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Author de Backer, A.
  Title Quantitative atomic resolution electron microscopy using advanced statistical techniques Type Doctoral thesis
  Year 2015 Publication Abbreviated Journal
  Volume Issue Pages (up)
  Keywords Doctoral thesis; Electron microscopy for materials research (EMAT)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:125636 Serial 2747
Permanent link to this record
 
 
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
  Volume Issue Pages (up)
  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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000784103500001 Publication Date 2022-04-21
  Series Editor Series Title Abbreviated Series Title
  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
Permanent link to this record
 
 
Author Van Holsbeke, C.S.; Leemans, G.; Vos, W.G.; de Backer, J.W.; Vinchurkar, S.C.; Geldof, M.; Verdonck, P.R.; Parizel, P.M.; van Schil, P.E.; de Backer, W.A.
  Title Functional Respiratory Imaging as a tool to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis Type A1 Journal article
  Year 2013 Publication Respiratory care Abbreviated Journal Resp Care
  Volume Issue Pages (up) 1-20
  Keywords A1 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract In two subjects with a unilateral diaphragmatic paralysis and complaints of dyspnea, a completely different treatment approach was chosen despite similar anatomical and physiological abnormalities. These decisions were supported by the results generated by Functional Respiratory Imaging (FRI). FRI was able to generate functional information with respect to lobar ventilation and local drug deposition. In one subject, it was found that some lobes were poorly ventilated and drug deposition simulation showed that some regions were undertreated. This subject underwent a diaphragm plication to restore the ventilation. In the other subject, it was found that all lobes were still ventilated. A conservative approach with regular follow-up was chosen to wait for spontaneous recovery of the diaphragmatic function. Both subjects improved subjectively and objectively. These cases demonstrate how novel medical imaging techniques such as FRI can be used to personalize respiratory treatment in subjects with unilateral diaphragmatic paralysis.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Dallas, Tex. Editor
  Language Wos 000349200100024 Publication Date 2013-12-11
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0020-1324;1943-3654; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 1.733 Times cited 5 Open Access
  Notes ; ; Approved Most recent IF: 1.733; 2013 IF: 1.840
  Call Number UA @ lucian @ c:irua:112982 Serial 1303
Permanent link to this record
 
 
Author De Backer, J.; Razzokov, J.; Hammerschmid, D.; Mensch, C.; Hafideddine, Z.; Kumar, N.; van Raemdonck, G.; Yusupov, M.; Van Doorslaer, S.; Johannessen, C.; Sobott, F.; Bogaerts, A.; Dewilde, S.
  Title The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor Type A1 Journal article
  Year 2018 Publication Redox Biology Abbreviated Journal Redox Biol
  Volume 19 Issue Pages (up) 1-10
  Keywords A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); Molecular Spectroscopy (MolSpec)
  Abstract Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000449722100002 Publication Date 2018-07-24
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2213-2317 ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 6.337 Times cited Open Access OpenAccess
  Notes M.Y. and N.K. gratefully acknowledge financial support from the Research Foundation – Flanders (FWO), Grant nos. 1200216N and 12J5617N. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI). C.M acknowledges the financial support provided by the Flemish Community and the University of Antwerp (BOF-NOI) for the pre-doctoral scholarship is under grant number/project ID: 28465. S.V.D., S. D. and Z.H. acknowledge the FWO (Grant G.0687.13) and the GOA-BOF UA 2013–2016 (project-ID 28312) for funding. The computational resources and services used in this work were provided by the HPC core facility CalcUA of the Universiteit Antwerpen, and VSC (Flemish Supercomputer Center), funded by the Research Foundation – Flanders (FWO) and the Flemish Government – department EWI. Approved Most recent IF: 6.337
  Call Number PLASMANT @ plasmant @c:irua:152818 Serial 5006
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Introduction 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 (up) 1-28
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  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:177525 Serial 6784
Permanent link to this record
 
 
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 (up) 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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000854930500001 Publication Date 2022-09-19
  Series Editor Series Title Abbreviated Series Title
  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
Permanent link to this record
 
 
Author Goris, B.; De Beenhouwer, J.; de Backer, A.; Zanaga, D.; Batenburg, J.; Sanchez-Iglesias, A.; Liz-Marzan, L.; Van Aert, S.; Sijbers, J.; Van Tendeloo, G.; Bals, S.
  Title Investigating lattice strain in Au nanodecahedrons Type P1 Proceeding
  Year 2016 Publication Abbreviated Journal
  Volume Issue Pages (up) 11-12
  Keywords P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos Publication Date 2016-12-21
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 978-3-527-80846-5 ISBN Additional Links UA library record
  Impact Factor Times cited Open Access Not_Open_Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:145813 Serial 5144
Permanent link to this record
 
 
Author Martinez, G.T.; Rosenauer, A.; de Backer, A.; Verbeeck, J.; Van Aert, S.
  Title Quantitative composition determination at the atomic level using model-based high-angle annular dark field scanning transmission electron microscopy Type A1 Journal article
  Year 2014 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 137 Issue Pages (up) 12-19
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract High angle annular dark field scanning transmission electron microscopy (HAADF STEM) images provide sample information which is sensitive to the chemical composition. The image intensities indeed scale with the mean atomic number Z. To some extent, chemically different atomic column types can therefore be visually distinguished. However, in order to quantify the atomic column composition with high accuracy and precision, model-based methods are necessary. Therefore, an empirical incoherent parametric imaging model can be used of which the unknown parameters are determined using statistical parameter estimation theory (Van Aert et al., 2009, [1]). In this paper, it will be shown how this method can be combined with frozen lattice multislice simulations in order to evolve from a relative toward an absolute quantification of the composition of single atomic columns with mixed atom types. Furthermore, the validity of the model assumptions are explored and discussed.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Amsterdam Editor
  Language Wos 000331092200003 Publication Date 2013-11-09
  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 74 Open Access
  Notes FWO; FP7; ERC Countatoms; ESTEEM2; esteem2_ta Approved Most recent IF: 2.843; 2014 IF: 2.436
  Call Number UA @ lucian @ c:irua:111579UA @ admin @ c:irua:111579 Serial 2749
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 (up) 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
Permanent link to this record
 
 
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 (up) 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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  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
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 (up) 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 Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S.
  Title Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 177 Issue 177 Pages (up) 36-42
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000401219800006 Publication Date 2016-11-09
  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 13 Open Access OpenAccess
  Notes The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843
  Call Number EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 Serial 4316
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 (up) 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 (up) 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
 
 
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 (up) 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, 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 (up) 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 Martinez, G.T.; de Backer, A.; Rosenauer, A.; Verbeeck, J.; Van Aert, S.
  Title The effect of probe inaccuracies on the quantitative model-based analysis of high angle annular dark field scanning transmission electron microscopy images Type A1 Journal article
  Year 2014 Publication Micron Abbreviated Journal Micron
  Volume 63 Issue Pages (up) 57-63
  Keywords A1 Journal article; Engineering Management (ENM); Electron microscopy for materials research (EMAT)
  Abstract Quantitative structural and chemical information can be obtained from high angle annular dark field scanning transmission electron microscopy (HAADF STEM) images when using statistical parameter estimation theory. In this approach, we assume an empirical parameterized imaging model for which the total scattered intensities of the atomic columns are estimated. These intensities can be related to the material structure or composition. Since the experimental probe profile is assumed to be known in the description of the imaging model, we will explore how the uncertainties in the probe profile affect the estimation of the total scattered intensities. Using multislice image simulations, we analyze this effect for Cs corrected and non-Cs corrected microscopes as a function of inaccuracies in cylindrically symmetric aberrations, such as defocus and spherical aberration of third and fifth order, and non-cylindrically symmetric aberrations, such as 2-fold and 3-fold astigmatism and coma.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Oxford Editor
  Language Wos 000338402500011 Publication Date 2014-01-02
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0968-4328; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 1.98 Times cited 25 Open Access
  Notes FWO (G.0393.11; G.0064.10; G.0374.13; G.0044.13); European Research Council under the 7th Framework Program (FP7); ERC GrantNo. 246791-COUNTATOMS and ERC Starting Grant No. 278510-VORTEX. A.R. thanks the DFG under contract number RO2057/8-1.The research leading to these results has received funding fromthe European Union 7th Framework Programme [FP7/2007-2013]under grant agreement no. 312483 (ESTEEM2).; esteem2ta ECASJO; Approved Most recent IF: 1.98; 2014 IF: 1.988
  Call Number UA @ lucian @ c:irua:113857UA @ admin @ c:irua:113857 Serial 831
Permanent link to this record
 
 
Author De wael, A.; De Backer, A.; Jones, L.; Nellist, P.D.; Van Aert, S.
  Title Hybrid statistics-simulations based method for atom-counting from ADF STEM images Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 177 Issue 177 Pages (up) 69-77
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
  Abstract A hybrid statistics-simulations based method for atom-counting from annular dark field scanning transmission electron microscopy (ADF STEM) images of monotype crystalline nanostructures is presented. Different atom-counting methods already exist for model-like systems. However, the increasing relevance of radiation damage in the study of nanostructures demands a method that allows atom-counting from low dose images with a low signal-to-noise ratio. Therefore, the hybrid method directly includes prior knowledge from image simulations into the existing statistics-based method for atom-counting, and accounts in this manner for possible discrepancies between actual and simulated experimental conditions. It is shown by means of simulations and experiments that this hybrid method outperforms the statistics-based method, especially for low electron doses and small nanoparticles. The analysis of a simulated low dose image of a small nanoparticle suggests that this method allows for far more reliable quantitative analysis of beam-sensitive materials.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000401219800010 Publication Date 2017-01-25
  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 8 Open Access OpenAccess
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0368.15N, G.0369.15N, and WO.010.16N), and a postdoctoral research Grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). The authors are grateful to G.T. Martinez for providing image simulations. Approved Most recent IF: 2.843
  Call Number EMAT @ emat @ c:irua:141718 Serial 4486
Permanent link to this record
 
 
Author Van Aert, S.; De Backer, A.; Martinez, G.T.; den Dekker, A.J.; Van Dyck, D.; Bals, S.; Van Tendeloo, G.
  Title Advanced electron crystallography through model-based imaging Type A1 Journal article
  Year 2016 Publication IUCrJ Abbreviated Journal Iucrj
  Volume 3 Issue 3 Pages (up) 71-83
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab; Engineering Management (ENM)
  Abstract The increasing need for precise determination of the atomic arrangement of non-periodic structures in materials design and the control of nanostructures explains the growing interest in quantitative transmission electron microscopy. The aim is to extract precise and accurate numbers for unknown structure parameters including atomic positions, chemical concentrations and atomic numbers. For this purpose, statistical parameter estimation theory has been shown to provide reliable results. In this theory, observations are considered purely as data planes, from which structure parameters have to be determined using a parametric model describing the images. As such, the positions of atom columns can be measured with a precision of the order of a few picometres, even though the resolution of the electron microscope is still one or two orders of magnitude larger. Moreover, small differences in average atomic number, which cannot be distinguished visually, can be quantified using high-angle annular dark-field scanning transmission electron microscopy images. In addition, this theory allows one to measure compositional changes at interfaces, to count atoms with single-atom sensitivity, and to reconstruct atomic structures in three dimensions. This feature article brings the reader up to date, summarizing the underlying theory and highlighting some of the recent applications of quantitative model-based transmisson electron microscopy.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000368590900010 Publication Date 2015-11-13
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 2052-2525; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 5.793 Times cited 30 Open Access OpenAccess
  Notes The authors gratefully acknowledge the Research Foundation Flanders (FWO, Belgium) for funding and for a PhD grant to ADB. The research leading to these results has received funding from the European Union 7th Framework Program (FP7/20072013) under grant agreement No. 312483 (ESTEEM2). SB and GVT acknowledge the European Research Council under the 7th Framework Program (FP7), ERC grant No. 335078 – COLOURATOMS and ERC grant No. 246791 – COUNTATOMS.; esteem2jra2; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:can); Approved Most recent IF: 5.793
  Call Number c:irua:129589 c:irua:129589 Serial 3965
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Efficient fitting algorithm 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 (up) 73-90
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT)
  Abstract An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic-resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighboring columns, enabling the analysis of a large field of view. To provide end-users with this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. In this chapter, this efficient algorithm is applied to three different nanostructures for which the analysis of a large field of view is required.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  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:177528 Serial 6778
Permanent link to this record
 
 
Author Vinchurkar, S.; De Backer, L.; Vos, W.; Van Holsbeke, C.; de Backer, J.; de Backer, W.
  Title A case series on lung deposition analysis of inhaled medication using functional imaging based computational fluid dynamics in asthmatic patients : effect of upper airway morphology and comparison with in vivo data Type A1 Journal article
  Year 2012 Publication Inhalation Toxicology Abbreviated Journal Inhal Toxicol
  Volume 24 Issue 2 Pages (up) 81-88
  Keywords A1 Journal article; Pharmacology. Therapy; Biophysics and Biomedical Physics; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract Context: Asthma affects 20 million Americans resulting in an economic burden of approximately $18 billion in the US alone (Allergies and Asthma Foundation 2000; National Center for Environmental Health (NCEH) 1999). Research studies based on differences in patient-specific airway morphology for asthma and the associated effect on deposition of inhaled aerosols are currently not available in the literature. Therefore, the role of morphological variations such as upper airway (extrathoracic) occlusion is not well documented. Objective: Functional imaging based computational fluid dynamics (CFD) of the respiratory airways for five asthmatic subjects is performed in this study using computed tomography (CT) based patient-specific airway models and boundary conditions. Methods: CT scans for 5 asthma patients were used to reconstruct 3D lung models using segmentation software. An averaged inhalation profile and patient-specific lobar flow distribution were used to perform the simulation. The simulations were used to obtain deposition for BDP/Formoterol (R) HFA pMDI in the patient-specific airway models. Results: The lung deposition obtained using CFD was in excellent agreement with available in vivo data using the same product. Specifically, CFD resulted in 30% lung deposition, whereas in vivo lung deposition was reported to be approximately 31%. Conclusion: It was concluded that a combination of patient-specific airway models and lobar boundary conditions can be used to obtain accurate lung deposition estimates. Lower lung deposition can be expected for patients with higher extrathoracic resistance. Novel respiratory drug delivery devices need to accommodate population subgroups based on these morphological and anatomical differences in addition to subject age.
  Address
  Corporate Author Thesis
  Publisher Place of Publication New York, N.Y. Editor
  Language Wos 000299744800001 Publication Date 2012-01-20
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN 0895-8378;1091-7691; ISBN Additional Links UA library record; WoS full record; WoS citing articles
  Impact Factor 1.751 Times cited 36 Open Access
  Notes ; ; Approved Most recent IF: 1.751; 2012 IF: 1.894
  Call Number UA @ lucian @ c:irua:96238 Serial 286
Permanent link to this record
 
 
Author de Backer, A.; Fatermans, J.; den Dekker, A.J.; Van Aert, S.
  Title Atom counting 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 (up) 91-144
  Keywords H2 Book chapter; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this chapter, a statistical model-based method to count the number of atoms of monotype crystalline nanostructures from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images is discussed in detail together with a thorough study on the possibilities and inherent limitations. We show that this method can be applied to nanocrystals of arbitrary shape, size, and atom type. The validity of the atom-counting results is confirmed by means of detailed image simulations and it is shown that the high sensitivity of our method enables us to count atoms with single atom sensitivity.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  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:177529 Serial 6776
Permanent link to this record
 
 
Author De Backer, A.; van den Bos, K.H.W.; Van den Broek, W.; Sijbers, J.; Van Aert, S.
  Title StatSTEM: An efficient approach for accurate and precise model-based quantification of atomic resolution electron microscopy images Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 171 Issue 171 Pages (up) 104-116
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
  Abstract An efficient model-based estimation algorithm is introduced to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, has been investigated. The highest attainable precision is reached even for low dose images. Furthermore, the advantages of the model-based approach taking into account overlap between neighbouring columns are highlighted. This is done for the estimation of the distance between two neighbouring columns as a function of their distance and for the estimation of the scattering cross-section which is compared to the integrated intensity from a Voronoi cell. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000389106200014 Publication Date 2016-09-09
  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 43 Open Access
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0393.11, G.0064.10 and G.0374.13), a Ph.D. research grant to K.H.W. van den Bos, and a postdoctoral research grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A. Rosenauer is acknowledged for providing the STEMsim program.; esteem2_jra2 Approved Most recent IF: 2.843
  Call Number EMAT @ emat @ c:irua:135516 Serial 4280
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 (up) 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 Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S.
  Title Atom-counting in High Resolution Electron Microscopy: TEM or STEM – that's the question Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 174 Issue 174 Pages (up) 112-120
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this work, a recently developed quantitative approach based on the principles of detection theory is used in order to determine the possibilities and limitations of High Resolution Scanning Transmission Electron Microscopy (HR STEM) and HR TEM for atom-counting. So far, HR STEM has been shown to be an appropriate imaging mode to count the number of atoms in a projected atomic column. Recently, it has been demonstrated that HR TEM, when using negative spherical aberration imaging, is suitable for atom-counting as well. The capabilities of both imaging techniques are investigated and compared using the probability of error as a criterion. It is shown that for the same incoming electron dose, HR STEM outperforms HR TEM under common practice standards, i.e. when the decision is based on the probability function of the peak intensities in HR TEM and of the scattering cross-sections in HR STEM. If the atom-counting decision is based on the joint probability function of the image pixel values, the dependence of all image pixel intensities as a function of thickness should be known accurately. Under this assumption, the probability of error may decrease significantly for atom-counting in HR TEM and may, in theory, become lower as compared to HR STEM under the predicted optimal experimental settings. However, the commonly used standard for atom-counting in HR STEM leads to a high performance and has been shown to work in practice.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000403342200013 Publication Date 2016-10-27
  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 2 Open Access
  Notes The authors gratefully acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15N, G.0369.15N, G.0374.13N, and WO.010.16N) and a postdoctoral grant to A. De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). Approved Most recent IF: 2.843
  Call Number EMAT @ emat @ c:irua:137102 Serial 4315
Permanent link to this record
 
 
Author Gonnissen, J.; De Backer, A.; den Dekker, A.J.; Sijbers, J.; Van Aert, S.
  Title Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 170 Issue 170 Pages (up) 128-138
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramer-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms.
  Address Electron Microscopy for Materials Science (EMAT), University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium. Electronic address: sandra.vanaert@uantwerpen.be
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language English Wos 000386925500014 Publication Date 2016-07-26
  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 6 Open Access
  Notes The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0368.15, G.0369.15 and G.0374.13) and a postdoctoral research grant to A. De Backer. The research leading to these results has also received funding from the European Union Seventh Framework Programme [FP7/2007-2013] under Grant agreement no. 312483 (ESTEEM2). The authors would also like to thank A. Rosenauer for providing access to the STEMsim software and Gerardo T. Martinez for fruitful discussions.; esteem2_jra2 Approved Most recent IF: 2.843
  Call Number c:irua:135337 c:irua:135337 Serial 4128
Permanent link to this record
 
 
Author Parizel, P.M.; Corthouts, B.; Snoeckx, A.; de Backer, J.; de Backer, W.
  Title Klinische semiologie en radiologie Type H3 Book chapter
  Year 2007 Publication Abbreviated Journal
  Volume Issue Pages (up) 133-146
  Keywords H3 Book chapter; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Acco Place of Publication Leuven Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:63801 Serial 1765
Permanent link to this record
 
 
Author Alania, M.; De Backer, A.; Lobato, I.; Krause, F.F.; Van Dyck, D.; Rosenauer, A.; Van Aert, S.
  Title How precise can atoms of a nanocluster be located in 3D using a tilt series of scanning transmission electron microscopy images? Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy
  Volume 181 Issue 181 Pages (up) 134-143
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
  Abstract In this paper, we investigate how precise atoms of a small nanocluster can ultimately be located in three dimensions (3D) from a tilt series of images acquired using annular dark field (ADF) scanning transmission electron microscopy (STEM). Therefore, we derive an expression for the statistical precision with which the 3D atomic position coordinates can be estimated in a quantitative analysis. Evaluating this statistical precision as a function of the microscope settings also allows us to derive the optimal experimental design. In this manner, the optimal angular tilt range, required electron dose, optimal detector angles, and number of projection images can be determined.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  Language Wos 000411170800016 Publication Date 2016-12-15
  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 The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N, G.0368.15N, and WO.010.16N) and a post-doctoral grant to A. De Backer, and from the DFG under contract No. RO-2057/4-2. Approved Most recent IF: 2.843
  Call Number EMAT @ emat @ c:irua:144432 Serial 4618
Permanent link to this record
 
 
Author de Backer, J.; Vanderveken, O.; Vos, W.; Devolder, A.; Verhulst, S.; Verbraecken, J.
  Title Functional imaging to predict treatment success of mandibular advancement devices in sleep-disordered breathing Type H3 Book chapter
  Year 2008 Publication Abbreviated Journal
  Volume Issue Pages (up) 141-155
  Keywords H3 Book chapter; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP); Translational Neurosciences (TNW)
  Abstract
  Address
  Corporate Author Thesis
  Publisher Place of Publication Antwerpen Editor
  Language Wos Publication Date 0000-00-00
  Series Editor Series Title Abbreviated Series Title
  Series Volume Series Issue Edition
  ISSN ISBN Additional Links UA library record
  Impact Factor Times cited Open Access
  Notes Approved Most recent IF: NA
  Call Number UA @ lucian @ c:irua:72885 Serial 1298
Permanent link to this record
 
 
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 (up) 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.
  Address
  Corporate Author Thesis
  Publisher Place of Publication Editor
  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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