dependence on the thickness and atomic column type. Columns containing light and heavy elements can be imaged simultaneously and are distinguishable. The combination of super-resolution, good noise robustness, and intuitive image contrast characteristics makes the approach unique among live imaging methods in 4D-STEM. |
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Corporate Author |
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Wos |
001033590800038 |
Publication Date |
2023-01-12 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1431-9276 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.8 |
Times cited |
1 |
Open Access |
OpenAccess |
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Notes |
We acknowledge funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement no. 770887 PICOMETRICS) and funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 823717 ESTEEM3. J.V. and S.V.A acknowledge funding from the University of Antwerp through a TOP BOF project. The direct electron detector (Merlin, Medipix3, Quantum Detectors) was funded by the Hercules fund from the Flemish Government. This work was supported by the FWO and FNRS within the 2Dto3D project of the EOS program (grant number 30489208). |
Approved |
Most recent IF: 2.8; 2023 IF: 1.891 |
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Call Number |
UA @ admin @ c:irua:198221 |
Serial |
8912 |
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Permanent link to this record |
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Author |
Fatermans, J.; Van Aert, S.; den Dekker, A.J. |
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Title |
The maximum a posteriori probability rule for atom column detection from HAADF STEM images |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
201 |
Issue |
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Pages |
81-91 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
Recently, the maximum a posteriori (MAP) probability rule has been proposed as an objective and quantitative method to detect atom columns and even single atoms from high-resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images. The method combines statistical parameter estimation and model-order selection using a Bayesian framework and has been shown to be especially useful for the analysis of the structure of beam-sensitive nanomaterials. In order to avoid beam damage, images of such materials are usually acquired using a limited incoming electron dose resulting in a low contrast-to-noise ratio (CNR) which makes visual inspection unreliable. This creates a need for an objective and quantitative approach. The present paper describes the methodology of the MAP probability rule, gives its step-by-step derivation and discusses its algorithmic implementation for atom column detection. In addition, simulation results are presented showing that the performance of the MAP probability rule to detect the correct number of atomic columns from HAADF STEM images is superior to that of other model-order selection criteria, including the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Moreover, the MAP probability rule is used as a tool to evaluate the relation between STEM image quality measures and atom detectability resulting in the introduction of the so-called integrated CNR (ICNR) as a new image quality measure that better correlates with atom detectability than conventional measures such as signal-to-noise ratio (SNR) and CNR. |
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Wos |
000466343800009 |
Publication Date |
2019-02-04 |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
1 |
Open Access |
OpenAccess |
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Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (No. W.O.010.16N, No. G.0368.15N, No. G.0502.18N). This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant Agreement No. 770887). |
Approved |
Most recent IF: 2.843 |
|
|
Call Number |
EMAT @ emat @UA @ admin @ c:irua:157176 |
Serial |
5153 |
|
Permanent link to this record |
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|
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Author |
Fatermans, J.; Romolini, G.; Altantzis, T.; Hofkens, J.; Roeffaers, M.B.J.; Bals, S.; Van Aert, S. |
|
|
Title |
Atomic-scale detection of individual lead clusters confined in Linde Type A zeolites |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Nanoscale |
Abbreviated Journal |
Nanoscale |
|
|
Volume |
|
Issue |
|
Pages |
|
|
|
Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) |
|
|
Abstract |
Structural analysis of metal clusters confined in nanoporous materials is typically performed by X-ray-driven techniques. Although X-ray analysis has proved its strength in the characterization of metal clusters, it provides averaged structural information. Therefore, we here present an alternative workflow for bringing the characterization of confined metal clusters towards the local scale. This workflow is based on the combination of aberration-corrected transmission electron microscopy (TEM), TEM image simulations, and powder X-ray diffraction (XRD) with advanced statistical techniques. In this manner, we were able to characterize the clustering of Pb atoms in Linde Type A (LTA) zeolites with Pb loadings as low as 5 wt%. Moreover, individual Pb clusters could be directly detected. The proposed methodology thus enables a local-scale characterization of confined metal clusters in zeolites. This is important for further elucidation of the connection between the structure and the physicochemical properties of such systems. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000809619900001 |
Publication Date |
0000-00-00 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
2040-3364 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
|
Impact Factor |
6.7 |
Times cited |
2 |
Open Access |
OpenAccess |
|
|
Notes |
The authors acknowledge the Research Foundation Flanders through project fundings (FWO, G026718N, G050218N, ZW15_09-G0H6316N, and W002221N) and through a PhD scholarship to G.R. (grant 11C6920N), as well as iBOF-21-085 PERSIST. T.A. and S.V.A. acknowledge funding from the University of Antwerp Research fund (BOF). J.H. acknowledges the Flemish government through long-term structural funding Methusalem (CASAS2, Meth/15/04) and the MPI as MPI fellow. M.R. acknowledges funding by the KU Leuven Research Fund (C14/19/079). S.B. and S.V.A. acknowledge funding from the European Research Council under the European Union’s Horizon 2020 research and innovation program (ERC Consolidator Grants No. 815128−REALNANO and No. 770887−PICOMETRICS). The authors thank Dr. D. Chernyshov for the collection of XRD measurements. |
Approved |
Most recent IF: 6.7 |
|
|
Call Number |
EMAT @ emat @c:irua:189061 |
Serial |
7076 |
|
Permanent link to this record |
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Author |
Fatermans, J.; den Dekker, Aj.; Müller-Caspary, K.; Gauquelin, N.; Verbeeck, J.; Van Aert, S. |
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|
Title |
Atom column detection from simultaneously acquired ABF and ADF STEM images |
Type |
A1 Journal article |
|
Year |
2020 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
|
Volume |
219 |
Issue |
|
Pages |
113046 |
|
|
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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|
Abstract |
In electron microscopy, the maximum a posteriori (MAP) probability rule has been introduced as a tool to determine the most probable atomic structure from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images exhibiting low contrast-to-noise ratio (CNR). Besides ADF imaging, STEM can also be applied in the annular bright-field (ABF) regime. The ABF STEM mode allows to directly visualize light-element atomic columns in the presence of heavy columns. Typically, light-element nanomaterials are sensitive to the electron beam, limiting the incoming electron dose in order to avoid beam damage and leading to images exhibiting low CNR. Therefore, it is of interest to apply the MAP probability rule not only to ADF STEM images, but to ABF STEM images as well. In this work, the methodology of the MAP rule, which combines statistical parameter estimation theory and model-order selection, is extended to be applied to simultaneously acquired ABF and ADF STEM images. For this, an extension of the commonly used parametric models in STEM is proposed. Hereby, the effect of specimen tilt has been taken into account, since small tilts from the crystal zone axis affect, especially, ABF STEM intensities. Using simulations as well as experimental data, it is shown that the proposed methodology can be successfully used to detect light elements in the presence of heavy elements. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000594768500005 |
Publication Date |
2020-06-01 |
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Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.2 |
Times cited |
9 |
Open Access |
OpenAccess |
|
|
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (No. W.O.010.16N, No. G.0368.15N, No. G.0502.18N, EOS 30489208). 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). The authors acknowledge funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 823717 – ESTEEM3. The direct electron detector (Medipix3, Quantum Detectors) was funded by the Hercules fund from the Flemish Government. K. M. C. acknowledges funding from the Initiative and Network Fund of the Helmholtz Association (Germany) under contract VH-NG-1317. The authors thank Mark Huijben from the University of Twente (Enschede, The Netherlands) for providing the LiMn2O4 sample used in section 4.2 of this study. N. G., J. V., and S. V. A. acknowledge funding from the University of Antwerp through the Concerted Research Actions (GOA) project Solarpaint and the TOP project. |
Approved |
Most recent IF: 2.2; 2020 IF: 2.843 |
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|
Call Number |
EMAT @ emat @c:irua:169706 |
Serial |
6373 |
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Permanent link to this record |
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Author |
Fatermans, J.; den Dekker, A. J.; Müller-Caspary, K.; Lobato, I.; O’Leary, C. M.; Nellist, P. D.; Van Aert, S. |
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Title |
Single Atom Detection from Low Contrast-to-Noise Ratio Electron Microscopy Images |
Type |
A1 Journal article |
|
Year |
2018 |
Publication |
Physical review letters |
Abbreviated Journal |
Phys Rev Lett |
|
|
Volume |
121 |
Issue |
5 |
Pages |
056101 |
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|
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
Single atom detection is of key importance to solving a wide range of scientific and technological problems. The strong interaction of electrons with matter makes transmission electron microscopy one of the most promising techniques. In particular, aberration correction using scanning transmission electron microscopy has made a significant step forward toward detecting single atoms. However, to overcome radiation damage, related to the use of high-energy electrons, the incoming electron dose should be kept low enough. This results in images exhibiting a low signal-to-noise ratio and extremely weak contrast, especially for light-element nanomaterials. To overcome this problem, a combination of physics-based model fitting and the use of a model-order selection method is proposed, enabling one to detect single atoms with high reliability. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000440143200007 |
Publication Date |
2018-07-30 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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ISSN |
0031-9007 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.462 |
Times cited |
6 |
Open Access |
OpenAccess |
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|
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Project fundings (No. WO.010.16N, No. G.0368.15N, No. G.0502.18N). The authors are grateful to M. Van Bael and P. Lievens (KU Leuven) and to L. M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (Grant Agreement No. 770887). |
Approved |
Most recent IF: 8.462 |
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Call Number |
EMAT @ emat @c:irua:152819 |
Serial |
5004 |
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Permanent link to this record |
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Author |
Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S. |
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Title |
Atom column detection |
Type |
H2 Book chapter |
|
Year |
2021 |
Publication |
Advances in imaging and electron physics
T2 – Advances in imaging and electron physics |
Abbreviated Journal |
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Volume |
|
Issue |
|
Pages |
177-214 |
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Keywords |
H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
By combining statistical parameter estimation and model-order selection using a Bayesian framework, the maximum a posteriori (MAP) probability rule is proposed in this chapter as an objective and quantitative method to detect atom columns from high-resolution scanning transmission electron microscopy (HRSTEM) images. The validity and usefulness of this approach is demonstrated to both simulated and experimental annular dark-field (ADF) STEM images, but also to simultaneously acquired annular bright-field (ABF) and ADF STEM image data. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
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Publication Date |
2021-03-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
217 |
Series Issue |
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Edition |
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ISSN |
|
ISBN |
978-0-12-824607-8; 1076-5670 |
Additional Links |
UA library record |
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Impact Factor |
|
Times cited |
|
Open Access |
Not_Open_Access |
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Notes |
ERC Consolidator project funded by the European Union grant #770887 Picometrics |
Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:177531 |
Serial |
6775 |
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Permanent link to this record |
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Author |
Fatermans, J.; de Backer, A.; den Dekker, A.J.; Van Aert, S. |
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Title |
Image-quality evaluation and model selection with maximum a posteriori probability |
Type |
H2 Book chapter |
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Year |
2021 |
Publication |
Advances in imaging and electron physics
T2 – Advances in imaging and electron physics |
Abbreviated Journal |
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Volume |
|
Issue |
|
Pages |
215-242 |
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Keywords |
H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
The maximum a posteriori (MAP) probability rule for atom column detection can also be used as a tool to evaluate the relation between scanning transmission electron microscopy (STEM) image quality and atom detectability. In this chapter, a new image-quality measure is proposed that correlates well with atom detectability, namely the integrated contrast-to-noise ratio (ICNR). Furthermore, the working principle of the MAP probability rule is described in detail showing a close relation to the principles of model-selection methods. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
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Publication Date |
2021-03-06 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
217 |
Series Issue |
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Edition |
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ISSN |
|
ISBN |
978-0-12-824607-8; 1076-5670 |
Additional Links |
UA library record |
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Impact Factor |
|
Times cited |
|
Open Access |
Not_Open_Access |
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|
Notes |
ERC Consolidator project funded by the European Union grant #770887 Picometrics |
Approved |
Most recent IF: NA |
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Call Number |
UA @ admin @ c:irua:177532 |
Serial |
6782 |
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Permanent link to this record |
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Author |
Egoavil, R.; Gauquelin, N.; Martinez, G.T.; Van Aert, S.; Van Tendeloo, G.; Verbeeck, J. |
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Title |
Atomic resolution mapping of phonon excitations in STEM-EELS experiments |
Type |
A1 Journal article |
|
Year |
2014 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
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Volume |
147 |
Issue |
|
Pages |
1-7 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Atomically resolved electron energy-loss spectroscopy experiments are commonplace in modern aberration-corrected transmission electron microscopes. Energy resolution has also been increasing steadily with the continuous improvement of electron monochromators. Electronic excitations however are known to be delocalized due to the long range interaction of the charged accelerated electrons with the electrons in a sample. This has made several scientists question the value of combined high spatial and energy resolution for mapping interband transitions and possibly phonon excitation in crystals. In this paper we demonstrate experimentally that atomic resolution information is indeed available at very low energy losses around 100 meV expressed as a modulation of the broadening of the zero loss peak. Careful data analysis allows us to get a glimpse of what are likely phonon excitations with both an energy loss and gain part. These experiments confirm recent theoretical predictions on the strong localization of phonon excitations as opposed to electronic excitations and show that a combination of atomic resolution and recent developments in increased energy resolution will offer great benefit for mapping phonon modes in real space. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000343157400001 |
Publication Date |
2014-05-29 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
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ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
2.843 |
Times cited |
22 |
Open Access |
|
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|
Notes |
246102 IFOX; 278510 VORTEX; 246791 COUNTATOMS; Hercules; 312483 ESTEEM2; esteem2jra3 ECASJO; |
Approved |
Most recent IF: 2.843; 2014 IF: 2.436 |
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Call Number |
UA @ lucian @ c:irua:118332UA @ admin @ c:irua:118332 |
Serial |
177 |
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Permanent link to this record |
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Author |
Dunin-Borkowski, R.E.; Lichte, H.; Tillmann, K.; Van Aert, S.; Van Tendeloo, G. |
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Title |
Introduction to a special issue in honour of W. Owen Saxton, David J. Smith and Dirk Van Dyck on the occasion of their 65th birthdays |
Type |
Editorial |
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Year |
2013 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
134 |
Issue |
|
Pages |
1-1 |
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Keywords |
Editorial; Electron microscopy for materials research (EMAT) |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
Elsevier science bv |
Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000324474900001 |
Publication Date |
2013-07-24 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
2.843 |
Times cited |
1 |
Open Access |
|
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|
Notes |
|
Approved |
Most recent IF: 2.843; 2013 IF: 2.745 |
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Call Number |
UA @ lucian @ c:irua:109917 |
Serial |
1721 |
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Permanent link to this record |
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Author |
den Dekker, A.J.; Van Aert, S.; van Dyck, D.; van den Bos, A.; Geuens, P. |
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Title |
Does a monochromator improve the precision in quantitative HRTEM? |
Type |
A1 Journal article |
|
Year |
2001 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
89 |
Issue |
|
Pages |
275-290 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000172667000004 |
Publication Date |
2002-07-25 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
|
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ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
2.843 |
Times cited |
22 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.843; 2001 IF: 1.890 |
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Call Number |
UA @ lucian @ c:irua:47518 |
Serial |
746 |
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Permanent link to this record |
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Author |
den Dekker, A.J.; Van Aert, S.; van den Bos, A.; van Dyck, D. |
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Title |
Maximum likelihood estimation of structure parameters from high resolution electron microscopy images: part 1: a theoretical framework |
Type |
A1 Journal article |
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Year |
2005 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
104 |
Issue |
2 |
Pages |
83-106 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000230526400001 |
Publication Date |
2005-04-09 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
|
Series Issue |
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Edition |
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ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
2.843 |
Times cited |
70 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.843; 2005 IF: 2.490 |
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Call Number |
UA @ lucian @ c:irua:57229 |
Serial |
1959 |
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Permanent link to this record |
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Author |
den Dekker, A.J.; Gonnissen, J.; de Backer, A.; Sijbers, J.; Van Aert, S. |
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Title |
Estimation of unknown structure parameters from high-resolution (S)TEM images : what are the limits? |
Type |
A1 Journal article |
|
Year |
2013 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
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Volume |
134 |
Issue |
|
Pages |
34-43 |
|
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
Statistical parameter estimation theory is proposed as a quantitative method to measure unknown structure parameters from electron microscopy images. Images are then purely considered as data planes from which structure parameters have to be determined as accurately and precisely as possible using a parametric statistical model of the observations. For this purpose, an efficient algorithm is proposed for the estimation of atomic column positions and intensities from high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. Furthermore, the so-called CramérRao lower bound (CRLB) is reviewed to determine the limits to the precision with which continuous parameters such as atomic column positions and intensities can be estimated. Since this lower bound can only be derived for continuous parameters, alternative measures using the principles of detection theory are introduced for problems concerning the estimation of discrete parameters such as atomic numbers. An experimental case study is presented to show the practical use of these measures for the optimization of the experiment design if the purpose is to decide between the presence of specific atom types using STEM images. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000324474900006 |
Publication Date |
2013-06-01 |
|
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Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
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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 |
31 |
Open Access |
|
|
|
Notes |
FWO; FP 2007-2013; Esteem2; esteem2_jra2 |
Approved |
Most recent IF: 2.843; 2013 IF: 2.745 |
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|
Call Number |
UA @ lucian @ c:irua:109240 |
Serial |
1083 |
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Permanent link to this record |
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Author |
Delfino, C.L.; Hao, Y.; Martin, C.; Minoia, A.; Gopi, E.; Mali, K.S.; Van der Auweraer, M.; Geerts, Y.H.; Van Aert, S.; Lazzaroni, R.; De Feyter, S. |
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Title |
Conformation-Dependent Monolayer and Bilayer Structures of an Alkylated TTF Derivative Revealed using STM and Molecular Modeling |
Type |
A1 Journal Article |
|
Year |
2023 |
Publication |
The Journal of Physical Chemistry C |
Abbreviated Journal |
J. Phys. Chem. C |
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Volume |
127 |
Issue |
47 |
Pages |
23023-23033 |
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Keywords |
A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; |
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Abstract |
In this study, the multi-layer self-assembled molecular network formation of an alkylated tetrathiafulvalene compound is studied at the liquid-solid interface between 1-phenyloctane and graphite. A combined theoretical/experimental approach associating force-field and quantum-chemical calculations with scanning tunnelling microscopy is used to determine the two-dimensional self-assembly beyond the monolayer, but also to further the understanding of the molecular adsorption conformation and its impact on the molecular packing within the assemblies at the monolayer and bilayer level. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
001111637100001 |
Publication Date |
2023-11-30 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
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ISSN |
1932-7447 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
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Impact Factor |
3.7 |
Times cited |
|
Open Access |
OpenAccess |
|
|
Notes |
Financial support from the Research Foundation-Flanders (FWO G081518N, G0A3220N) and KU Leuven–Internal Funds (C14/19/079) is acknowledged. This work was in part supported by FWO and F. R. S.-FNRS under the Excellence of Science EOS program (project 30489208 and 40007495). C.M. acknowledges the financial support: Grants PID2021-128761OA-C22 and CNS2022-136052 funded by MCIN/AEI/10.13039/501100011033 by the “European Union” and SBPLY/21/180501/000127 funded by JCCM and by the EU through “Fondo Europeo de Desarollo Regional” (FEDER). Research in Mons is also supported by the Belgian National Fund for Scientific Research (FRS-FNRS) within the Consortium des Équipements de Calcul Intensif – CÉCI, under Grant 2.5020.11, and by the Walloon Region (ZENOBE Tier-1 supercomputer, under grant 1117545). |
Approved |
Most recent IF: 3.7; 2023 IF: 4.536 |
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Call Number |
EMAT @ emat @c:irua:201671 |
Serial |
8974 |
|
Permanent link to this record |
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Author |
De wael, A.; De Backer, A.; Yu, C.-P.; Sentürk, D.G.; Lobato, I.; Faes, C.; Van Aert, S. |
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|
Title |
Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
Microscopy and microanalysis |
Abbreviated Journal |
Microsc Microanal |
|
|
Volume |
|
Issue |
|
Pages |
1-9 |
|
|
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
|
|
Abstract |
A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000854930500001 |
Publication Date |
2022-09-19 |
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Series Editor |
|
Series Title |
|
Abbreviated Series Title |
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|
Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
1431-9276 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
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|
Impact Factor |
2.8 |
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. The authors are grateful to L.M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.8 |
|
|
Call Number |
EMAT @ emat @c:irua:190585 |
Serial |
7119 |
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Permanent link to this record |
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|
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Author |
De wael, A.; De Backer, A.; Van Aert, S. |
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|
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 |
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|
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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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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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000594770500003 |
Publication Date |
2020-10-03 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
|
|
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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|
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 |
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Call Number |
EMAT @ emat @c:irua:172449 |
Serial |
6417 |
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Permanent link to this record |
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Author |
De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S. |
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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 |
|
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Volume |
|
Issue |
|
Pages |
113391 |
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|
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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|
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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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000704334200001 |
Publication Date |
2021-09-24 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
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Series Volume |
|
Series Issue |
|
Edition |
|
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ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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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 |
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|
Call Number |
EMAT @ emat @c:irua:181462 |
Serial |
6810 |
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Permanent link to this record |
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Author |
De wael, A.; De Backer, A.; Jones, L.; Varambhia, A.; Nellist, P.D.; Van Aert, S. |
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Title |
Measuring Dynamic Structural Changes of Nanoparticles at the Atomic Scale Using Scanning Transmission Electron Microscopy |
Type |
A1 Journal article |
|
Year |
2020 |
Publication |
Physical Review Letters |
Abbreviated Journal |
Phys Rev Lett |
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Volume |
124 |
Issue |
10 |
Pages |
106105 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We propose a new method to measure atomic scale dynamics of nanoparticles from experimental high-resolution annular dark field scanning transmission electron microscopy images. By using the so-called hidden Markov model, which explicitly models the possibility of structural changes, the number of atoms in each atomic column can be quantified over time. This newly proposed method outperforms the current atom-counting procedure and enables the determination of the probabilities and cross sections for surface diffusion. This method is therefore of great importance for revealing and quantifying the atomic structure when it evolves over time via adatom dynamics, surface diffusion, beam effects, or during in situ experiments. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000519718100015 |
Publication Date |
2020-03-13 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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ISSN |
0031-9007 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
8.6 |
Times cited |
|
Open Access |
OpenAccess |
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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. L.J. acknowledges the SFI AMBER Centre for support. A.V. and P.D.N. acknowledge the UK Engineering and Physical Sciences Council (EPSRC) for support (EP/K040375/1 and 1772738). A.V. also acknowledges Johnson-Matthey for support. We would like to thank Brian Theobald and Jonathan Sharman from JMTC Sonning for provision of the Pt sample. |
Approved |
Most recent IF: 8.6; 2020 IF: 8.462 |
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Call Number |
EMAT @ emat @c:irua:167148 |
Serial |
6347 |
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Permanent link to this record |
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Author |
De wael, A.; De Backer, A.; Jones, L.; Nellist, P.D.; Van Aert, S. |
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Title |
Hybrid statistics-simulations based method for atom-counting from ADF STEM images |
Type |
A1 Journal article |
|
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
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Volume |
177 |
Issue |
177 |
Pages |
69-77 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000401219800010 |
Publication Date |
2017-01-25 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
|
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Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
OpenAccess |
|
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Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0368.15N, G.0369.15N, and WO.010.16N), and a postdoctoral research Grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). The authors are grateful to G.T. Martinez for providing image simulations. |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:141718 |
Serial |
4486 |
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Permanent link to this record |
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Author |
De Backer, A.; Zhang, Z.; van den Bos, K.H.W.; Bladt, E.; Sánchez‐Iglesias, A.; Liz‐Marzán, L.M.; Nellist, P.D.; Bals, S.; Van Aert, S. |
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Title |
Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Small methods |
Abbreviated Journal |
Small Methods |
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Volume |
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Issue |
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Pages |
2200875 |
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Keywords |
A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) |
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Abstract |
A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000862072700001 |
Publication Date |
2022-09-30 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
|
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ISSN |
2366-9608 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
12.4 |
Times cited |
5 |
Open Access |
OpenAccess |
|
|
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A., Grant 815128 REALNANO to S.B., and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B.; esteem3reported; esteem3JRA |
Approved |
Most recent IF: 12.4 |
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Call Number |
EMAT @ emat @c:irua:191570 |
Serial |
7109 |
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Permanent link to this record |
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Author |
De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S. |
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Title |
StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images |
Type |
A1 Journal article |
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Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
|
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Volume |
171 |
Issue |
171 |
Pages |
104-116 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000389106200014 |
Publication Date |
2016-09-09 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
43 |
Open Access |
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Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0393.11, G.0064.10 and G.0374.13), a Ph.D. research grant to K.H.W. van den Bos, and a postdoctoral research grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A. Rosenauer is acknowledged for providing the STEMsim program.; esteem2_jra2 |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:135516 |
Serial |
4280 |
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Permanent link to this record |
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Author |
De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S. |
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Title |
StatSTEM: An efficient program for accurate and precise model-based quantification of atomic resolution electron microscopy images |
Type |
P1 Proceeding |
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Year |
2017 |
Publication |
Journal of physics : conference series
T2 – Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK |
Abbreviated Journal |
J. Phys.: Conf. Ser. |
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Volume |
902 |
Issue |
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Pages |
012013 |
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Keywords |
P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
An efficient model-based estimation algorithm is introduced in order to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model- based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
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Editor |
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Language |
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Wos |
000416370700013 |
Publication Date |
2017-10-16 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
1742-6588 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
|
Times cited |
1 |
Open Access |
OpenAccess |
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Notes |
The authors acknowledge nancial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0374.13N, G.0368.15N, G.0369.15N, WO.010.16N) and a PhD research grant to K H W van den Bos, and a postdoctoral research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A Rosenauer is acknowledged for providing the STEMsim program. |
Approved |
Most recent IF: NA |
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Call Number |
EMAT @ emat @c:irua:147188 |
Serial |
4764 |
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Permanent link to this record |
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Author |
de Backer, A.; Van Aert, S.; van Dyck, D. |
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Title |
High precision measurements of atom column positions using model-based exit wave reconstruction |
Type |
A1 Journal article |
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Year |
2011 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
111 |
Issue |
9/10 |
Pages |
1475-1482 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
In this paper, it has been investigated how to measure atom column positions as accurately and precisely as possible using a focal series of images. In theory, it is expected that the precision would considerably improve using a maximum likelihood estimator based on the full series of focal images. As such, the theoretical lower bound on the variances of the unknown atom column positions can be attained. However, this approach is numerically demanding. Therefore, maximum likelihood estimation has been compared with the results obtained by fitting a model to a reconstructed exit wave rather than to the full series of focal images. Hence, a real space model-based exit wave reconstruction technique based on the channelling theory is introduced. Simulations show that the reconstructed complex exit wave contains the same amount of information concerning the atom column positions as the full series of focal images. Only for thin samples, which act as weak phase objects, this information can be retrieved from the phase of the reconstructed complex exit wave. |
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Address |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Amsterdam |
Editor |
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Language |
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Wos |
000300461200004 |
Publication Date |
2011-07-28 |
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Series Editor |
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Series Title |
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Abbreviated Series Title |
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Series Volume |
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Series Issue |
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Edition |
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ISSN |
0304-3991; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
|
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Notes |
Fwo |
Approved |
Most recent IF: 2.843; 2011 IF: 2.471 |
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Call Number |
UA @ lucian @ c:irua:91879 |
Serial |
1438 |
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Permanent link to this record |
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Author |
De Backer, A.; Van Aert, S.; Faes, C.; Arslan Irmak, E.; Nellist, P.D.; Jones, L. |
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Title |
Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm |
Type |
A1 Journal article |
|
Year |
2022 |
Publication |
N P J Computational Materials |
Abbreviated Journal |
npj Comput Mater |
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Volume |
8 |
Issue |
1 |
Pages |
216 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
We introduce a Bayesian genetic algorithm for reconstructing atomic models of monotype crystalline nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning transmission electron microscopy images serves as an input for the initial three-dimensional model. The algorithm minimizes the energy of the structure while utilizing a priori information about the finite precision of the atom-counting results and neighbor-mass relations. The results show promising prospects for obtaining reliable reconstructions of beam-sensitive nanoparticles during dynamical processes from images acquired with sufficiently low incident electron doses. |
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000866500900001 |
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2022-10-12 |
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2057-3960 |
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UA library record; WoS full record; WoS citing articles |
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OpenAccess |
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Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A. and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B. L.J. acknowledges Science Foundation Ireland (SFI – grant number URF/RI/191637), the Royal Society, and the AMBER Centre. The authors acknowledge Aakash Varambhia for his assistance and expertise with the experimental recording and use of characterization facilities within the David Cockayne Centre for Electron Microscopy, Department of Materials, University of Oxford, and in particular the EPSRC (EP/K040375/1 South of England Analytical Electron Microscope).; esteem3reported; esteem3JRA |
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Most recent IF: NA |
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EMAT @ emat @c:irua:191398 |
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7114 |
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