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	Author	Koo, J.; Dahl, A.B.; Bærentzen, J.A.; Chen, Q.; Bals, S.; Dahl, V.A.
	Title	Shape from projections via differentiable forward projector for computed tomography			Type	A1 Journal article
	Year	2021	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	224	Issue		Pages	113239
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	In computed tomography, the reconstruction is typically obtained on a voxel grid. In this work, however, we propose a mesh-based reconstruction method. For tomographic problems, 3D meshes have mostly been studied to simulate data acquisition, but not for reconstruction, for which a 3D mesh means the inverse process of estimating shapes from projections. In this paper, we propose a differentiable forward model for 3D meshes that bridge the gap between the forward model for 3D surfaces and optimization. We view the forward projection as a rendering process, and make it differentiable by extending recent work in differentiable rendering. We use the proposed forward model to reconstruct 3D shapes directly from projections. Experimental results for single-object problems show that the proposed method outperforms traditional voxel-based methods on noisy simulated data. We also apply the proposed method on electron tomography images of nanoparticles to demonstrate the applicability of the method on real data.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000744576800008	Publication Date	2021-03-11
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	3	Open Access	OpenAccess
	Notes	EU Horizon 2020 MSCA Innovative Training Network MUMMERING Grant Number 765604.			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @c:irua:183267			Serial	6825
Permanent link to this record



	Author	Jannis, D.; Hofer, C.; Gao, C.; Xie, X.; Béché, A.; Pennycook, Tj.; Verbeeck, J.
	Title	Event driven 4D STEM acquisition with a Timepix3 detector: Microsecond dwell time and faster scans for high precision and low dose applications			Type	A1 Journal article
	Year	2022	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	233	Issue		Pages	113423
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	Four dimensional scanning transmission electron microscopy (4D STEM) records the scattering of electrons in a material in great detail. The benefits offered by 4D STEM are substantial, with the wealth of data it provides facilitating for instance high precision, high electron dose efficiency phase imaging via centre of mass or ptychography based analysis. However the requirement for a 2D image of the scattering to be recorded at each probe position has long placed a severe bottleneck on the speed at which 4D STEM can be performed. Recent advances in camera technology have greatly reduced this bottleneck, with the detection efficiency of direct electron detectors being especially well suited to the technique. However even the fastest frame driven pixelated detectors still significantly limit the scan speed which can be used in 4D STEM, making the resulting data susceptible to drift and hampering its use for low dose beam sensitive applications. Here we report the development of the use of an event driven Timepix3 direct electron camera that allows us to overcome this bottleneck and achieve 4D STEM dwell times down to 100 ns; orders of magnitude faster than what has been possible with frame based readout. We characterize the detector for different acceleration voltages and show that the method is especially well suited for low dose imaging and promises rich datasets without compromising dwell time when compared to conventional STEM imaging.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000734396800003	Publication Date	2021-11-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited	31	Open Access	OpenAccess
	Notes	This project has received funding from the Euro- pean Union’s Horizon 2020 Research Infrastructure – Integrating Activities for Advanced Communities under grant agreement No 823717 – ESTEEM3. J.V. and A.B. acknowledge funding from FWO project G093417N (‘Compressed sensing enabling low dose imaging in transmission electron microscopy’). J.V. and D.J. ac- knowledge funding from FWO project G042920N ‘Co- incident event detection for advanced spectroscopy in transmission electron microscopy’. We acknowledge funding under the European Union’s Horizon 2020 re- search and innovation programme (J.V. and D.J un- der grant agreement No 101017720, FET-Proactive EBEAM, and C.H., C.G., X.X. and T.J.P. from the Eu- ropean Research Council (ERC) Grant agreement No. 802123-HDEM).; esteem3JRA; esteem3reported			Approved	Most recent IF: 2.2
	Call Number	EMAT @ emat @c:irua:183948			Serial	6828
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	Author	Madsen, J.; Pennycook, T.J.; Susi, T.
	Title	ab initio description of bonding for transmission electron microscopy			Type	A1 Journal article
	Year	2021	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	231	Issue		Pages
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and structural biology. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and fairly accurate, especially for scanning TEM (STEM) annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory, which was previously mainly required for holography. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We argue that a physically better justified ab initio description of the scattering potential is both useful and viable for an increasing number of systems, and we expect such simulations to steadily gain in popularity and importance.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000744190300006	Publication Date	2021-03-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited		Open Access	OpenAccess
	Notes				Approved	Most recent IF: 2.843
	Call Number	UA @ admin @ c:irua:183955			Serial	6850
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	Author	Robert, Hl.; Lobato, I.; Lyu, Fj.; Chen, Q.; Van Aert, S.; Van Dyck, D.; Müller-Caspary, K.
	Title	Dynamical diffraction of high-energy electrons investigated by focal series momentum-resolved scanning transmission electron microscopy at atomic resolution			Type	A1 Journal article
	Year	2022	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	233	Issue		Pages	113425
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	We report a study of scattering dynamics in crystals employing momentum-resolved scanning transmission electron microscopy under varying illumination conditions. As we perform successive changes of the probe focus, multiple real-space signals are obtained in dependence of the shape of the incident electron wave. With support from extensive simulations, each signal is shown to be characterised by an optimum focus for which the contrast is maximum and which differs among different signals. For instance, a systematic focus mismatch is found between images formed by high-angle scattering, being sensitive to thickness and chemical composition, and the first moment in diffraction space, being sensitive to electric fields. It follows that a single recording at one specific probe focus is usually insufficient to characterise materials comprehensively. Most importantly, we demonstrate in experiment and simulation that the second moment (
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000734396800009	Publication Date	2021-11-13
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	We thank Dr. Florian Winkler for valuable discussions and experimental work at the early stages of this study. This work was supported by the Initiative and Network Fund of the Helmholtz Association (Germany) under contracts VH-NG-1317 and ZT-I-0025. This project furthermore received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement No. 770887).			Approved	Most recent IF: 2.2
	Call Number	EMAT @ emat @c:irua:184833			Serial	6898
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	Author	Jannis, D.; Velazco, A.; Béché, A.; Verbeeck, J.
	Title	Reducing electron beam damage through alternative STEM scanning strategies, Part II: Attempt towards an empirical model describing the damage process			Type	A1 Journal article
	Year	2022	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume		Issue		Pages	113568
	Keywords	A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
	Abstract	In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific zeolite sample. We make use of a 2D diffusion model that describes the dissipation of the deposited beam energy in the sequence of probe positions that are visited during the scan pattern. The diffusion process allows for the concept of trying to ‘outrun’ the beam damage by carefully tuning the dwell time and distance between consecutively visited probe positions. We add a non linear function to include a threshold effect and evaluate the accumulated damage in each part of the image as a function of scan pattern details. Together, these ingredients are able to describe qualitatively all aspects of the experimental data and provide us with a model that could guide a further optimisation towards even lower beam damage without lowering the applied electron dose. We deliberately remain vague on what is diffusing here which avoids introducing too many sample specific details. This provides hope that the model can be applied also in sample classes that were not yet studied in such great detail by adjusting higher level parameters: a sample dependent diffusion constant and damage threshold.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000832788000003	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited	4	Open Access	OpenAccess
	Notes	D.J., A.V, A.B. and J.V. acknowledge funding from FWO project G093417N (’Compressed sensing enabling low dose imaging in transmission electron microscopy’) and G042920N (’Coincident event detection for advanced spectroscopy in transmission electron microscopy’). This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 823717 ESTEEM3. The Qu-Ant-EM microscope was partly funded by the Hercules fund from the Flemish Government. J.V. acknowledges funding from GOA project “Solarpaint” of the University of Antwerp .; esteem3reported; esteem3jra;			Approved	Most recent IF: 2.2
	Call Number	EMAT @ emat @c:irua:188535			Serial	7071
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	Author	Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S.
	Title	Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors			Type	A1 Journal article
	Year	2022	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	242	Issue		Pages	113626
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000873778100001	Publication Date	0000-00-00
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra			Approved	Most recent IF: 2.2
	Call Number	EMAT @ emat @c:irua:190925			Serial	7118
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	Author	Lobato, I.; De Backer, A.; Van Aert, S.
	Title	Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network			Type	A1 Journal article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	251	Issue		Pages	113769
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag, Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS values for a wide range of input parameters that are commonly used for aberration-corrected transmission electron microscopes.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001011617200001	Publication Date	2023-06-01
	Series Editor		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
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	Author	Denisov, N.; Jannis, D.; Orekhov, A.; Müller-Caspary, K.; Verbeeck, J.
	Title	Characterization of a Timepix detector for use in SEM acceleration voltage range			Type	A1 Journal article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	253	Issue		Pages	113777
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15–30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001026912700001	Publication Date	2023-06-08
	Series Editor		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	The authors acknowledge the financial support of the Research Foundation Flanders (FWO, Belgium) project SBO S000121N. The authors are grateful to Dr. Lobato for productive discussion of methods.			Approved	Most recent IF: 2.2; 2023 IF: 2.843
	Call Number	EMAT @ emat @c:irua:198258			Serial	8815
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	Author	Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S.
	Title	Atom counting from a combination of two ADF STEM images			Type	A1 Journal article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	255	Issue		Pages	113859
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001089064200001	Publication Date	2023-09-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).			Approved	Most recent IF: 2.2; 2024 IF: 2.843
	Call Number	EMAT @ emat @c:irua:201008			Serial	8964
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	Author	Şentürk, D.G.; De Backer, A.; Van Aert, S.
	Title	Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination			Type	A1 Journal Article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	259	Issue		Pages	113941
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2024-02-19
	Series Editor		Series Title		Abbreviated Series Title
	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
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	Author	Verbeeck, J.; Béché, A.; Müller-Caspary, K.; Guzzinati, G.; Luong, M.A.; Den Hertog, M.
	Title	Demonstration of a 2 × 2 programmable phase plate for electrons			Type	A1 Journal article
	Year	2018	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	190	Issue		Pages	58-65
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	First results on the experimental realisation of a 2 × 2 programmable phase plate for electrons are presented. The design consists of an array of electrostatic elements that influence the phase of electron waves passing through 4 separately controllable aperture holes. This functionality is demonstrated in a conventional transmission electron microscope operating at 300 kV and results are in very close agreement with theoretical predictions. The dynamic creation of a set of electron probes with different phase symmetry is demonstrated, thereby bringing adaptive optics in TEM one step closer to reality. The limitations of the current design and how to overcome these in the future are discussed. Simulations show how further evolved versions of the current proof of concept might open new and exciting application prospects for beam shaping and aberration correction.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000432868800007	Publication Date	2018-04-18
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	73	Open Access	Not_Open_Access: Available from 19.04.2020
	Notes	J.V. and A.B. acknowledge funding from the Fund for Scientific Research Flanders FWO project G093417N and the European Research Council under the 7th Framework Program (FP7), ERC Starting Grant 278510 VORTEX and ERC proof of concept project DLV-789598 ADAPTEM. The Qu-Ant-EM microscope used in this work was partly funded by the Hercules fund from the Flemish Government. MdH acknowledges financial support from the ANRCOSMOS (ANR-12-JS10-0002). MdH and ML acknowledge funding from the Laboratoire d’excellence LANEF in Grenoble (ANR-10-LABX-51-01).			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @c:irua:150459UA @ admin @ c:irua:150459			Serial	4920
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	Author	Martinez, G.T.; van den Bos, K.H.W.; Alania, M.; Nellist, P.D.; Van Aert, S.
	Title	Thickness dependence of scattering cross-sections in quantitative scanning transmission electron microscopy			Type	A1 Journal article
	Year	2018	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	187	Issue		Pages	84-92
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	In quantitative scanning transmission electron microscopy (STEM), scattering cross-sections have been shown to be very sensitive to the number of atoms in a column and its composition. They correspond to the integrated intensity over the atomic column and they outperform other measures. As compared to atomic column peak intensities, which saturate at a given thickness, scattering cross-sections increase monotonically. A study of the electron wave propagation is presented to explain the sensitivity of the scattering cross-sections. Based on the multislice algorithm, we analyse the wave propagation inside the crystal and its link to the scattered signal for the different probe positions contained in the scattering cross-section for detector collection in the low-, middle- and high-angle regimes. The influence to the signal from scattering of neighbouring columns is also discussed.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000428131200011	Publication Date	2018-01-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	4	Open Access	Not_Open_Access: Available from 01.02.2020
	Notes	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 PhD grant to K.H.W.v.d.B. The research leading to these results has received funding from the European Union 7th Framework Programme [ FP7 /2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors are grateful to A. Rosenauer for providing access to the StemSim software.			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @c:irua:149384			Serial	4809
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	Author	Stefan Löffler; Matthieu Bugnet; Nicolas Gauquelin; Sorin Lazar; Elias Assmann; Karsten Held; Gianluigi A. Botton; Peter Schattschneider
	Title	Real-space mapping of electronic orbitals			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	177	Issue	177	Pages	26-29
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Electronic states are responsible for most material properties, including chemical bonds, electrical and thermal conductivity, as well as optical and magnetic properties. Experimentally, however, they remain mostly elusive. Here, we report the real-space mapping of selected transitions between p and d states on the Ångström scale in bulk rutile (TiO2) using electron energy-loss spectrometry (EELS), revealing information on individual bonds between atoms. On the one hand, this enables the experimental verification of theoretical predictions about electronic states. On the other hand, it paves the way for directly investigating electronic states under conditions that are at the limit of the current capabilities of numerical simulations such as, e.g., the electronic states at defects, interfaces, and quantum dots.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	000401219800004	Publication Date	2017-01-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record
	Impact Factor	2.843	Times cited		Open Access	Not_Open_Access
	Notes	; St.L. thanks Walid Hetaba for discussions about WIEN2k. St.L. and P.S. thank Ralf Hambach and Ute Kaiser for many valuable discussions. M.B. thanks Vienna University of Technology for travel support. St.L. and P.S. acknowledge financial support by the Austrian Science Fund (FWF) under grant number 1543-N20, SFB F45 FOXSI; St.L. also acknowledges financial support by the Austrian Science Fund (FWF) under grant number J3732-N27. M.B., N.G., S.L. and G.A.B. performed the experimental work at the Canadian Center for Electron Microscopy, a national facility supported by McMaster University and the Natural Sciences and Engineering Research Council of Canada (NSERC). G.A.B. is grateful to NSERC for supporting this work. ;			Approved	Most recent IF: 2.843
	Call Number	EMAT @ emat @ c:irua:142201			Serial	4539
Permanent link to this record



	Author	Vatanparast, M.; Egoavil, R.; Reenaas, T.W.; Verbeeck, J.; Holmestad, R.; Vullum, P.E.
	Title	Bandgap measurement of high refractive index materials by off-axis EELS			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	182	Issue		Pages	92-98
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	In the present work Cs aberration corrected and monochromated scanning transmission electron microscopy electron energy loss spectroscopy (STEM-EELS) has been used to explore experimental setups that allow bandgaps of high refractive index materials to be determined. Semi-convergence and collection angles in the mu rad range were combined with off-axis or dark field EELS to avoid relativistic losses and guided light modes in the low loss range to contribute to the acquired EEL spectra. Off-axis EELS further supressed the zero loss peak and the tail of the zero loss peak. The bandgap of several GaAs-based materials were successfully determined by simple regression analyses of the background subtracted EEL spectra. The presented set-up does not require that the acceleration voltage is set to below the. Cerenkov limit and can be applied over the entire acceleration voltage range of modern TEMs and for a wide range of specimen thicknesses. (C) 2017 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000413436500013	Publication Date	2017-06-21
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	3	Open Access	Not_Open_Access
	Notes	; The authors would like to thank Professor Shu Min Wang and Mahdad Sadeghi at the Nanofabrication Laboratory at Chalmers University, Sweden for providing the samples. The Norwegian Research Council is acknowledged for funding the HighQ-IB project under contract no. 10415201. M.V. and T.W.R. acknowledge funding from the EEA Financial Mechanism 2009-2014 under the project contract no 23SEE/30.06.2014. 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) through the system of transnational access. R.E. and J.V. acknowledge funding from GOA project “Solarpaint” of the University of Antwerp. ;			Approved	Most recent IF: 2.843
	Call Number	UA @ lucian @ c:irua:146639UA @ admin @ c:irua:146639			Serial	4778
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	Author	Grieb, T.; Krause, F.F.; Mahr, C.; Zillmann, D.; Müller-Caspary, K.; Schowalter, M.; Rosenauer, A.
	Title	Optimization of NBED simulations for disc-detection measurements			Type	A1 Journal article
	Year	2017	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	181	Issue		Pages	50-60
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Nano-beam electron diffraction (NBED) is a method which can be applied to measure lattice strain and polarisation fields in strained layer heterostructures and transistors. To investigate precision, accuracy and spatial resolution of such measurements in dependence of properties of the specimen as well as electron optical parameters, simulations of NBED patterns are required which allow to predict the result of common disc-detection algorithms. In this paper we demonstrate by focusing on the detection of the central disc in crystalline silicon that such simulations require to take several experimental characteristics into account in order to obtain results which are comparable to those from experimental NBED patterns. These experimental characteristics are the background intensity, the presence of Poisson noise caused by electron statistics and blurring caused by inelastic scattering and by the transfer quality of the microscope camera. By means of these optimized simulations, different effects of specimen properties on disc detection – such as strain, surface morphology and compositional changes on the nanometer scale – are investigated and discussed in the context of misinterpretation in experimental NBED evaluations. It is shown that changes in surface morphology and chemical composition lead to measured shifts of the central disc in the NBED pattern of tens to hundreds of grad. These shifts are of the same order of magnitude or even larger than shifts that could be caused by an electric polarisation field in the range of MV/cm. (C) 2017 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000411170800006	Publication Date	2017-05-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	6	Open Access	Not_Open_Access
	Notes	; This work was supported by the German Research Foundation (DFG) under Contract No. R02057/11-1, R02057/4-2 and MU3660/1-1. ;			Approved	Most recent IF: 2.843
	Call Number	UA @ lucian @ c:irua:146725			Serial	4792
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	Author	Grieb, T.; Tewes, M.; Schowalter, M.; Müller-Caspary, K.; Krause, F.F.; Mehrtens, T.; Hartmann, J.-M.; Rosenauer, A.
	Title	Quantitative HAADF STEM of SiGe in presence of amorphous surface layers from FIB preparation			Type	A1 Journal article
	Year	2018	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	184	Issue	B	Pages	29-36
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	<script type='text/javascript'>document.write(unpmarked('The chemical composition of four Si1-xGex layers grown on silicon was determined from quantitative scanning transmission electron microscopy (STEM). The chemical analysis was performed by a comparison of the high-angle annular dark field (HAADF) intensity with multislice simulations. It could be shown that amorphous surface layers originating from the preparation process by focused-ion beam (FIB) at 30 kV have a strong influence on the quantification: the local specimen thickness is overestimated by approximately a factor of two, and the germanium concentration is substantially underestimated. By means of simulations, the effect of amorphous surface layers on the HAADF intensity of crystalline silicon and germanium is investigated. Based on these simulations, a method is developed to analyze the experimental HAADF-STEM images by taking the influence of the amorphous layers into account which is done by a reduction of the intensities by multiplication with a constant factor. This suggested modified HAADF analysis gives germanium concentrations which are in agreement with the nominal values. The same TEM lamella was treated with low-voltage ion milling which removed the amorphous surface layers completely. The results from subsequent quantitative HAADF analyses are in agreement with the nominal concentrations which validates the applicability of the used frozen-lattice based multislice simulations to describe the HAADF scattering of Si1-xGex in STEM. (C) 2017 Elsevier B.V. All rights reserved.'));
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000417779800004	Publication Date	2017-10-14
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	7	Open Access	Not_Open_Access
	Notes	; This work was supported by the German Research Foundation (DFG) under Contract No. RO2057/11-1. ;			Approved	Most recent IF: 2.843
	Call Number	UA @ lucian @ c:irua:148500			Serial	4893
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	Author	Hofer, C.; Gao, C.; Chennit, T.; Yuan, B.; Pennycook, T.J.
	Title	Phase offset method of ptychographic contrast reversal correction			Type	A1 Journal article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume		Issue		Pages	113922
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001164447000001	Publication Date	2024-01-08
	Series Editor		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	Not_Open_Access
	Notes	FWO, G013122N ; Horizon 2020 Framework Programme; European Research Council, 802123-HDEM ; European Research Council;			Approved	Most recent IF: 2.2; 2024 IF: 2.843
	Call Number	EMAT @ emat @c:irua:202379			Serial	8988
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	Author	Van den Broek, W.; Jannis, D.; Verbeeck, J.
	Title	Convexity constraints on linear background models for electron energy-loss spectra			Type	A1 Journal Article
	Year	2023	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	254	Issue		Pages	113830
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	In this paper convexity constraints are derived for a background model of electron energy loss spectra (EELS) that is linear in the fitting parameters. The model outperforms a power-law both on experimental and simulated backgrounds, especially for wide energy ranges, and thus improves elemental quantification results. Owing to the model’s linearity, the constraints can be imposed through fitting by quadratic programming. This has important advantages over conventional nonlinear power-law fitting such as high speed and a guaranteed unique solution without need for initial parameters. As such, the need for user input is significantly reduced, which is essential for unsupervised treatment of large datasets. This is demonstrated on a demanding spectrum image of a semiconductor device sample with a high number of elements over a wide energy range.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2023-08-15
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record
	Impact Factor	2.2	Times cited		Open Access	Not_Open_Access
	Notes	ECSEL, 875999 ; Horizon 2020; Horizon 2020 Framework Programme; Electronic Components and Systems for European Leadership;			Approved	Most recent IF: 2.2; 2023 IF: 2.843
	Call Number	EMAT @ emat @c:irua:200588			Serial	8961
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	Author	Wang, A.; Turner, S.; Van Aert, S.; van Dyck, D.
	Title	An alternative approach to determine attainable resolution directly from HREM images			Type	A1 Journal article
	Year	2013	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	133	Issue		Pages	50-61
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	The concept of resolution in high-resolution electron microscopy (HREM) is the power to resolve neighboring atoms. Since the resolution is related to the width of the point spread function of the microscope, it could in principle be determined from the image of a point object. However, in electron microscopy there are no ideal point objects. The smallest object is an individual atom. If the width of an atom is much smaller than the resolution of the microscope, this atom can still be considered as a point object. As the resolution of the microscope enters the sub-Å regime, information about the microscope is strongly entangled with the information about the atoms in HREM images. Therefore, we need to find an alternative method to determine the resolution in an object-independent way. In this work we propose to use the image wave of a crystalline object in zone axis orientation. Under this condition, the atoms of a column act as small lenses so that the electron beam channels through the atom column periodically. Because of this focusing, the image wave of the column can be much more peaked than the constituting atoms and can thus be a much more sensitive probe to measure the resolution. Our approach is to use the peakiness of the image wave of the atom column to determine the resolution. We will show that the resolution can be directly linked to the total curvature of the atom column wave. Moreover, we can then directly obtain the resolution of the microscope given that the contribution from the object is known, which is related to the bounding energy of the atom. The method is applied on an experimental CaTiO3 image wave.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000324471800007	Publication Date	2013-05-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record
	Impact Factor	2.843	Times cited		Open Access
	Notes	FWO; Hercules; Esteem2; esteem2_jra2			Approved	Most recent IF: 2.843; 2013 IF: 2.745
	Call Number	UA @ lucian @ c:irua:109919			Serial	90
Permanent link to this record



	Author	de Backer, A.; Martinez, G.T.; Rosenauer, A.; Van Aert, S.
	Title	Atom counting in HAADF STEM using a statistical model-based approach : methodology, possibilities, and inherent limitations			Type	A1 Journal article
	Year	2013	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	134	Issue		Pages	23-33
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	In the present paper, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high resolution high-angle annular dark-field (HAADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. In order to count the number of atoms, it is assumed that the total scattered intensity scales with the number of atoms per atom column. These intensities are quantitatively determined using model-based statistical parameter estimation theory. The distribution describing the probability that intensity values are generated by atomic columns containing a specific number of atoms is inferred on the basis of the experimental scattered intensities. Finally, the number of atoms per atom column is quantified using this estimated probability distribution. The number of atom columns available in the observed STEM image, the number of components in the estimated probability distribution, the width of the components of the probability distribution, and the typical shape of a criterion to assess the number of components in the probability distribution directly affect the accuracy and precision with which the number of atoms in a particular atom column can be estimated. It is shown that single atom sensitivity is feasible taking the latter aspects into consideration.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000324474900005	Publication Date	2013-05-17
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	48	Open Access
	Notes	FWO; Esteem2; FP 2007-2013; esteem2_jra2			Approved	Most recent IF: 2.843; 2013 IF: 2.745
	Call Number	UA @ lucian @ c:irua:109916			Serial	162
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	Author	Egoavil, R.; Gauquelin, N.; Martinez, G.T.; Van Aert, S.; Van Tendeloo, G.; Verbeeck, J.
	Title	Atomic resolution mapping of phonon excitations in STEM-EELS experiments			Type	A1 Journal article
	Year	2014	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	147	Issue		Pages	1-7
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Atomically resolved electron energy-loss spectroscopy experiments are commonplace in modern aberration-corrected transmission electron microscopes. Energy resolution has also been increasing steadily with the continuous improvement of electron monochromators. Electronic excitations however are known to be delocalized due to the long range interaction of the charged accelerated electrons with the electrons in a sample. This has made several scientists question the value of combined high spatial and energy resolution for mapping interband transitions and possibly phonon excitation in crystals. In this paper we demonstrate experimentally that atomic resolution information is indeed available at very low energy losses around 100 meV expressed as a modulation of the broadening of the zero loss peak. Careful data analysis allows us to get a glimpse of what are likely phonon excitations with both an energy loss and gain part. These experiments confirm recent theoretical predictions on the strong localization of phonon excitations as opposed to electronic excitations and show that a combination of atomic resolution and recent developments in increased energy resolution will offer great benefit for mapping phonon modes in real space.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000343157400001	Publication Date	2014-05-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	22	Open Access
	Notes	246102 IFOX; 278510 VORTEX; 246791 COUNTATOMS; Hercules; 312483 ESTEEM2; esteem2jra3 ECASJO;			Approved	Most recent IF: 2.843; 2014 IF: 2.436
	Call Number	UA @ lucian @ c:irua:118332UA @ admin @ c:irua:118332			Serial	177
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	Author	van den Broek, W.; Rosenauer, A.; Goris, B.; Martinez, G.T.; Bals, S.; Van Aert, S.; van Dyck, D.
	Title	Correction of non-linear thickness effects in HAADF STEM electron tomography			Type	A1 Journal article
	Year	2012	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	116	Issue		Pages	8-12
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	In materials science, high angle annular dark field scanning transmission electron microscopy is often used for tomography at the nanometer scale. In this work, it is shown that a thickness dependent, non-linear damping of the recorded intensities occurs. This results in an underestimated intensity in the interior of reconstructions of homogeneous particles, which is known as the cupping artifact. In this paper, this non-linear effect is demonstrated in experimental images taken under common conditions and is reproduced with a numerical simulation. Furthermore, an analytical derivation shows that these non-linearities can be inverted if the imaging is done quantitatively, thus preventing cupping in the reconstruction.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000304473700002	Publication Date	2012-03-09
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	67	Open Access
	Notes	Fwo			Approved	Most recent IF: 2.843; 2012 IF: 2.470
	Call Number	UA @ lucian @ c:irua:96558			Serial	518
Permanent link to this record



	Author	de Backer, A.; Martinez, G.T.; MacArthur, K.E.; Jones, L.; Béché, A.; Nellist, P.D.; Van Aert, S.
	Title	Dose limited reliability of quantitative annular dark field scanning transmission electron microscopy for nano-particle atom-counting			Type	A1 Journal article
	Year	2015	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	151	Issue	151	Pages	56-61
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Quantitative annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique to characterise nano-particles on an atomic scale. Because of their limited size and beam sensitivity, the atomic structure of such particles may become extremely challenging to determine. Therefore keeping the incoming electron dose to a minimum is important. However, this may reduce the reliability of quantitative ADF STEM which will here be demonstrated for nano-particle atom-counting. Based on experimental ADF STEM images of a real industrial catalyst, we discuss the limits for counting the number of atoms in a projected atomic column with single atom sensitivity. We diagnose these limits by combining a thorough statistical method and detailed image simulations.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000351237800008	Publication Date	2014-12-03
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	29	Open Access
	Notes	312483 Esteem2; 278510 Vortex; Fwo G039311; G006410; G037413; esteem2ta; ECASJO;			Approved	Most recent IF: 2.843; 2015 IF: 2.436
	Call Number	c:irua:123927 c:irua:123927			Serial	753
Permanent link to this record



	Author	Lubk, A.; Javon, E.; Cherkashin, N.; Reboh, S.; Gatel, C.; Hytch, M.
	Title	Dynamic scattering theory for dark-field electron holography of 3D strain fields			Type	A1 Journal article
	Year	2014	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	136	Issue		Pages	42-49
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Dark-held electron holography maps strain in crystal lattices into reconstructed phases over large fields of view. Here we investigate the details of the lattice strain-reconstructed phase relationship by applying dynamic scattering theory both analytically and numerically. We develop efficient analytic linear projection rules for 3D strain fields, facilitating a straight-forward calculation of reconstructed phases from 3D strained materials. They are used in the following to quantify the influence of various experimental parameters like strain magnitude, specimen thickness, excitation error and surface relaxation. (C) 2013 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000327884700006	Publication Date	2013-07-29
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	18	Open Access
	Notes	European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative (Reference312483 – ESTEEM2); esteem2_jra4			Approved	Most recent IF: 2.843; 2014 IF: 2.436
	Call Number	UA @ lucian @ c:irua:112836			Serial	766
Permanent link to this record



	Author	den Dekker, A.J.; Gonnissen, J.; de Backer, A.; Sijbers, J.; Van Aert, S.
	Title	Estimation of unknown structure parameters from high-resolution (S)TEM images : what are the limits?			Type	A1 Journal article
	Year	2013	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	134	Issue		Pages	34-43
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	Statistical parameter estimation theory is proposed as a quantitative method to measure unknown structure parameters from electron microscopy images. Images are then purely considered as data planes from which structure parameters have to be determined as accurately and precisely as possible using a parametric statistical model of the observations. For this purpose, an efficient algorithm is proposed for the estimation of atomic column positions and intensities from high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. Furthermore, the so-called CramérRao lower bound (CRLB) is reviewed to determine the limits to the precision with which continuous parameters such as atomic column positions and intensities can be estimated. Since this lower bound can only be derived for continuous parameters, alternative measures using the principles of detection theory are introduced for problems concerning the estimation of discrete parameters such as atomic numbers. An experimental case study is presented to show the practical use of these measures for the optimization of the experiment design if the purpose is to decide between the presence of specific atom types using STEM images.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000324474900006	Publication Date	2013-06-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	31	Open Access
	Notes	FWO; FP 2007-2013; Esteem2; esteem2_jra2			Approved	Most recent IF: 2.843; 2013 IF: 2.745
	Call Number	UA @ lucian @ c:irua:109240			Serial	1083
Permanent link to this record



	Author	Verbeeck, J.; Béché, A.; van den Broek, W.
	Title	A holographic method to measure the source size broadening in STEM			Type	A1 Journal article
	Year	2012	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	120	Issue		Pages	35-40
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	Source size broadening is an important resolution limiting effect in modern STEM experiments. Here, we propose an alternative method to measure the source size broadening making use of a holographic biprism to create interference patterns in an empty Ronchigram. This allows us to measure the exact shape of the source size broadening with a much better sampling than previously possible. We find that the shape of the demagnified source deviates considerably from a Gaussian profile that is often assumed. We fit the profile with a linear combination of a Gaussian and a bivariate Cauchy distribution showing that even though the full width at half maximum is similar to previously reported measurements, the tails of the profile are considerable wider. This is of fundamental importance for quantitative comparison of STEM simulations with experiments as these tails make the image contrast dependent on the interatomic distance, an effect that cannot be reproduced by a single Gaussian profile of fixed width alone.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000308082600005	Publication Date	2012-06-01
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	29	Open Access
	Notes	This work was supported by funding from the European Research Council under the 7th Framework Program (FP7), ERC Grant no. 246791 COUNTATOMS and ERC Starting Grant 278510 VORTEX. The Qu-Ant-EM microscope was partly funded by the Hercules fund from the Flemish Government. W. Van den Broek acknowledges funding from the Condor project, a project under the supervision of the Embedded Systems Institute (ESI) and FEI. This project is partially supported by the Dutch Ministry of Economic Affairs under the BSIK program. ECASJO_;			Approved	Most recent IF: 2.843; 2012 IF: 2.470
	Call Number	UA @ lucian @ c:irua:100466UA @ admin @ c:irua:100466			Serial	1483
Permanent link to this record



	Author	Krause, F.F.; Ahl, J.P.; Tytko, D.; Choi, P.P.; Egoavil, R.; Schowalter, M.; Mehrtens, T.; Müller-Caspary, K.; Verbeeck, J.; Raabe, D.; Hertkorn, J.; Engl, K.; Rosenauer, A.
	Title	Homogeneity and composition of AlInGaN : a multiprobe nanostructure study			Type	A1 Journal article
	Year	2015	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	156	Issue	156	Pages	29-36
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	The electronic properties of quaternary AlInGaN devices significantly depend on the homogeneity of the alloy. The identification of compositional fluctuations or verification of random-alloy distribution is hence of grave importance. Here, a comprehensive multiprobe study of composition and compositional homogeneity is presented, investigating AlInGaN layers with indium concentrations ranging from 0 to 17 at% and aluminium concentrations between 0 and 39 at% employing high-angle annular dark field scanning electron microscopy (HAADF STEM), energy dispersive X-ray spectroscopy (EDX) and atom probe tomography (APT). EDX mappings reveal distributions of local concentrations which are in good agreement with random alloy atomic distributions. This was hence investigated with HAADF STEM by comparison with theoretical random alloy expectations using statistical tests. To validate the performance of these tests, HAADF STEM image simulations were carried out for the case of a random-alloy distribution of atoms and for the case of In-rich clusters with nanometer dimensions. The investigated samples, which were grown by metal-organic vapor phase epitaxy (MOVPE), were thereby found to be homogeneous on this nanometer scale. Analysis of reconstructions obtained from APT measurements yielded matching results. Though HAADF STEM only allows for the reduction of possible combinations of indium and aluminium concentrations to the proximity of isolines in the two-dimensional composition space. The observed ranges of composition are in good agreement with the EDX and APT results within the respective precisions.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000361001800006	Publication Date	2015-04-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	11	Open Access
	Notes	312483 Esteem2; esteem2_ta			Approved	Most recent IF: 2.843; 2015 IF: 2.436
	Call Number	c:irua:126965 c:irua:126965UA @ admin @ c:irua:126965			Serial	1485
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	Author	Schattschneider, P.; Löffler, S.; Stöger-Pollach, M.; Verbeeck, J.
	Title	Is magnetic chiral dichroism feasible with electron vortices?			Type	A1 Journal article
	Year	2014	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	136	Issue		Pages	81-85
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	We discuss the feasibility of detecting magnetic transitions with focused electron vortex probes, suggested by selection rules for the magnetic quantum number. We theoretically estimate the dichroic signal strength in the L2,3 edge of ferromagnetic d metals. It is shown that under realistic conditions, the dichroic signal is undetectable for nanoparticles larger than View the MathML source. This is confirmed by a key experiment with nanometer-sized vortices.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000327884700011	Publication Date	2013-07-26
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	64	Open Access
	Notes	Countatoms; Vortex; Esteem2; esteem2jra3 ECASJO;			Approved	Most recent IF: 2.843; 2014 IF: 2.436
	Call Number	UA @ lucian @ c:irua:110952UA @ admin @ c:irua:110952			Serial	1750
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	Author	Van den Broek, W.; Rosenauer, A.; Van Aert, S.; Sijbers, J.; van Dyck, D.
	Title	A memory efficient method for fully three-dimensional object reconstruction with HAADF STEM			Type	A1 Journal article
	Year	2014	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	141	Issue		Pages	22-31
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
	Abstract	The conventional approach to object reconstruction through electron tomography is to reduce the three-dimensional problem to a series of independent two-dimensional slice-by-slice reconstructions. However, at atomic resolution the image of a single atom extends over many such slices and incorporating this image as prior knowledge in tomography or depth sectioning therefore requires a fully three-dimensional treatment. Unfortunately, the size of the three-dimensional projection operator scales highly unfavorably with object size and readily exceeds the available computer memory. In this paper, it is shown that for incoherent image formation the memory requirement can be reduced to the fundamental lower limit of the object size, both for tomography and depth sectioning. Furthermore, it is shown through multislice calculations that high angle annular dark field scanning transmission electron microscopy can be sufficiently incoherent for the reconstruction of single element nanocrystals, but that dynamical diffraction effects can cause classification problems if more than one element is present. (C) 2014 Elsevier B.V. All rights reserved.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000335766600004	Publication Date	2014-03-22
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	6	Open Access
	Notes	ResearchFoundationFlanders(FWO;G.0393.11; G.0064.10;andG.0374.13); European Union Seventh Frame- workProgramme [FP7/2007-2013]under Grant agreement no. 312483 (ESTEEM2).; esteem2jra2; esteem2jra4			Approved	Most recent IF: 2.843; 2014 IF: 2.436
	Call Number	UA @ lucian @ c:irua:117650			Serial	1992
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	Author	Verbeeck, J.; Tian, H.; Béché, A.
	Title	A new way of producing electron vortex probes for STEM			Type	A1 Journal article
	Year	2012	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	113	Issue		Pages	83-87
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	A spiral holographic aperture is used in the condensor plane of a scanning transmission electron microscope to produce a focussed electron vortex probe carrying a topological charge of either −1, 0 or +1. The spiral aperture design has a major advantage over the previously used forked aperture in that the three beams with topological charge m=−1, 0, and 1 are not side by side in the specimen plane, but rather on top of each other, focussed at different heights. This allows us to have only one selected beam in focus on the sample while the others contribute only to a background signal. In this paper we describe the working principle as well as first experimental results demonstrating atomic resolution HAADF STEM images obtained with electron vortex probes. These results pave the way for atomic resolution magnetic information when combined with electron energy loss spectroscopy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication	Amsterdam	Editor
	Language		Wos	000300554400002	Publication Date	2011-10-31
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991;	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.843	Times cited	62	Open Access
	Notes	J.V. wants to thank Miles Padgett for suggesting this setup and pointing to the relevant optics literature. Peter Schattschneider is acknowledged for in depth discussions on related topics. J.V acknowledges funding from the European Research Council under the 7th Framework Program (FP7), ERC Grant no. 46791-COUN-TATOMS and ERC Starting Grant no. 278510 VORTEX. The Qu-Ant-EM microscope is partially funded by the Hercules fund of the Flemish Government. ECASJO_;			Approved	Most recent IF: 2.843; 2012 IF: 2.470
	Call Number	UA @ lucian @ c:irua:93624UA @ admin @ c:irua:93624			Serial	2336
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