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| Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
| Title | Optimal experiment design for nanoparticle atom counting from ADF STEM images | Type | H2 Book chapter | ||
| Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
| Volume | Issue  |
Pages | 145-175 | ||
| Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
| Abstract | In this chapter, the principles of detection theory are used to quantify the probability of error for atom counting from high-resolution scanning transmission electron microscopy (HRSTEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom counting using the expression of the probability of error. We show that for very thin objects the low-angle annular dark-field (LAADF) regime is optimal and that for thicker objects the optimal inner detector angle increases. | ||||
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| Language | Wos | Publication Date | 2021-03-06 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | 217 | Series Issue | Edition | ||
| ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
| Impact Factor | Times cited | Open Access | Not_Open_Access | ||
| Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
| Call Number | UA @ admin @ c:irua:177530 | Serial | 6785 | ||
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| Author | de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S. | ||||
| Title | Statistical parameter estimation theory : principles and simulation studies | Type | H2 Book chapter | ||
| Year | 2021 | Publication | Advances in imaging and electron physics T2 – Advances in imaging and electron physics | Abbreviated Journal | |
| Volume | Issue |
Pages | 29-72 | ||
| Keywords | H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab | ||||
| Abstract | In this chapter, the principles of statistical parameter estimation theory for a quantitative analysis of atomic-resolution electron microscopy images are introduced. Within this framework, electron microscopy images are described by a parametric statistical model. Here, parametric models are introduced for different types of electron microscopy images: reconstructed exit waves, annular dark-field (ADF) scanning transmission electron microscopy (STEM) images, and simultaneously acquired ADF and annular bright-field (ABF) STEM images. Furthermore, the Cramér-Rao lower bound (CRLB) is introduced, i.e. a theoretical lower bound on the variance of any unbiased estimator. This CRLB is used to quantify the precision of the structure parameters of interest, such as the atomic column positions and the integrated atomic column intensities. | ||||
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| Language | Wos | Publication Date | 2021-03-06 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | 217 | Series Issue | Edition | ||
| ISSN | ISBN | 978-0-12-824607-8; 1076-5670 | Additional Links | UA library record | |
| Impact Factor | Times cited | Open Access | Not_Open_Access | ||
| Notes | ERC Consolidator project funded by the European Union grant #770887 Picometrics | Approved | Most recent IF: NA | ||
| Call Number | UA @ admin @ c:irua:177527 | Serial | 6788 | ||
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| Author | De wael, A.; De Backer, A.; Lobato, I.; Van Aert, S. | ||||
| Title | Modelling ADF STEM images using elliptical Gaussian peaks and its effects on the quantification of structure parameters in the presence of sample tilt | Type | A1 Journal article | ||
| Year | 2021 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
| Volume | Issue |
Pages | 113391 | ||
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | A small sample tilt away from a main zone axis orientation results in an elongation of the atomic columns in ADF STEM images. An often posed research question is therefore whether the ADF STEM image intensities of tilted nanomaterials should be quantified using a parametric imaging model consisting of elliptical rather than the currently used symmetrical peaks. To this purpose, simulated ADF STEM images corresponding to different amounts of sample tilt are studied using a parametric imaging model that consists of superimposed 2D elliptical Gaussian peaks on the one hand and symmetrical Gaussian peaks on the other hand. We investigate the quantification of structural parameters such as atomic column positions and scattering cross sections using both parametric imaging models. In this manner, we quantitatively study what can be gained from this elliptical model for quantitative ADF STEM, despite the increased parameter space and computational effort. Although a qualitative improvement can be achieved, no significant quantitative improvement in the estimated structure parameters is achieved by the elliptical model as compared to the symmetrical model. The decrease in scattering cross sections with increasing sample tilt is even identical for both types of parametric imaging models. This impedes direct comparison with zone axis image simulations. Nonetheless, we demonstrate how reliable atom-counting can still be achieved in the presence of small sample tilt. | ||||
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| Language | Wos | 000704334200001 | Publication Date | 2021-09-24 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.843 | Times cited | Open Access | OpenAccess | |
| Notes | This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp.; esteem3JRA; esteem3reported | Approved | Most recent IF: 2.843 | ||
| Call Number | EMAT @ emat @c:irua:181462 | Serial | 6810 | ||
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| Author | Hudry, D.; De Backer, A.; Popescu, R.; Busko, D.; Howard, I.A.; Bals, S.; Zhang, Y.; Pedrazo‐Tardajos, A.; Van Aert, S.; Gerthsen, D.; Altantzis, T.; Richards, B.S. | ||||
| Title | Interface Pattern Engineering in Core‐Shell Upconverting Nanocrystals: Shedding Light on Critical Parameters and Consequences for the Photoluminescence Properties | Type | A1 Journal article | ||
| Year | 2021 | Publication | Small | Abbreviated Journal | Small |
| Volume | Issue |
Pages | 2104441 | ||
| Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT) | ||||
| Abstract | Advances in controlling energy migration pathways in core-shell lanthanide (Ln)-based hetero-nanocrystals (HNCs) have relied heavily on assumptions about how optically active centers are distributed within individual HNCs. In this article, it is demonstrated that different types of interface patterns can be formed depending on shell growth conditions. Such interface patterns are not only identified but also characterized with spatial resolution ranging from the nanometer- to the atomic-scale. In the most favorable cases, atomic-scale resolved maps of individual particles are obtained. It is also demonstrated that, for the same type of core-shell architecture, the interface pattern can be engineered with thicknesses of just 1 nm up to several tens of nanometers. Total alloying between the core and shell domains is also possible when using ultra-small particles as seeds. Finally, with different types of interface patterns (same architecture and chemical composition of the core and shell domains) it is possible to modify the output color (yellow, red, and green-yellow) or change (improvement or degradation) the absolute upconversion quantum yield. The results presented in this article introduce an important paradigm shift and pave the way toward the emergence of a new generation of core-shell Ln-based HNCs with better control over their atomic-scale organization. | ||||
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| Language | Wos | 000710758000001 | Publication Date | 2021-10-25 | |
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| ISSN | 1613-6810 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 8.643 | Times cited | 17 | Open Access | OpenAccess |
| Notes | The authors would like to acknowledge the financial support provided by the Helmholtz Recruitment Initiative Fellowship (B.S.R.) and the Helmholtz Association's Research Field Energy (Materials and Technologies for the Energy Transition program, Topic 1 Photovoltaics and Wind Energy). The authors would like to thank the Karlsruhe Nano Micro Facility (KNMF) for STEM access. 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 PICOMETRICS to S.V.A. and Grant agreement no. 815128 REALNANO to S.B.). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through Projects no. G.0502.18N, G.0267.18N, and a postdoctoral grant to A.D.B. T.A. acknowledges funding from the University of Antwerp Research fund (BOF). This project had received funding (EUSMI proposal #E181100205) from the European Union's Horizon 2020 Research and Innovation Programme under Grant agreement no 731019 (EUSMI). D.H. would like to thank “CGFigures” for helpful tutorials on 3D graphics with Blender.; sygmaSB | Approved | Most recent IF: 8.643 | ||
| Call Number | EMAT @ emat @c:irua:183285 | Serial | 6817 | ||
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| Author | Lin, A.; De Backer, J.; Quatannens, D.; Cuypers, B.; Verswyvel, H.; De La Hoz, E.C.; Ribbens, B.; Siozopoulou, V.; Van Audenaerde, J.; Marcq, E.; Lardon, F.; Laukens, K.; Vanlanduit, S.; Smits, E.; Bogaerts, A. | ||||
| Title | The effect of local non‐thermal plasma therapy on the<scp>cancer‐immunity</scp>cycle in a melanoma mouse model | Type | University Hospital Antwerp | ||
| Year | 2022 | Publication | Bioengineering & Translational Medicine | Abbreviated Journal | Bioengineering & Transla Med |
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Pages | |||
| Keywords | University Hospital Antwerp; A1 Journal article; Pharmacology. Therapy; Engineering sciences. Technology; ADReM Data Lab (ADReM); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES) | ||||
| Abstract | Melanoma remains a deadly cancer despite significant advances in immune checkpoint blockade and targeted therapies. The incidence of melanoma is also growing worldwide, which highlights the need for novel treatment options and strategic combination of therapies. Here, we investigate non-thermal plasma (NTP), an ionized gas, as a promising, therapeutic option. In a melanoma mouse model, direct treatment of tumors with NTP results in reduced tumor burden and prolonged survival. Physical characterization of NTP treatment in situ reveals the deposited NTP energy and temperature associated with therapy response, and whole transcriptome analysis of the tumor identified several modulated pathways. NTP treatment also enhances the cancer-immunity cycle, as immune cells in both the tumor and tumor-draining lymph nodes appear more stimulated to perform their anti-cancer functions. Thus, our data suggest that local NTP therapy stimulates systemic, anti-cancer immunity. We discuss, in detail, how these fundamental insights will help direct the translation of NTP technology into the clinic and inform rational combination strategies to address the challenges in melanoma therapy. | ||||
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| Language | Wos | 000784103500001 | Publication Date | 2022-04-21 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 2380-6761 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | Open Access | OpenAccess | ||
| Notes | Vlaamse regering, 1S67621N 1S76421N G044420N 12S9221N 12S9218N ; The authors would like to thank and acknowledge Christophe Hermans, Ho Wa Lau, and Hilde Lambrechts for their help with sectioning and preparing the IHC slides. The authors would also like to thank Dani Banner for designing the ergonomic NTP applicator handle and Hasan Baysal for 3D printing the pieces used in this experiment. We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr Willy Floren, and the Vereycken family. Some of the resources and services used in this work were provided by the VSC (Flemish Supercomputer Center) The data that support the findings of this study are available from the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9218N (Abraham Lin), 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaert, and Steve Vanlanduit), 1S76421N (Delphine Quatannens), and 1S67621N (Hanne Verswyvel). Figure 7 was created with BioRender.com. | Approved | Most recent IF: NA | ||
| Call Number | PLASMANT @ plasmant @c:irua:187909 | Serial | 7056 | ||
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| Author | De Backer, J.; Lin, A.; Berghe, W.V.; Bogaerts, A.; Hoogewijs, D. | ||||
| Title | Cytoglobin inhibits non-thermal plasma-induced apoptosis in melanoma cells through regulation of the NRF2-mediated antioxidant response | Type | A1 Journal article | ||
| Year | 2022 | Publication | Redox Biology | Abbreviated Journal | Redox Biol |
| Volume | 55 | Issue |
Pages | 102399 | |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Proteinscience, proteomics and epigenetic signaling (PPES) | ||||
| Abstract | Melanoma arises from pigment-producing cells called melanocytes located in the basal layers of the epidermis of the skin. Cytoglobin (CYGB) is a ubiquitously expressed hexacoordinated globin that is highly enriched in melanocytes and frequently downregulated during melanomagenesis. Previously, we showed that non-thermal plasma (NTP)-produced reactive oxygen and nitrogen species (RONS) lead to the formation of an intra molecular disulfide bridge that would allow CYGB to function as a redox-sensitive protein. Here, we investigate the cytotoxic effect of indirect NTP treatment in two melanoma cell lines with divergent endogenous CYGB expression levels, and we explore the role of CYGB in determining treatment outcome. Our findings are consistent with previous studies supporting that NTP cytotoxicity is mediated through the production of RONS and leads to apoptotic cell death in melanoma cells. Furthermore, we show that NTP-treated solutions elicit an antioxidant response through the activation of nuclear factor erythroid 2–related factor 2 (NRF2). The knock down and overexpression of CYGB respectively sensitizes and protects melanoma cells from RONS-induced apoptotic cell death. The presence of CYGB enhances heme-oxygenase 1 (HO-1) and NRF2 protein expression levels, whereas the absence impairs their expression. Moreover, analysis of the CYGB-dependent transcriptome demonstrates the tumor suppressor long non-coding RNA maternally expressed 3 (MEG3) as a hitherto unde scribed link between CYGB and NRF2. Thus, the presence of CYGB, at least in melanoma cells, seems to play a central role in determining the therapeutic outcome of RONS-inducing anticancer therapies, like NTP-treated solutions, possessing both tumor-suppressive and oncogenic features. Hence, CYGB expression could be of in terest either as a biomarker or as a candidate for future targeted therapies in melanoma. | ||||
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| Language | Wos | 000844595100002 | Publication Date | 0000-00-00 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 2213-2317 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 11.4 | Times cited | Open Access | OpenAccess | |
| Notes | This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work include: 12S9221 N (Abraham Lin) and G044420 N (Abraham Lin and Annemie Bogaerts). Joey De Backer acknowledges a visiting fellowship from the University of Fribourg. David Hoogewijs acknowledges support by the Swiss National Science Foundation (grants 31003A173000 and 310030207460). | Approved | Most recent IF: 11.4 | ||
| Call Number | PLASMANT @ plasmant @c:irua:190635 | Serial | 7101 | ||
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| Author | De Backer, A.; Zhang, Z.; van den Bos, K.H.W.; Bladt, E.; Sánchez‐Iglesias, A.; Liz‐Marzán, L.M.; Nellist, P.D.; Bals, S.; Van Aert, S. | ||||
| Title | Element Specific Atom Counting at the Atomic Scale by Combining High Angle Annular Dark Field Scanning Transmission Electron Microscopy and Energy Dispersive X‐ray Spectroscopy | Type | A1 Journal article | ||
| Year | 2022 | Publication | Small methods | Abbreviated Journal | Small Methods |
| Volume | Issue |
Pages | 2200875 | ||
| Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) | ||||
| Abstract | A new methodology is presented to count the number of atoms in multimetallic nanocrystals by combining energy dispersive X-ray spectroscopy (EDX) and high angle annular dark field scanning transmission electron microscopy (HAADF STEM). For this purpose, the existence of a linear relationship between the incoherent HAADF STEM and EDX images is exploited. Next to the number of atoms for each element in the atomic columns, the method also allows quantification of the error in the obtained number of atoms, which is of importance given the noisy nature of the acquired EDX signals. Using experimental images of an Au@Ag core–shell nanorod, it is demonstrated that 3D structural information can be extracted at the atomic scale. Furthermore, simulated data of an Au@Pt core–shell nanorod show the prospect to characterize heterogeneous nanostructures with adjacent atomic numbers. | ||||
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| Language | Wos | 000862072700001 | Publication Date | 2022-09-30 | |
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| ISSN | 2366-9608 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 12.4 | Times cited | 5 | Open Access | OpenAccess |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A., Grant 815128 REALNANO to S.B., and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B.; esteem3reported; esteem3JRA | Approved | Most recent IF: 12.4 | ||
| Call Number | EMAT @ emat @c:irua:191570 | Serial | 7109 | ||
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| Author | De wael, A.; De Backer, A.; Yu, C.-P.; Sentürk, D.G.; Lobato, I.; Faes, C.; Van Aert, S. | ||||
| Title | Three Approaches for Representing the Statistical Uncertainty on Atom-Counting Results in Quantitative ADF STEM | Type | A1 Journal article | ||
| Year | 2022 | Publication | Microscopy and microanalysis | Abbreviated Journal | Microsc Microanal |
| Volume | Issue |
Pages | 1-9 | ||
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | A decade ago, a statistics-based method was introduced to count the number of atoms from annular dark-field scanning transmission electron microscopy (ADF STEM) images. In the past years, this method was successfully applied to nanocrystals of arbitrary shape, size, and composition (and its high accuracy and precision has been demonstrated). However, the counting results obtained from this statistical framework are so far presented without a visualization of the actual uncertainty about this estimate. In this paper, we present three approaches that can be used to represent counting results together with their statistical error, and discuss which approach is most suited for further use based on simulations and an experimental ADF STEM image. | ||||
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| Language | Wos | 000854930500001 | Publication Date | 2022-09-19 | |
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| Series Volume | Series Issue | Edition | |||
| ISSN | 1431-9276 | ISBN | Additional Links | UA library record; WoS full record | |
| Impact Factor | 2.8 | Times cited | Open Access | OpenAccess | |
| Notes | This project has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N, G.0267.18N, and EOS 30489208. S.V.A. acknowledges TOP BOF funding from the University of Antwerp. The authors are grateful to L.M. Liz-Marzán (CIC biomaGUNE and Ikerbasque) for providing the samples. esteem3reported; esteem3jra | Approved | Most recent IF: 2.8 | ||
| Call Number | EMAT @ emat @c:irua:190585 | Serial | 7119 | ||
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| Author | Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. | ||||
| Title | Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors | Type | A1 Journal article | ||
| Year | 2022 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
| Volume | 242 | Issue |
Pages | 113626 | |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
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| Language | Wos | 000873778100001 | Publication Date | 0000-00-00 | |
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra | Approved | Most recent IF: 2.2 | ||
| Call Number | EMAT @ emat @c:irua:190925 | Serial | 7118 | ||
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| Author | De Backer, A.; Bals, S.; Van Aert, S. | ||||
| 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 | ||
| Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal | |
| Volume | Issue |
Pages | 113702 | ||
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| 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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| Language | Wos | 000953765800001 | Publication Date | 2023-02-10 | |
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| ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.2 | Times cited | 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 | ||
| Call Number | EMAT @ emat @c:irua:195896 | Serial | 7236 | ||
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| Author | Lin, A.; Sahun, M.; Biscop, E.; Verswyvel, H.; De Waele, J.; De Backer, J.; Theys, C.; Cuypers, B.; Laukens, K.; Berghe, W.V.; Smits, E.; Bogaerts, A. | ||||
| Title | Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma | Type | A1 Journal article | ||
| Year | 2023 | Publication | Drug resistance updates | Abbreviated Journal | |
| Volume | 67 | Issue |
Pages | 100914 | |
| Keywords | A1 Journal article; Pharmacology. Therapy; ADReM Data Lab (ADReM); Center for Oncological Research (CORE); Proteinscience, proteomics and epigenetic signaling (PPES); Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | To gain insights into the underlying mechanisms of NTP therapy sensitivity and resistance, using the firstever NTP-resistant cell line derived from sensitive melanoma cells (A375). Methods: Melanoma cells were exposed to NTP and re-cultured for 12 consecutive weeks before evaluation against the parental control cells. Whole transcriptome sequencing analysis was performed to identify differentially expressed genes and enriched molecular pathways. Glucose uptake, extracellular lactate, media acidification, and mitochondrial respiration was analyzed to determine metabolic changes. Cell death inhibitors were used to assess the NTP-induced cell death mechanisms, and apoptosis and ferroptosis was further validated via Annexin V, Caspase 3/7, and lipid peroxidation analysis. Results: Cells continuously exposed to NTP became 10 times more resistant to NTP compared to the parental cell line of the same passage, based on their half-maximal inhibitory concentration (IC50). Sequencing and metabolic analysis indicated that NTP-resistant cells had a preference towards aerobic glycolysis, while cell death analysis revealed that NTP-resistant cells exhibited less apoptosis but were more vulnerable to lipid peroxidation and ferroptosis. Conclusions: A preference towards aerobic glycolysis and ferroptotic cell death are key physiological changes in NTP-resistance cells, which opens new avenues for further, in-depth research into other cancer types. |
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| Language | Wos | 000925156500001 | Publication Date | 2022-12-29 | |
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| ISSN | 1368-7646 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 24.3 | Times cited | Open Access | OpenAccess | |
| Notes | The authors would like to thank Dr. Christophe Deben and Ms. Hannah Zaryouh (Center for Oncological Research, University of Antwerp) for the use and their help with the D300e Digital Dispenser and Spark® Cyto, as well as Ms. Rapha¨elle Corremans (Laboratory Pathophysiology, University of Antwerp) for the use of their lactate meter. The authors would also like to acknowledge the help from Ms. Tias Verhezen and Mr. Cyrus Akbari, who was involved at the start of the project but could not continue due to the COVID-19 pandemic. The authors also acknowledge the resources and services provided by the VSC (Flemish Supercomputer Center). This work was funded in part by the Research Foundation – Flanders (FWO) and the Flemish Government. The FWO fellowships and grants that funded this work also include: 12S9221N (Abraham Lin), G044420N (Abraham Lin, Annemie Bogaerts), and 1S67621N (Hanne Verswyvel). We would also like to thank several patrons, as part of this research was funded by donations from different donors, including Dedert Schilde vzw, Mr. Willy Floren, and the Vereycken family. We would also like to acknowledge the support from the European Cooperation in Science & Technology (COST) Action on Therapeutical applications of Cold Plasmas (CA20114; PlasTHER). | Approved | Most recent IF: 24.3; 2023 IF: 10.906 | ||
| Call Number | PLASMANT @ plasmant @c:irua:193167 | Serial | 7240 | ||
| Permanent link to this record | |||||
| Author | Zhang, Z.; Lobato, I.; De Backer, A.; Van Aert, S.; Nellist, P. | ||||
| 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 | |
| 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. | ||||
| Address | |||||
| Corporate Author | Zezhong Zhang | Thesis | |||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000995063900001 | Publication Date | 2022-12-28 | |
| 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 | 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 | |||||
| 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 | ||
| 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. | ||||
| 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 | ||
| 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. | ||||
| 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 | ||
| Permanent link to this record | |||||
| Author | Van Holsbeke, C.S.; Verhulst, S.L.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Verdonck, P.R.; van Doorn, J.W.D.; Nadjmi, N.; de Backer, W.A. | ||||
| Title | Change in upper airway geometry between upright and supine position during tidal nasal breathing | Type | A1 Journal article | ||
| Year | 2014 | Publication | Journal Of Aerosol Medicine And Pulmonary Drug Delivery | Abbreviated Journal | J Aerosol Med Pulm D |
| Volume | 27 | Issue |
1 | Pages | 51-57 |
| Keywords | A1 Journal article; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000331144500007 | Publication Date | 2013-03-19 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1941-2711;1941-2703; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.528 | Times cited | 16 | Open Access | |
| Notes | ; ; | Approved | Most recent IF: 2.528; 2014 IF: 2.798 | ||
| Call Number | UA @ lucian @ c:irua:115759 | Serial | 308 | ||
| Permanent link to this record | |||||
| Author | de Backer, J.W.; Vos, W.G.; Devolder, A.; Verhulst, S.L.; Germonpré, P.; Wuyts, F.L.; Parizel, P.M.; de Backer, W. | ||||
| 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 |
| Keywords | A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | New York, N.Y. | Editor | ||
| Language | Wos | 000253062100014 | Publication Date | 2007-08-15 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| 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 | 53 | Open Access | |
| Notes | Approved | Most recent IF: 2.664; 2008 IF: 2.784 | |||
| Call Number | UA @ lucian @ c:irua:64859 | Serial | 456 | ||
| Permanent link to this record | |||||
| Author | De Backer, A.; Van Aert, S.; Faes, C.; Arslan Irmak, E.; Nellist, P.D.; Jones, L. | ||||
| Title | Experimental reconstructions of 3D atomic structures from electron microscopy images using a Bayesian genetic algorithm | Type | A1 Journal article | ||
| Year | 2022 | Publication | N P J Computational Materials | Abbreviated Journal | npj Comput Mater |
| Volume | 8 | Issue |
1 | Pages | 216 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | We introduce a Bayesian genetic algorithm for reconstructing atomic models of monotype crystalline nanoparticles from a single projection using Z-contrast imaging. The number of atoms in a projected atomic column obtained from annular dark field scanning transmission electron microscopy images serves as an input for the initial three-dimensional model. The algorithm minimizes the energy of the structure while utilizing a priori information about the finite precision of the atom-counting results and neighbor-mass relations. The results show promising prospects for obtaining reliable reconstructions of beam-sensitive nanoparticles during dynamical processes from images acquired with sufficiently low incident electron doses. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000866500900001 | Publication Date | 2022-10-12 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2057-3960 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | Times cited | Open Access | OpenAccess | ||
| Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S.V.A. and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0267.18N, G.0502.18N, G.0346.21N) and a postdoctoral grant to A.D.B. L.J. acknowledges Science Foundation Ireland (SFI – grant number URF/RI/191637), the Royal Society, and the AMBER Centre. The authors acknowledge Aakash Varambhia for his assistance and expertise with the experimental recording and use of characterization facilities within the David Cockayne Centre for Electron Microscopy, Department of Materials, University of Oxford, and in particular the EPSRC (EP/K040375/1 South of England Analytical Electron Microscope).; esteem3reported; esteem3JRA | Approved | Most recent IF: NA | ||
| Call Number | EMAT @ emat @c:irua:191398 | Serial | 7114 | ||
| Permanent link to this record | |||||
| Author | Arteaga Cardona, F.; Jain, N.; Popescu, R.; Busko, D.; Madirov, E.; Arús, B.A.; Gerthsen, D.; De Backer, A.; Bals, S.; Bruns, O.T.; Chmyrov, A.; Van Aert, S.; Richards, B.S.; Hudry, D. | ||||
| Title | Preventing cation intermixing enables 50% quantum yield in sub-15 nm short-wave infrared-emitting rare-earth based core-shell nanocrystals | Type | A1 Journal article | ||
| Year | 2023 | Publication | Nature communications | Abbreviated Journal | Nat Commun |
| Volume | 14 | Issue |
1 | Pages | 4462 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT) | ||||
| Abstract | Short-wave infrared (SWIR) fluorescence could become the new gold standard in optical imaging for biomedical applications due to important advantages such as lack of autofluorescence, weak photon absorption by blood and tissues, and reduced photon scattering coefficient. Therefore, contrary to the visible and NIR regions, tissues become translucent in the SWIR region. Nevertheless, the lack of bright and biocompatible probes is a key challenge that must be overcome to unlock the full potential of SWIR fluorescence. Although rare-earth-based core-shell nanocrystals appeared as promising SWIR probes, they suffer from limited photoluminescence quantum yield (PLQY). The lack of control over the atomic scale organization of such complex materials is one of the main barriers limiting their optical performance. Here, the growth of either homogeneous (α-NaYF<sub>4</sub>) or heterogeneous (CaF<sub>2</sub>) shell domains on optically-active α-NaYF<sub>4</sub>:Yb:Er (with and without Ce<sup>3+</sup>co-doping) core nanocrystals is reported. The atomic scale organization can be controlled by preventing cation intermixing only in heterogeneous core-shell nanocrystals with a dramatic impact on the PLQY. The latter reached 50% at 60 mW/cm<sup>2</sup>; one of the highest reported PLQY values for sub-15 nm nanocrystals. The most efficient nanocrystals were utilized for in vivo imaging above 1450 nm. | ||||
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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 001037058500022 | Publication Date | 2023-07-25 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 2041-1723 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 16.6 | Times cited | 1 | Open Access | OpenAccess |
| Notes | D.H. would like to thank Dominique Ectors (Bruker AXS GmbH, Karlsruhe, Germany) for assistance and discussion on the PXRD data and TOPAS evaluations. The authors would like to acknowledge the financial support provided by the Helmholtz Association via: i) the Professorial Recruitment Initiative Funding (B.S.R.); ii) the Research Field Energy – Program Materials and Technologies for the Energy Transition – Topic 1 Photovoltaics (F.A.C., D.B., E.M., B.S.R., D.H.). This project received funding from the European Union’s Horizon 2020 innovation programme under grant agreement 823717. This work was supported by the European Research Council (grant 770887-PICOMETRICS to S.V.A. and Grant 815128-REALNANO to S.B.). The authors acknowledge financial support from the ResearchFoundation Flanders (FWO, Belgium) through project fundings (G.0346.21 N to S.V.A. and S.B.) and a postdoctoral grant (A.D.B.). The authors (B.A.A., O.T.B. and A.C.) acknowledge funding from the Helmholtz Zentrum München, the DFG-Emmy Noether program (BR 5355/2-1) and from the CZI Deep Tissue Imaging (DTI-0000000248). The authors (O.T.B. and D.H.) would like to thank the Helmholtz Imaging (ZT-I-PF-4-038-BENIGN). | Approved | Most recent IF: 16.6; 2023 IF: 12.124 | ||
| Call Number | EMAT @ emat @c:irua:198158 | Serial | 8808 | ||
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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. | ||||
| 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 |
| 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) | ||||
| Abstract | |||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | New York, N.Y. | Editor | ||
| Language | Wos | 000248468000011 | Publication Date | 2006-12-19 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| 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 | 86 | Open Access | |
| Notes | Approved | Most recent IF: 2.664; 2007 IF: 2.897 | |||
| Call Number | UA @ lucian @ c:irua:62425 | Serial | 523 | ||
| Permanent link to this record | |||||
| Author | De wael, A.; De Backer, A.; Jones, L.; Varambhia, A.; Nellist, P.D.; Van Aert, S. | ||||
| 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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| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000519718100015 | Publication Date | 2020-03-13 | |
| Series Editor | Series Title | 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 | ||
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| Author | Guzzinati, G.; Altantzis, T.; Batuk, M.; De Backer, A.; Lumbeeck, G.; Samaee, V.; Batuk, D.; Idrissi, H.; Hadermann, J.; Van Aert, S.; Schryvers, D.; Verbeeck, J.; Bals, S. | ||||
| Title | Recent Advances in Transmission Electron Microscopy for Materials Science at the EMAT Lab of the University of Antwerp | Type | A1 Journal article | ||
| Year | 2018 | Publication | Materials | Abbreviated Journal | Materials |
| Volume | 11 | Issue |
11 | Pages | 1304 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | The rapid progress in materials science that enables the design of materials down to the nanoscale also demands characterization techniques able to analyze the materials down to the same scale, such as transmission electron microscopy. As Belgium’s foremost electron microscopy group, among the largest in the world, EMAT is continuously contributing to the development of TEM techniques, such as high-resolution imaging, diffraction, electron tomography, and spectroscopies, with an emphasis on quantification and reproducibility, as well as employing TEM methodology at the highest level to solve real-world materials science problems. The lab’s recent contributions are presented here together with specific case studies in order to highlight the usefulness of TEM to the advancement of materials science. | ||||
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| Language | Wos | 000444112800041 | Publication Date | 2018-07-28 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1996-1944 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.654 | Times cited | 15 | Open Access | OpenAccess |
| Notes | Fonds Wetenschappelijk Onderzoek, G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N AUHA13009 ; European Research Council, COLOURATOM 335078 ; Universiteit Antwerpen, GOA Solarpaint ; G. Guzzinati, T. Altantzis and A. De Backer have been supported by postdoctoral fellowship grants from the Research Foundation Flanders (FWO). Funding was also received from the European Research Council (starting grant no. COLOURATOM 335078), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 770887), the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N, G.0401.16N) and from the University of Antwerp through GOA project Solarpaint. Funding for the TopSPIN precession system under grant AUHA13009, as well as for the Qu-Ant-EM microscope, is acknowledged from the HERCULES Foundation. H. Idrissi is mandated by the Belgian National Fund for Scientific Research (F.R.S.-FNRS). (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; | Approved | Most recent IF: 2.654 | ||
| Call Number | EMAT @ emat @c:irua:153737UA @ admin @ c:irua:153737 | Serial | 5064 | ||
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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. | ||||
| 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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| Language | Wos | 000378059500010 | Publication Date | 2016-06-17 | |
| Series Editor | Series Title | 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 | 8.462 | 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 | ||
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| Author | Verhulst, S.L.; de Backer, J.; Van Gaal, L.; de Backer, W.; Desager, K. | ||||
| Title | Adenotonsillectomy as first-line treatment for sleep-disordered breathing in obese children | Type | L1 Letter to the editor | ||
| Year | 2008 | Publication | American journal of respiratory and critical care medicine | Abbreviated Journal | Am J Resp Crit Care |
| Volume | 177 | Issue |
12 | Pages | 1399 |
| Keywords | L1 Letter to the editor; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP) | ||||
| Abstract | |||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | New York | Editor | ||
| Language | Wos | Publication Date | 0000-00-00 | ||
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1073-449x; 1535-4970 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 13.204 | Times cited | Open Access | ||
| Notes | Approved | Most recent IF: 13.204; 2008 IF: 9.792 | |||
| Call Number | UA @ lucian @ c:irua:68864 | Serial | 59 | ||
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| Author | Vermeylen, S.; De Waele, J.; Vanuytsel, S.; De Backer, J.; Van der Paal, J.; Ramakers, M.; Leyssens, K.; Marcq, E.; Van Audenaerde, J.; L. J. Smits, E.; Dewilde, S.; Bogaerts, A. | ||||
| Title | Cold atmospheric plasma treatment of melanoma and glioblastoma cancer cells | Type | A1 Journal article | ||
| Year | 2016 | Publication | Plasma processes and polymers | Abbreviated Journal | Plasma Process Polym |
| Volume | 13 | Issue |
13 | Pages | 1195-1205 |
| Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
| Abstract | In this paper, two types of melanoma and glioblastoma cancer cell lines are treated with cold atmospheric plasma to assess the effect of several parameters on the cell viability. The cell viability decreases with treatment duration and time until analysis in all cell lines with varying sensitivity. The majority of dead cells stains both AnnexinV (AnnV) and propidium iodide, indicating that the plasma-treated non-viable cells are mostly late apoptotic or necrotic. Genetic mutations might be involved in the response to plasma. Comparing the effects of two gas mixtures, as well as indirect plasma-activated medium versus direct treatment, gives different results per cell line. In conclusion, this study confirms the potential of plasma for cancer therapy and emphasizes the influence of experimental parameters on therapeutic outcome. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | Wos | 000393131600007 | Publication Date | 2016-10-31 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1612-8850 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 2.846 | Times cited | 26 | Open Access | |
| Notes | The authors acknowledge the University of Antwerp for providing research funds. The authors are very grateful to V. Schulz-von der Gathen and J. Benedikt (Bochum University) for providing the COST RF plasma jet. The authors would also like to thank Eva Santermans (University of Hasselt) for statistical advice. J. De Waele, J. Van Audenaerde and J. Van der Paal are research fellows of the Research Foundation Flanders (fellowship numbers: 1121016N, 1S32316N and 11U5416N), E. Marcq of Flanders Innovation & Entrepreneurship (fellowship number: 141433). | Approved | Most recent IF: 2.846 | ||
| Call Number | PLASMANT @ plasmant @ c:irua:138722 | Serial | 4328 | ||
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| Author | Goris, B.; de Beenhouwer, J.; de Backer, A.; Zanaga, D.; Batenburg, K.J.; Sánchez-Iglesias, A.; Liz-Marzán, L.M.; Van Aert, S.; Bals, S.; Sijbers, J.; Van Tendeloo, G. | ||||
| Title | Measuring lattice strain in three dimensions through electron microscopy | Type | A1 Journal article | ||
| Year | 2015 | Publication | Nano letters | Abbreviated Journal | Nano Lett |
| Volume | 15 | Issue |
15 | Pages | 6996-7001 |
| Keywords | A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Vision lab | ||||
| Abstract | The three-dimensional (3D) atomic structure of nanomaterials, including strain, is crucial to understand their properties. Here, we investigate lattice strain in Au nanodecahedra using electron tomography. Although different electron tomography techniques enabled 3D characterizations of nanostructures at the atomic level, a reliable determination of lattice strain is not straightforward. We therefore propose a novel model-based approach from which atomic coordinates are measured. Our findings demonstrate the importance of investigating lattice strain in 3D. | ||||
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| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Washington | Editor | ||
| Language | Wos | 000363003100108 | Publication Date | 2015-09-04 | |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1530-6984;1530-6992; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 12.712 | Times cited | 87 | Open Access | OpenAccess |
| Notes | Fwo; 335078 Colouratom; 267867 Plasmaquo; 312483 Esteem2; 262348 Esmi; esteem2jra4; ECASSara; (ROMEO:white; preprint:; postprint:restricted 12 months embargo; pdfversion:cannot); | Approved | Most recent IF: 12.712; 2015 IF: 13.592 | ||
| Call Number | c:irua:127639 c:irua:127639 | Serial | 1965 | ||
| Permanent link to this record | |||||
| Author | Geuchies, J.J.; van Overbeek, C.; Evers, W.H.; Goris, B.; de Backer, A.; Gantapara, A.P.; Rabouw, F.T.; Hilhorst, J.; Peters, J.L.; Konovalov, O.; Petukhov, A.V.; Dijkstra, M.; Siebbeles, L.D.A.; van Aert, S.; Bals, S.; Vanmaekelbergh, D. | ||||
| Title | In situ study of the formation mechanism of two-dimensional superlattices from PbSe nanocrystals | Type | A1 Journal article | ||
| Year | 2016 | Publication | Nature materials | Abbreviated Journal | Nat Mater |
| Volume | 15 | Issue |
15 | Pages | 1248-1254 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | Oriented attachment of PbSe nanocubes can result in the formation of two-dimensional (2D) superstructures with long-range nanoscale and atomic order. This questions the applicability of classic models in which the superlattice grows by first forming a nucleus, followed by sequential irreversible attachment of nanocrystals, as one misaligned attachment would disrupt the 2D order beyond repair. Here, we demonstrate the formation mechanism of 2D PbSe superstructures with square geometry by using in situ grazing-incidence X-ray scattering (small angle and wide angle), ex situ electron microscopy, and Monte Carlo simulations. We observed nanocrystal adsorption at the liquid/gas interface, followed by the formation of a hexagonal nanocrystal monolayer. The hexagonal geometry transforms gradually through a pseudo-hexagonal phase into a phase with square order, driven by attractive interactions between the {100} planes perpendicular to the liquid substrate, which maximize facet-to-facet overlap. The nanocrystals then attach atomically via a necking process, resulting in 2D square superlattices. | ||||
| Address | Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands | ||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Editor | |||
| Language | English | Wos | 000389104400011 | Publication Date | 2016-09-05 |
| Series Editor | Series Title | Abbreviated Series Title | |||
| Series Volume | Series Issue | Edition | |||
| ISSN | 1476-1122 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
| Impact Factor | 39.737 | Times cited | 182 | Open Access | OpenAccess |
| Notes | This research is part of the programme ‘Designing Dirac Carriers in semiconductor honeycomb superlattices (DDC13),’ which is supported by the Foundation for Fundamental Research on Matter (FOM), which is part of the Dutch Research Council (NWO). J.J.G. acknowledges funding from the Debye and ESRF Graduate Programs. The authors gratefully acknowledge funding from the Research Foundation Flanders (G.036915 G.037413 and funding of postdoctoral grants to B.G. and A.d.B). S.B. acknowledges the European Research Council, ERC grant No 335078—Colouratom. The authors gratefully acknowledge I. Swart and M. van Huis for fruitful discussions. We acknowledge funding from NWO-CW TOPPUNT ‘Superficial Superstructures’. The X-ray scattering measurements were performed at the ID10 beamline at ESRF under proposal numbers SC-4125 and SC-3786. The authors thank G. L. Destri and F. Zontone for their support during the experiments.; ECAS_Sara; (ROMEO:yellow; preprint:; postprint:restricted ; pdfversion:cannot); | Approved | Most recent IF: 39.737 | ||
| Call Number | EMAT @ emat @ c:irua:136165 | Serial | 4289 | ||
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| 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 | de Backer, A.; De wael, A.; Gonnissen, J.; Van Aert, S. | ||||
| Title | Optimal experimental design for nano-particle atom-counting from high-resolution STEM images | Type | A1 Journal article | ||
| Year | 2015 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
| Volume | 151 | Issue |
151 | Pages | 46-55 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | In the present paper, the principles of detection theory are used to quantify the probability of error for atom-counting from high resolution scanning transmission electron microscopy (HR STEM) images. Binary and multiple hypothesis testing have been investigated in order to determine the limits to the precision with which the number of atoms in a projected atomic column can be estimated. The probability of error has been calculated when using STEM images, scattering cross-sections or peak intensities as a criterion to count atoms. Based on this analysis, we conclude that scattering cross-sections perform almost equally well as images and perform better than peak intensities. Furthermore, the optimal STEM detector design can be derived for atom-counting using the expression for the probability of error. We show that for very thin objects LAADF is optimal and that for thicker objects the optimal inner detector angle increases. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Amsterdam | Editor | ||
| Language | Wos | 000351237800007 | Publication Date | 2014-11-11 | |
| 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 | 24 | Open Access | |
| Notes | 312483 Esteem2; Fwo G039311; G037413; esteem2_jra2 | Approved | Most recent IF: 2.843; 2015 IF: 2.436 | ||
| Call Number | c:irua:123926 c:irua:123926 | Serial | 2481 | ||
| Permanent link to this record | |||||
| Author | Martinez, G.T.; Jones, L.; de Backer, A.; Béché, A.; Verbeeck, J.; Van Aert, S.; Nellist, P.D. | ||||
| Title | Quantitative STEM normalisation : the importance of the electron flux | Type | A1 Journal article | ||
| Year | 2015 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
| Volume | 159 | Issue |
159 | Pages | 46-58 |
| Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
| Abstract | Annular dark-field (ADF) scanning transmission electron microscopy (STEM) has become widely used in quantitative studies based on the opportunity to directly compare experimental and simulated images. This comparison merely requires the experimental data to be normalised and expressed in units of fractional beam-current. However, inhomogeneities in the response of electron detectors can complicate this normalisation. The quantification procedure becomes both experiment and instrument specific, requiring new simulations for the particular response of each instrument's detector, and for every camera-length used. This not only impedes the comparison between different instruments and research groups, but can also be computationally very time consuming. Furthermore, not all image simulation methods allow for the inclusion of an inhomogeneous detector response. In this work, we propose an alternative method for normalising experimental data in order to compare these with simulations that consider a homogeneous detector response. To achieve this, we determine the electron flux distribution reaching the detector by means of a camera-length series or a so-called atomic column cross-section averaged convergent beam electron diffraction (XSACBED) pattern. The result is then used to determine the relative weighting of the detector response. Here we show that the results obtained by this new electron flux weighted (EFW) method are comparable to the currently used method, while considerably simplifying the needed simulation libraries. The proposed method also allows one to obtain a metric that describes the quality of the detector response in comparison with the ideal detector response. | ||||
| Address | |||||
| Corporate Author | Thesis | ||||
| Publisher | Place of Publication | Amsterdam | Editor | ||
| Language | Wos | 000366220000006 | Publication Date | 2015-08-01 | |
| 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 | 27 | Open Access | |
| Notes | 246791 Countatoms; 278510 Vortex; 312483 Esteem2; Fwo G036815; G036915; G037413; G004413; esteem2ta ECASJO; | Approved | Most recent IF: 2.843; 2015 IF: 2.436 | ||
| Call Number | c:irua:127293 c:irua:127293UA @ admin @ c:irua:127293 | Serial | 2762 | ||
| Permanent link to this record | |||||