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Records |
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Author |
Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S. |
| |
Title |
Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
177 |
Issue |
177 |
Pages |
36-42 |
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
Abstract |
Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod. |
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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 |
000401219800006 |
Publication Date |
2016-11-09 |
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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 |
|
| |
ISSN  |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.843 |
Times cited |
13 |
Open Access |
OpenAccess |
| |
Notes |
The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 |
Serial |
4316 |
| Permanent link to this record |
| |
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Author |
Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S. |
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Title |
How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images? |
Type |
A1 Journal article |
| |
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
181 |
Issue |
181 |
Pages |
134-143 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined. |
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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 |
000411170800016 |
Publication Date |
2016-12-15 |
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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 |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.843 |
Times cited |
3 |
Open Access |
OpenAccess |
| |
Notes |
The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2. |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @ c:irua:144432 |
Serial |
4618 |
| 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 |
| |
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 |
|
Series Issue |
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Edition |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.843 |
Times cited |
8 |
Open Access |
OpenAccess |
| |
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 |
| Permanent link to this record |
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Author |
Schryvers, D.; Salje, E.K.H.; Nishida, M.; De Backer, A.; Idrissi, H.; Van Aert, S. |
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Title |
Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations |
Type |
A1 Journal article |
| |
Year |
2017 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
176 |
Issue |
|
Pages |
194-199 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective 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 |
000403992200026 |
Publication Date |
2017-01-09 |
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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 |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.843 |
Times cited |
1 |
Open Access |
OpenAccess |
| |
Notes |
The authors acknowledge financial support from the Fund for Scientific Research-Flanders (G.0064.10N, G.0393.11N, G.0374.13N, G.0368.15N, G.0369.15N) and the Flemish Hercules 3 program for large infrastructure as well as financial support from the European Union Seventh Framework Programme (FP7/2007 – 2013) under Grant agreement no. 312483 (ESTEEM2). EKHS thanks EPSRC (EP/ K009702/1) and the Leverhulme trust (EM-2016-004) for support. DS and MN acknowledge financial support from the Japan Society for the Promotion of Science (JSPS, Japan) through the Grant-in-Aid for Scientific Research (A: No. 26249090) and the Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation (R2408). |
Approved |
Most recent IF: 2.843 |
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Call Number |
EMAT @ emat @c:irua:149654 |
Serial |
4914 |
| Permanent link to this record |
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Author |
van den Bos, K.H.W.; Janssens, L.; De Backer, A.; Nellist, P.D.; Van Aert, S. |
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Title |
The atomic lensing model: new opportunities for atom-by-atom metrology of heterogeneous nanomaterials |
Type |
A1 Journal article |
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Year |
2019 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
203 |
Issue |
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Pages |
155 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
The atomic lensing model has been proposed as a promising method facilitating atom-counting in heterogeneous nanocrystals [1]. Here, image simulations will validate the model, which describes dynamical diffraction as a superposition of individual atoms focussing the incident electrons. It will be demonstrated that the model is reliable in the annular dark field regime for crystals having columns containing dozens of atoms. By using the principles of statistical detection theory, it will be shown that this model gives new opportunities for detecting compositional differences. |
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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 |
000465021000020 |
Publication Date |
2018-12-06 |
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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 |
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Series Issue |
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Edition |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.843 |
Times cited |
4 |
Open Access |
OpenAccess |
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0369.15N, G.0502.18N and WO.010.16N), and by personal grants to K.H.W. van den Bos and A. De Backer. 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:155721 |
Serial |
5074 |
| Permanent link to this record |
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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 |
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Year |
2020 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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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 |
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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 |
| |
Impact Factor |
2.2 |
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. |
Approved |
Most recent IF: 2.2; 2020 IF: 2.843 |
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Call Number |
EMAT @ emat @c:irua:172449 |
Serial |
6417 |
| 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 |
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Year |
2021 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
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Volume |
|
Issue |
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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 |
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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 |
| |
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 |
| Permanent link to this record |
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Author |
Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. |
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Title |
Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors |
Type |
A1 Journal article |
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Year |
2022 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
242 |
Issue |
|
Pages |
113626 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In
addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
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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 |
000873778100001 |
Publication Date |
0000-00-00 |
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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 |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra |
Approved |
Most recent IF: 2.2 |
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Call Number |
EMAT @ emat @c:irua:190925 |
Serial |
7118 |
| Permanent link to this record |
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Author |
De Backer, A.; Bals, S.; Van Aert, S. |
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Title |
A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection |
Type |
A1 Journal article |
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Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
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Volume |
|
Issue |
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Pages |
113702 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted. |
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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 |
000953765800001 |
Publication Date |
2023-02-10 |
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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 |
2.2 |
Times cited |
3 |
Open Access |
OpenAccess |
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert, Grant 815128 REALNANO to S. Bals, 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 EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF) . The authors also thank the colleagues who have contributed to this work over the years, including T. Altantzis, E. Arslan Irmak, K.J. Batenburg, E. Bladt, A. De wael, R. Erni, C. Faes, B. Goris, L. Jones, L.M. Liz-Marzán, I. Lobato, G.T. Martinez, P.D. Nellist, M.D. Rosell, A. Rosenauer, K.H.W. van den Bos, A. Varambhia, and Z. Zhang.; esteem3reported; esteem3JRA |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
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Call Number |
EMAT @ emat @c:irua:195896 |
Serial |
7236 |
| Permanent link to this record |
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Author |
Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P. |
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Title |
Fast generation of calculated ADF-EDX scattering cross-sections under channelling conditions |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
|
| |
Volume |
246 |
Issue |
|
Pages |
113671 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
Abstract |
Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements. |
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Address |
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Corporate Author |
Zezhong Zhang |
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 |
000995063900001 |
Publication Date |
2022-12-28 |
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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 |
|
Series Issue |
|
Edition |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
European Research Council 770887 PICOMETRICS; Fonds Wetenschappelijk Onderzoek No.G.0502.18N; Horizon 2020, 770887 ; Horizon 2020 Framework Programme; European Research Council, 823717 ESTEEM3 ; esteem3reported; esteem3JRa |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
| |
Call Number |
EMAT @ emat @c:irua:195890 |
Serial |
7251 |
| Permanent link to this record |
| |
|
| |
|
Author |
Lobato, I.; De Backer, A.; Van Aert, S. |
| |
Title |
Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network |
Type |
A1 Journal article |
| |
Year |
2023 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
251 |
Issue |
|
Pages |
113769 |
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
Abstract |
Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms
of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In
order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for
a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such
simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently
parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most
research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will
only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and
present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as
a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag,
Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope
parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS
values for a wide range of input parameters that are commonly used for aberration-corrected transmission
electron microscopes. |
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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 |
001011617200001 |
Publication Date |
2023-06-01 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record |
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. |
Approved |
Most recent IF: 2.2; 2023 IF: 2.843 |
| |
Call Number |
EMAT @ emat @c:irua:197275 |
Serial |
8812 |
| Permanent link to this record |
| |
|
| |
|
Author |
Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S. |
| |
Title |
Atom counting from a combination of two ADF STEM images |
Type |
A1 Journal article |
| |
Year |
2024 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
255 |
Issue |
|
Pages |
113859 |
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
Abstract |
To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures. |
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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 |
001089064200001 |
Publication Date |
2023-09-23 |
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Series Editor |
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Series Title |
|
Abbreviated Series Title |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). |
Approved |
Most recent IF: 2.2; 2024 IF: 2.843 |
| |
Call Number |
EMAT @ emat @c:irua:201008 |
Serial |
8964 |
| Permanent link to this record |
| |
|
| |
|
Author |
Şentürk, D.G.; De Backer, A.; Van Aert, S. |
| |
Title |
Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination |
Type |
A1 Journal Article |
| |
Year |
2024 |
Publication |
Ultramicroscopy |
Abbreviated Journal |
Ultramicroscopy |
| |
Volume |
259 |
Issue |
|
Pages |
113941 |
| |
Keywords |
A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ; |
| |
Abstract |
In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy. |
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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 |
2024-02-19 |
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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 |
|
| |
ISSN |
0304-3991 |
ISBN |
|
Additional Links |
UA library record |
| |
Impact Factor |
2.2 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF). |
Approved |
Most recent IF: 2.2; 2024 IF: 2.843 |
| |
Call Number |
EMAT @ emat @c:irua:204353 |
Serial |
8996 |
| Permanent link to this record |
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|
| |
|
Author |
Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A. |
| |
Title |
Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study |
Type |
A1 Journal article |
| |
Year |
2020 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
| |
Volume |
163 |
Issue |
|
Pages |
2405-2414 |
| |
Keywords |
A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) |
| |
Abstract |
NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP. |
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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 |
000579839600233 |
Publication Date |
2020-09-19 |
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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 |
|
| |
ISSN |
0141-8130 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
8.2 |
Times cited |
|
Open Access |
|
| |
Notes |
European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 8.2; 2020 IF: 3.671 |
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Call Number |
PLASMANT @ plasmant @c:irua:172451 |
Serial |
6419 |
| Permanent link to this record |
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Author |
Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A. |
| |
Title |
Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells |
Type |
A1 Journal Article |
| |
Year |
2021 |
Publication |
International Journal Of Biological Macromolecules |
Abbreviated Journal |
Int J Biol Macromol |
| |
Volume |
182 |
Issue |
|
Pages |
1724-1736 |
| |
Keywords |
A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; |
| |
Abstract |
Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, fluorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modification of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme significantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug. |
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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 |
000675794700005 |
Publication Date |
2021-05-27 |
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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 |
|
| |
ISSN |
0141-8130 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
3.671 |
Times cited |
|
Open Access |
OpenAccess |
| |
Notes |
Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. |
Approved |
Most recent IF: 3.671 |
| |
Call Number |
PLASMANT @ plasmant @c:irua:178813 |
Serial |
6792 |
| Permanent link to this record |
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Author |
de Backer, J.W.; Vos, W.G.; Vinchurkar, S.C.; Claes, R.; Drollmann, A.; Wulfrank, D.; Parizel, P.M.; Germonpré, P.; de Backer, W. |
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Title |
Validation of computational fluid dynamics in CT-based airway models with SPECT/CT1 |
Type |
A1 Journal article |
| |
Year |
2010 |
Publication |
Radiology |
Abbreviated Journal |
Radiology |
| |
Volume |
257 |
Issue |
3 |
Pages |
854-862 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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Abstract |
Purpose: To compare the results obtained by using numerical flow simulations with the results of combined single photon emission computed tomography (SPECT) and computed tomography (CT) and to demonstrate the importance of correct boundary conditions for the numerical methods to account for the large amount of interpatient variability in airway geometry. Materials and Methods: This study was approved by all relevant institutional review boards. All patients gave their signed informed consent. In this study, six patients with mild asthma (three men; three women; overall mean age, 46 years ± 17 [standard deviation]) underwent CT at functional residual capacity and total lung capacity, as well as SPECT/CT. CT data were used for segmentation and computational fluid dynamics (CFD) simulations. A comparison was made between airflow distribution, as derived with (a) SPECT/CT through tracer concentration analysis, (b) CT through lobar expansion measurement, and (c) CFD through flow computer simulation. Also, the heterogeneity of the ventilation was examined. Results: Good agreement was found between SPECT/CT, CT, and CFD in terms of airflow distribution and hot spot detection. The average difference for the internal airflow distribution was less than 3% for CFD and CT versus SPECT/CT. Heterogeneity in ventilation patterns could be detected with SPECT/CT and CFD. Conclusion: This results of this study show that patient-specific computer simulations with appropriate boundary conditions yield information that is similar to that obtained with functional imaging tools, such as SPECT/CT. |
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Corporate Author |
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Thesis |
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Publisher |
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Place of Publication |
Easton, Pa |
Editor |
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Language |
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Wos |
000284469300031 |
Publication Date |
2010-11-17 |
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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 |
0033-8419;1527-1315; |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
7.296 |
Times cited |
100 |
Open Access |
|
| |
Notes |
; Supported by Novartis. ; |
Approved |
Most recent IF: 7.296; 2010 IF: 6.069 |
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Call Number |
UA @ lucian @ c:irua:85379 |
Serial |
3831 |
| Permanent link to this record |
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Author |
van den Bos, K.H. W.; De Backer, A.; Martinez, G.T.; Winckelmans, N.; Bals, S.; Nellist, P.D.; Van Aert, S. |
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Title |
Unscrambling Mixed Elements using High Angle Annular Dark Field Scanning Transmission Electron Microscopy |
Type |
A1 Journal article |
| |
Year |
2016 |
Publication |
Physical review letters |
Abbreviated Journal |
Phys Rev Lett |
| |
Volume |
116 |
Issue |
116 |
Pages |
246101 |
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
Abstract |
The development of new nanocrystals with outstanding physicochemical properties requires a full threedimensional (3D) characterization at the atomic scale. For homogeneous nanocrystals, counting the number of atoms in each atomic column from high angle annular dark field scanning transmission electron microscopy images has been shown to be a successful technique to get access to this 3D information. However, technologically important nanostructures often consist of more than one chemical element. In order to extend atom counting to heterogeneous materials, a new atomic lensing model is presented. This model takes dynamical electron diffraction into account and opens up new possibilities for unraveling the 3D composition at the atomic scale. Here, the method is applied to determine the 3D structure of Au@Ag core-shell nanorods, but it is applicable to a wide range of heterogeneous complex nanostructures. |
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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 |
000378059500010 |
Publication Date |
2016-06-17 |
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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 |
|
| |
ISSN |
0031-9007 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
8.462 |
Times cited |
46 |
Open Access |
OpenAccess |
| |
Notes |
The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Projects No. G.0374.13N, No. G.0368.15N, and No. G.0369.15N, and by grants to K. H.W. van den Bos and A. De Backer. S. Bals and N. Winckelmans acknowledge funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant No. 312483—ESTEEM2. The authors are grateful to A. Rosenauer for providing the STEMsim program.; esteem2jra2; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:can); |
Approved |
Most recent IF: 8.462 |
| |
Call Number |
c:irua:133954 c:irua:133954 |
Serial |
4084 |
| Permanent link to this record |
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Author |
Van Aert, S.; De Backer, A.; Jones, L.; Martinez, G.T.; Béché, A.; Nellist, P.D. |
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Title |
Control of Knock-On Damage for 3D Atomic Scale Quantification of Nanostructures: Making Every Electron Count in Scanning Transmission Electron Microscopy |
Type |
A1 Journal article |
| |
Year |
2019 |
Publication |
Physical review letters |
Abbreviated Journal |
Phys Rev Lett |
| |
Volume |
122 |
Issue |
6 |
Pages |
066101 |
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Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
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Abstract |
Understanding nanostructures down to the atomic level is the key to optimizing the design of advancedmaterials with revolutionary novel properties. This requires characterization methods capable of quantifying the three-dimensional (3D) atomic structure with the highest possible precision. A successful approach to reach this goal is to count the number of atoms in each atomic column from 2D annular dark field scanning transmission electron microscopy images. To count atoms with single atom sensitivity, a minimum electron dose has been shown to be necessary, while on the other hand beam damage, induced by the high energy electrons, puts a limit on the tolerable dose. An important challenge is therefore to develop experimental strategies to optimize the electron dose by balancing atom-counting fidelity vs the risk of knock-on damage. To achieve this goal, a statistical framework combined with physics-based modeling of the dose-dependent processes is here proposed and experimentally verified. This model enables an investigator to theoretically predict, in advance of an experimental measurement, the optimal electron dose resulting in an unambiguous quantification of nanostructures in their native state with the highest attainable precision. |
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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 |
000458824200008 |
Publication Date |
2019-02-13 |
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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 |
|
| |
ISSN |
0031-9007 |
ISBN |
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Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
8.462 |
Times cited |
3 |
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). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (WO.010.16N, G.0934.17N, G.0502.18N, G.0267.18N), and a grant to A. D. B. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement No. 312483— ESTEEM2 (Integrated Infrastructure Initiative-I3) and the UK EPSRC (Grant No. EP/M010708/1). |
Approved |
Most recent IF: 8.462 |
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Call Number |
EMAT @ emat @UA @ admin @ c:irua:157175 |
Serial |
5156 |
| 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 |
| |
Volume |
124 |
Issue |
10 |
Pages |
106105 |
| |
Keywords |
A1 Journal article; Electron microscopy for materials research (EMAT) |
| |
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 |
|
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 |
|
| |
Series Volume |
|
Series Issue |
|
Edition |
|
| |
ISSN |
0031-9007 |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
8.6 |
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. 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 |
| |
Call Number |
EMAT @ emat @c:irua:167148 |
Serial |
6347 |
| Permanent link to this record |
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|
| |
|
Author |
van Holsbeke, C.; de Backer, J.; Vos, W.; Verdonck, P.; van Ransbeeck, P.; Claessens, T.; Braem, M.; Vanderveken, O.; de Backer, W. |
| |
Title |
Anatomical and functional changes in the upper airways of sleep apnea patients due to mandibular repositioning: a large scale study |
Type |
A1 Journal article |
| |
Year |
2011 |
Publication |
Journal of biomechanics |
Abbreviated Journal |
J Biomech |
| |
Volume |
44 |
Issue |
3 |
Pages |
442-449 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW) |
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Abstract |
The obstructive sleep apnea-hypopnea syndrome (OSAHS) is a sleep related breathing disorder. A popular treatment is the use of a mandibular repositioning appliance (MRA) which advances the mandibula during the sleep and decreases the collapsibility of the upper airway. The success rate of such a device is, however, limited and very variable within a population of patients. Previous studies using computational fluid dynamics have shown that there is a decrease in upper airway resistance in patients who improve clinically due to an MRA. In this article, correlations between patient-specific anatomical and functional parameters are studied to examine how MRA induced biomechanical changes will have an impact on the upper airway resistance. Low-dose computed tomography (CT) scans are made from 143 patients suffering from OSAHS. A baseline scan and a scan after mandibular repositioning (MR) are performed in order to study variations in parameters. It is found that MR using a simulation bite is able to induce resistance changes by changing the pharyngeal lumen. The change in minimal cross-sectional area is the best parameter to predict the change in upper airway resistance. Looking at baseline values, the ideal patients for MR induced resistance decrease seem to be women with short airways, high initial resistance and no baseline occlusion. |
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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 |
New York, N.Y. |
Editor |
|
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Language |
|
Wos |
000287551000014 |
Publication Date |
2010-10-23 |
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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 |
0021-9290; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
2.664 |
Times cited |
23 |
Open Access |
|
| |
Notes |
; ; |
Approved |
Most recent IF: 2.664; 2011 IF: 2.434 |
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Call Number |
UA @ lucian @ c:irua:85305 |
Serial |
112 |
| Permanent link to this record |
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|
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|
Author |
de Backer, J.W.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Germonpré, P.; Wuyts, F.L.; Parizel, P.M.; de Backer, W. |
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Title |
Computational fluid dynamics can detect changes in airway resistance in asthmatics after acute bronchodilation |
Type |
A1 Journal article |
| |
Year |
2008 |
Publication |
Journal of biomechanics |
Abbreviated Journal |
J Biomech |
| |
Volume |
41 |
Issue |
1 |
Pages |
106-113 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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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 |
|
Place of Publication |
New York, N.Y. |
Editor |
|
| |
Language |
|
Wos |
000253062100014 |
Publication Date |
2007-08-15 |
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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 |
0021-9290; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.664 |
Times cited |
53 |
Open Access |
|
| |
Notes |
|
Approved |
Most recent IF: 2.664; 2008 IF: 2.784 |
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Call Number |
UA @ lucian @ c:irua:64859 |
Serial |
456 |
| Permanent link to this record |
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|
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|
Author |
Vos, W.; de Backer, J.; Devolder, A.; Vanderveken, O.; Verhulst, S.; Salgado, R.; Germonpré, P.; Partoens, B.; Wuyts, F.; Parizel, P.; de Backer, W. |
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Title |
Correlation between severity of sleep apnea and upper airway morphology based on advanced anatomical and functional imaging |
Type |
A1 Journal article |
| |
Year |
2007 |
Publication |
Journal of biomechanics |
Abbreviated Journal |
J Biomech |
| |
Volume |
40 |
Issue |
10 |
Pages |
2207-2213 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW) |
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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 |
|
Place of Publication |
New York, N.Y. |
Editor |
|
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Language |
|
Wos |
000248468000011 |
Publication Date |
2006-12-19 |
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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 |
0021-9290; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.664 |
Times cited |
86 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.664; 2007 IF: 2.897 |
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Call Number |
UA @ lucian @ c:irua:62425 |
Serial |
523 |
| Permanent link to this record |
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Author |
de Backer, J.W.; Vanderveken, O.M.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Verbraecken, J.A.; Parizel, P.M.; Braem, M.J.; van de Heyning, P.H.; de Backer, W.A. |
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Title |
Functional imaging using computational fluid dynamics to predict treatment success of mandibular advancement devices in sleep-disordered breathing |
Type |
A1 Journal article |
| |
Year |
2007 |
Publication |
Journal of biomechanics |
Abbreviated Journal |
J Biomech |
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Volume |
40 |
Issue |
16 |
Pages |
3708-3714 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW) |
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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 |
New York, N.Y. |
Editor |
|
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Language |
|
Wos |
000251845100020 |
Publication Date |
2007-08-01 |
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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 |
0021-9290; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
2.664 |
Times cited |
66 |
Open Access |
|
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Notes |
|
Approved |
Most recent IF: 2.664; 2007 IF: 2.897 |
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Call Number |
UA @ lucian @ c:irua:64860 |
Serial |
1299 |
| Permanent link to this record |
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Author |
Van Holsbeke, C.S.; Leemans, G.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Geldof, M.; Verdonck, P.R.; Parizel, P.M.; van Schil, P.E.; de Backer, W.A. |
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Title |
Functional Respiratory Imaging as a tool to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis |
Type |
A1 Journal article |
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Year |
2013 |
Publication |
Respiratory care |
Abbreviated Journal |
Resp Care |
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Volume |
|
Issue |
|
Pages |
1-20 |
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Keywords |
A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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Abstract |
In two subjects with a unilateral diaphragmatic paralysis and complaints of dyspnea, a completely different treatment approach was chosen despite similar anatomical and physiological abnormalities. These decisions were supported by the results generated by Functional Respiratory Imaging (FRI). FRI was able to generate functional information with respect to lobar ventilation and local drug deposition. In one subject, it was found that some lobes were poorly ventilated and drug deposition simulation showed that some regions were undertreated. This subject underwent a diaphragm plication to restore the ventilation. In the other subject, it was found that all lobes were still ventilated. A conservative approach with regular follow-up was chosen to wait for spontaneous recovery of the diaphragmatic function. Both subjects improved subjectively and objectively. These cases demonstrate how novel medical imaging techniques such as FRI can be used to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis. |
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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 |
Dallas, Tex. |
Editor |
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Language |
|
Wos |
000349200100024 |
Publication Date |
2013-12-11 |
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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 |
0020-1324;1943-3654; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
| |
Impact Factor |
1.733 |
Times cited |
5 |
Open Access |
|
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Notes |
; ; |
Approved |
Most recent IF: 1.733; 2013 IF: 1.840 |
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Call Number |
UA @ lucian @ c:irua:112982 |
Serial |
1303 |
| Permanent link to this record |
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Author |
Horemans, B.; Van Holsbeke, C.; Vos, W.; Darchuk, L.; Novakovic, V.; Fontan, A.C.; de Backer, J.; van Grieken, R.; de Backer, W.; De Wael, K. |
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Title |
Particle deposition in airways of chronic respiratory patients exposed to an urban aerosol |
Type |
A1 Journal article |
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Year |
2012 |
Publication |
Environmental science and technology |
Abbreviated Journal |
Environ Sci Technol |
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Volume |
46 |
Issue |
21 |
Pages |
12162-12169 |
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Keywords |
A1 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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Abstract |
Urban atmospheres in modern cities carry characteristic mixtures of particulate pollution which are potentially aggravating for chronic respiratory patients (CRP). Although air quality surveys can be detailed, the obtained information is not always useful to evaluate human health effects. This paper presents a novel approach to estimate particle deposition rates in airways of CRP, based on real air pollution data. By combining computational fluid dynamics with physical-chemical characteristics of particulate pollution, deposition rates are estimated for particles of different toxicological relevance, that is, minerals, iron oxides, sea salts, ammonium salts, and carbonaceous particles. Also, it enables some qualitative evaluation of the spatial, temporal, and patient specific effects on the particle dose upon exposure to the urban atmosphere. Results show how heavy traffic conditions increases the deposition of anthropogenic particles in the trachea and lungs of respiratory patients (here, +0.28 and +1.5 μg·h1, respectively). In addition, local and synoptic meteorological conditions were found to have a strong effect on the overall dose. However, the pathology and age of the patient was found to be more crucial, with highest deposition rates for toxic particles in adults with a mild anomaly, followed by mild asthmatic children and adults with severe respiratory dysfunctions (7, 5, and 3 μg·h1, respectively). |
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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 |
Easton, Pa |
Editor |
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Language |
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Wos |
000310665000082 |
Publication Date |
2012-10-04 |
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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 |
0013-936X;1520-5851; |
ISBN |
|
Additional Links |
UA library record; WoS full record; WoS citing articles |
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Impact Factor |
6.198 |
Times cited |
5 |
Open Access |
|
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Notes |
; We are grateful for the financial support of n.v. Vooruitzicht. Furthermore, co-workers at the environmental analysis research group are acknowledged for their help in the fieldwork. ; |
Approved |
Most recent IF: 6.198; 2012 IF: 5.257 |
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Call Number |
UA @ lucian @ c:irua:101411 |
Serial |
2557 |
| 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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Address |
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Corporate Author |
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Thesis |
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Publisher |
American Institute of Physics |
Place of Publication |
New York, N.Y. |
Editor |
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Language |
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Wos |
000341188700073 |
Publication Date |
2014-08-14 |
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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 |
0003-6951;1077-3118; |
ISBN |
|
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 |
| Permanent link to this record |
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Author |
de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W. |
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Title |
Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices |
Type |
A3 Journal article |
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Year |
2009 |
Publication |
Proceedings of the Society of Photo-optical Instrumentation Engineers |
Abbreviated Journal |
|
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Volume |
7262 |
Issue |
|
Pages |
72621p,1-72621p,9 |
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Keywords |
A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) |
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Abstract |
Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies. |
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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 |
2009-02-27 |
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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 |
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ISBN |
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Additional Links |
UA library record |
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Impact Factor |
|
Times cited |
|
Open Access |
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Notes |
|
Approved |
Most recent IF: NA |
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Call Number |
UA @ lucian @ c:irua:79497 |
Serial |
374 |
| 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 |
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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 |
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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 |
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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 |
| Permanent link to this record |
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Author |
de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. |
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Title |
Atom counting |
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 |
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Issue |
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Pages |
91-144 |
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Keywords |
H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab |
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Abstract |
In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity. |
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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 |
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ISBN |
978-0-12-824607-8; 1076-5670 |
Additional Links |
UA library record |
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Impact Factor |
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Times cited |
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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:177529 |
Serial |
6776 |
| Permanent link to this record |
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Author |
de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. |
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Title |
Efficient fitting algorithm |
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 |
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Pages |
73-90 |
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Keywords |
H2 Book chapter; Electron microscopy for materials research (EMAT) |
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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 neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required. |
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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 |
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ISBN |
978-0-12-824607-8; 1076-5670 |
Additional Links |
UA library record |
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Impact Factor |
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Times cited |
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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:177528 |
Serial |
6778 |
| Permanent link to this record |
