Home | << 1 2 3 4 >> |
![]() |
Records | |||||
---|---|---|---|---|---|
Author | de Backer, J.W.; Vos, W.G.; Germonpré, P.; Salgado, R.; Parizel, P.M.; de Backer, W. | ||||
Title | Clinical applications of image-based airway computational fluid dynamics: assessment of inhalation medication and endobronchial devices | Type | A3 Journal article | ||
Year | 2009 | Publication | Proceedings of the Society of Photo-optical Instrumentation Engineers | Abbreviated Journal | |
Volume ![]() |
7262 | Issue | Pages | 72621p,1-72621p,9 | |
Keywords | A3 Journal article; Condensed Matter Theory (CMT); Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) | ||||
Abstract | Computational fluid dynamics (CFD) is a technique that is used increasingly in the biomedical field. Solving the flow equations numerically provides a convenient way to assess the efficiency of therapies and devices, ranging from cardiovascular stents and heart valves to hemodialysis workflows. Also in the respiratory field CFD has gained increasing interest, especially through the combination of three dimensional image reconstruction which results in highend patient-specific models. This paper provides an overview of clinical applications of CFD through image based modeling, resulting from recent studies performed in our center. We focused on two applications: assessment of the efficiency of inhalation medication and analysis of endobronchial valve placement. In the first application we assessed the mode of action of a novel bronchodilator in 10 treated patients and 4 controls. We assessed the local volume increase and resistance change based on the combination of imaging and CFD. We found a good correlation between the changes in volume and resistance coming from the CFD results and the clinical tests. In the second application we assessed the placement and effect of one way endobronchial valves on respiratory function in 6 patients. We found a strong patientspecific result of the therapy where in some patients the therapy resulted in complete atelectasis of the target lobe while in others the lobe remained inflated. We concluded from these applications that CFD can provide a better insight into clinically relevant therapies. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | Publication Date | 2009-02-27 | ||
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:79497 | Serial | 374 | ||
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 program for accurate and precise model-based quantification of atomic resolution electron microscopy images | Type | P1 Proceeding | ||
Year | 2017 | Publication | Journal of physics : conference series T2 – Electron Microscopy and Analysis Group Conference 2017 (EMAG2017), 3-6 July 2017, Manchester, UK | Abbreviated Journal | J. Phys.: Conf. Ser. |
Volume ![]() |
902 | Issue | Pages | 012013 | |
Keywords | P1 Proceeding; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | An efficient model-based estimation algorithm is introduced in order to quantify the atomic column positions and intensities from atomic resolution (scanning) transmission electron microscopy ((S)TEM) images. This algorithm uses the least squares estimator on image segments containing individual columns fully accounting for the overlap between neighbouring columns, enabling the analysis of a large field of view. For this algorithm, the accuracy and precision with which measurements for the atomic column positions and scattering cross-sections from annular dark field (ADF) STEM images can be estimated, is investigated. The highest attainable precision is reached even for low dose images. Furthermore, advantages of the model- based approach taking into account overlap between neighbouring columns are highlighted. To provide end-users this well-established quantification method, a user friendly program, StatSTEM, is developed which is freely available under a GNU public license. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000416370700013 | Publication Date | 2017-10-16 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1742-6588 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | Times cited | 1 | Open Access | OpenAccess | |
Notes | The authors acknowledge nancial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0374.13N, G.0368.15N, G.0369.15N, WO.010.16N) and a PhD research grant to K H W van den Bos, and a postdoctoral research grant to A De Backer. The research leading to these results has received funding from the European Union Seventh Framework Programme under Grant Agreement 312483 – ESTEEM2 (Integrated Infrastructure Initiative-I3). A Rosenauer is acknowledged for providing the STEMsim program. | Approved | Most recent IF: NA | ||
Call Number | EMAT @ emat @c:irua:147188 | Serial | 4764 | ||
Permanent link to this record | |||||
Author | De Backer, A.; De Wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S. | ||||
Title | Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting: What are the limits? | Type | P1 Proceeding | ||
Year | 2015 | Publication | Journal of physics : conference series | Abbreviated Journal | |
Volume ![]() |
644 | Issue | 644 | Pages | 012034 |
Keywords | P1 Proceeding; Electron microscopy for materials research (EMAT) | ||||
Abstract | Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atom-counting diagnosed by combining a thorough statistical method and detailed image simulations. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000366826200034 | Publication Date | 2015-10-13 | |
Series Editor | Series Title | Abbreviated Series Title | Electron Microscopy and Analysis Group Conference (EMAG), JUN 02-JUL 02, 2015, Manchester, ENGLAND | ||
Series Volume | Series Issue | Edition | |||
ISSN | 1742-6588 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | Times cited | Open Access | |||
Notes | The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project funding (G.0368.15N, G.0369.15N, and G.0374.15N) and a PhD 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), ERC Starting Grant 278510 Vortex, and the UK Engineering and Physical Sciences Research Council (EP/K032518/1). The authors acknowledge Johnson-Matthey for providing the sample and PhD funding to K E MacArthur. A Rosenauer is acknowledged for providing the STEMsim program.; esteem2jra2; ECASJO; | Approved | Most recent IF: NA | ||
Call Number | c:irua:130314 c:irua:130314 | Serial | 4050 | ||
Permanent link to this record | |||||
Author | de Backer, A.; De wael, A.; Gonnissen, J.; Martinez, G.T.; Béché, A.; MacArthur, K.E.; Jones, L.; Nellist, P.D.; Van Aert, S. | ||||
Title | Quantitative annular dark field scanning transmission electron microscopy for nanoparticle atom-counting : what are the limits? | Type | A1 Journal article | ||
Year | 2015 | Publication | Journal of physics : conference series | Abbreviated Journal | |
Volume ![]() |
644 | Issue | Pages | 012034-4 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | Quantitative atomic resolution annular dark field scanning transmission electron microscopy (ADF STEM) has become a powerful technique for nanoparticle atom-counting. However, a lot of nanoparticles provide a severe characterisation challenge because of their limited size and beam sensitivity. Therefore, quantitative ADF STEM may greatly benefit from statistical detection theory in order to optimise the instrumental microscope settings such that the incoming electron dose can be kept as low as possible whilst still retaining single-atom precision. The principles of detection theory are used to quantify the probability of error for atom-counting. This enables us to decide between different image performance measures and to optimise the experimental detector settings for atom-counting in ADF STEM in an objective manner. To demonstrate this, ADF STEM imaging of an industrial catalyst has been conducted using the near-optimal detector settings. For this experiment, we discussed the limits for atomcounting diagnosed by combining a thorough statistical method and detailed image simulations. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Bristol | Editor | ||
Language | Wos | Publication Date | |||
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1742-6588; 1742-6596 | ISBN | Additional Links | UA library record | |
Impact Factor | Times cited | Open Access | |||
Notes | Approved | Most recent IF: NA | |||
Call Number | UA @ lucian @ c:irua:129198 | Serial | 4506 | ||
Permanent link to this record | |||||
Author | Vingerhoets, R.; Spiller, M.; De Backer, J.; Adriaens, A.; Vlaeminck, S.E.; Meers, E. | ||||
Title | Detailed nitrogen and phosphorus flow analysis, nutrient use efficiency and circularity in the agri-food system of a livestock-intensive region | Type | A1 Journal article | ||
Year | 2023 | Publication | Journal of cleaner production | Abbreviated Journal | |
Volume ![]() |
410 | Issue | Pages | 137278-13 | |
Keywords | A1 Journal article; Engineering sciences. Technology; Sustainable Energy, Air and Water Technology (DuEL) | ||||
Abstract | The agri-food value chain is a major cause of nitrogen (N) and phosphorus (P) emissions and associated environmental and health impacts. The EU's farm-to-fork strategy (F2F) demands an agri-food value chain approach to reduce nutrient emissions by 50% and fertilizer use by 20%. Substance flow analysis (SFA) is a method that can be applied to study complex systems such as the agri-food chain. A review of 60 SFA studies shows that they often lack detail by not sufficiently distinguishing between nodes, products and types of emissions. The present study aims to assess the added value of detail in SFAs and to illustrate that valuable indicators can be derived from detailed assessments. This aim will be attained by presenting a highly-detailed SFA for the livestock-intensive region of Flanders, Belgium. The SFA distinguishes 40 nodes and 1827 flows that are classified into eight different categories (e.g. by-products, point source emissions) following life cycle methods. Eight novel indicators were calculated, including indicators that assess the N and P recovery potential. Flanders has a low overall nutrient use efficiency (11% N, 18% P). About 55% of the N and 56% of the P embedded in recoverable streams are reused providing 35% and 37% of the total N and P input. Optimized nutrient recycling could replace 45% of N and 48% of P of the external nutrient input, exceeding the target set by the F2F strategy. Detailed accounting for N and P flows and nodes leads to the identification of more recoverable streams and larger N and P flows. More detailed flow accounting is a prerequisite for the quantification of technological intervention options. Future research should focus on including concentration and quality as a parameter in SFAs. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000991013600001 | Publication Date | 2023-04-21 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0959-6526 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 11.1 | Times cited | Open Access | OpenAccess | |
Notes | Approved | Most recent IF: 11.1; 2023 IF: 5.715 | |||
Call Number | UA @ admin @ c:irua:196227 | Serial | 7770 | ||
Permanent link to this record | |||||
Author | de Backer, J.W.; Vos, W.G.; Burnell, P.; Verhulst, S.L.; Salmon, P.; de Clerck, N.; de Backer, W. | ||||
Title | Study of the variability in upper and lower airway morphology in Sprague-Dawley rats using modern micro-CT scan-based segmentation techniques | Type | A1 Journal article | ||
Year | 2009 | Publication | The anatomical record: advances in integrative anatomy and evolutionary biology | Abbreviated Journal | Anat Rec |
Volume ![]() |
292 | Issue | 5 | Pages | 720-727 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Laboratory Experimental Medicine and Pediatrics (LEMP) | ||||
Abstract | Animal models are being used extensively in pre-clinical and safety assessment studies to assess the effectiveness and safety of new chemical entities and delivery systems. Although never entirely replacing the need for animal testing, the use of computer simulations could eventually reduce the amount of animals needed for research purposes and refine the data acquired from the animal studies. Computational fluid dynamics is a powerful tool that makes it possible to simulate flow and particle behavior in animal or patient-specific respiratory models, for purposes of inhaled delivery. This tool requires an accurate representation of the respiratory system, respiration and dose delivery attributes. The aim of this study is to develop a representative airway model of the Sprague-Dawley rat using static and dynamic micro-CT scans. The entire respiratory tract was modeled, from the snout and nares down to the central airways at the point where no distinction could be made between intraluminal air and the surrounding tissue. For the selection of the representative model, variables such as upper airway movement, segmentation length, airway volume and size are taken into account. Dynamic scans of the nostril region were used to illustrate the characteristic morphology of this region in anaesthetized animals. It could be concluded from this study that it was possible to construct a highly detailed representative model of a Sprague-Dawley rat based on imaging modalities such as micro-CT scans | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | New York, N.Y. | Editor | ||
Language | Wos | 000265766000010 | Publication Date | 2009-03-25 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 1932-8486;1932-8494; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 1.431 | Times cited | 16 | Open Access | |
Notes | Approved | Most recent IF: 1.431; 2009 IF: 1.490 | |||
Call Number | UA @ lucian @ c:irua:76455 | Serial | 3342 | ||
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 | de Backer, J.W.; Vos, W.G.; Vinchurkar, S.C.; Claes, R.; Drollmann, A.; Wulfrank, D.; Parizel, P.M.; Germonpré, P.; de Backer, W. | ||||
Title | Validation of computational fluid dynamics in CT-based airway models with SPECT/CT1 | Type | A1 Journal article | ||
Year | 2010 | Publication | Radiology | Abbreviated Journal | Radiology |
Volume ![]() |
257 | Issue | 3 | Pages | 854-862 |
Keywords | A1 Journal article; Condensed Matter Theory (CMT); Vision lab; Antwerp Surgical Training, Anatomy and Research Centre (ASTARC); Laboratory Experimental Medicine and Pediatrics (LEMP) | ||||
Abstract | Purpose: To compare the results obtained by using numerical flow simulations with the results of combined single photon emission computed tomography (SPECT) and computed tomography (CT) and to demonstrate the importance of correct boundary conditions for the numerical methods to account for the large amount of interpatient variability in airway geometry. Materials and Methods: This study was approved by all relevant institutional review boards. All patients gave their signed informed consent. In this study, six patients with mild asthma (three men; three women; overall mean age, 46 years ± 17 [standard deviation]) underwent CT at functional residual capacity and total lung capacity, as well as SPECT/CT. CT data were used for segmentation and computational fluid dynamics (CFD) simulations. A comparison was made between airflow distribution, as derived with (a) SPECT/CT through tracer concentration analysis, (b) CT through lobar expansion measurement, and (c) CFD through flow computer simulation. Also, the heterogeneity of the ventilation was examined. Results: Good agreement was found between SPECT/CT, CT, and CFD in terms of airflow distribution and hot spot detection. The average difference for the internal airflow distribution was less than 3% for CFD and CT versus SPECT/CT. Heterogeneity in ventilation patterns could be detected with SPECT/CT and CFD. Conclusion: This results of this study show that patient-specific computer simulations with appropriate boundary conditions yield information that is similar to that obtained with functional imaging tools, such as SPECT/CT. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Easton, Pa | Editor | ||
Language | Wos | 000284469300031 | Publication Date | 2010-11-17 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0033-8419;1527-1315; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 7.296 | Times cited | 100 | Open Access | |
Notes | ; Supported by Novartis. ; | Approved | Most recent IF: 7.296; 2010 IF: 6.069 | ||
Call Number | UA @ lucian @ c:irua:85379 | Serial | 3831 | ||
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 | Lobato, I.; De Backer, A.; Van Aert, S. | ||||
Title | Real-time simulations of ADF STEM probe position-integrated scattering cross-sections for single element fcc crystals in zone axis orientation using a densely connected neural network | Type | A1 Journal article | ||
Year | 2023 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
251 | Issue | Pages | 113769 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | Quantification of annular dark field (ADF) scanning transmission electron microscopy (STEM) images in terms of composition or thickness often relies on probe-position integrated scattering cross sections (PPISCS). In order to compare experimental PPISCS with theoretically predicted ones, expensive simulations are needed for a given specimen, zone axis orientation, and a variety of microscope settings. The computation time of such simulations can be in the order of hours using a single GPU card. ADF STEM simulations can be efficiently parallelized using multiple GPUs, as the calculation of each pixel is independent of other pixels. However, most research groups do not have the necessary hardware, and, in the best-case scenario, the simulation time will only be reduced proportionally to the number of GPUs used. In this manuscript, we use a learning approach and present a densely connected neural network that is able to perform real-time ADF STEM PPISCS predictions as a function of atomic column thickness for most common face-centered cubic (fcc) crystals (i.e., Al, Cu, Pd, Ag, Pt, Au and Pb) along [100] and [111] zone axis orientations, root-mean-square displacements, and microscope parameters. The proposed architecture is parameter efficient and yields accurate predictions for the PPISCS values for a wide range of input parameters that are commonly used for aberration-corrected transmission electron microscopes. |
||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 001011617200001 | Publication Date | 2023-06-01 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N and G0A7723N) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF), Belgium. | Approved | Most recent IF: 2.2; 2023 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:197275 | Serial | 8812 | ||
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 | Sentürk, D.G.; De Backer, A.; Friedrich, T.; Van Aert, S. | ||||
Title | Optimal experiment design for element specific atom counting using multiple annular dark field scanning transmission electron microscopy detectors | Type | A1 Journal article | ||
Year | 2022 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
242 | Issue | Pages | 113626 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose. |
||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000873778100001 | Publication Date | 0000-00-00 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert and Grant 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N and EOS 30489208) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).; esteem3reported; esteem3jra | Approved | Most recent IF: 2.2 | ||
Call Number | EMAT @ emat @c:irua:190925 | Serial | 7118 | ||
Permanent link to this record | |||||
Author | Klingstedt, M.; Sundberg, M.; Eriksson, L.; Haigh, S.; Kirkland, A.; Grüner, D.; de Backer, A.; Van Aert, S.; Tarasaki, O. | ||||
Title | Exit wave reconstruction from focal series of HRTEM images, single crystal XRD and total energy studies on SbxWO3+y (x\sim0.11) | Type | A1 Journal article | ||
Year | 2012 | Publication | Zeitschrift für Kristallographie | Abbreviated Journal | Z Krist-Cryst Mater |
Volume ![]() |
227 | Issue | 6 | Pages | 341-349 |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | A new tungsten bronze in the SbWO system has been prepared in a solid state reaction from Sb2O3, WO3 and W metal powder. The average structure was determined by single crystal X-ray diffraction. SbxWO3+y (x ∼ 0.11) crystallizes in the orthorhombic space group Pm21n (no. 31), a = 27.8135(9) Å, b = 7.3659(2) Å and c = 3.8672(1) Å. The structure belongs to the (n)-ITB class of intergrowth tungsten bronzes. It contains slabs of hexagonal channels formed by six WO6 octahedra. These slabs are separated by three layers of WO6 octahedra that are arranged in a WO3-type fashion. The WO6 octahedra share all vertices to build up a three-dimensional framework. The hexagonal channels are filled with Sb atoms to ∼80% and additional O atoms. The atoms are shifted out of the center of the channels. Exit-wave reconstruction of focal series of high resolution-transmission-electron-microscope (HRTEM) images combined with statistical paramäeter estimation techniques allowed to study local ordering in the channels. Sb atoms in neighbouring channels tend to be displaced in the same direction, which is in agreement with total energy calculations on ordered structure models, but the ratio of the occupation of the two possible Sb sites varies from channel to channel. The structure of SbxWO3+y exhibits pronounced local modulations. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | München | Editor | ||
Language | Wos | 000307314200003 | Publication Date | 2012-06-06 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 2194-4946; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.179 | Times cited | 4 | Open Access | |
Notes | Fwo; Esteem 026019 | Approved | Most recent IF: 3.179; 2012 IF: NA | ||
Call Number | UA @ lucian @ c:irua:101218 | Serial | 1131 | ||
Permanent link to this record | |||||
Author | De wael, A.; De Backer, A.; Van Aert, S. | ||||
Title | Hidden Markov model for atom-counting from sequential ADF STEM images: Methodology, possibilities and limitations | Type | A1 Journal article | ||
Year | 2020 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
219 | Issue | Pages | 113131 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000594770500003 | Publication Date | 2020-10-03 | |
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 | 2.2 | Times cited | Open Access | OpenAccess | |
Notes | This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 770887 and No. 823717 ESTEEM3). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through grants to A.D.w. and A.D.B. and projects G.0502.18N and EOS 30489208. | Approved | Most recent IF: 2.2; 2020 IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:172449 | Serial | 6417 | ||
Permanent link to this record | |||||
Author | van den Bos, K.H.W.; Janssens, L.; De Backer, A.; Nellist, P.D.; Van Aert, S. | ||||
Title | The atomic lensing model: new opportunities for atom-by-atom metrology of heterogeneous nanomaterials | Type | A1 Journal article | ||
Year | 2019 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
203 | Issue | Pages | 155 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | The atomic lensing model has been proposed as a promising method facilitating atom-counting in heterogeneous nanocrystals [1]. Here, image simulations will validate the model, which describes dynamical diffraction as a superposition of individual atoms focussing the incident electrons. It will be demonstrated that the model is reliable in the annular dark field regime for crystals having columns containing dozens of atoms. By using the principles of statistical detection theory, it will be shown that this model gives new opportunities for detecting compositional differences. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000465021000020 | Publication Date | 2018-12-06 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.843 | Times cited | 4 | Open Access | OpenAccess |
Notes | The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0369.15N, G.0502.18N and WO.010.16N), and by personal grants to K.H.W. van den Bos and A. De Backer. This project has received funding from the European Research Council (ERC) under the European Unions Horizon 2020 research and innovation programme (grant agreement No. 770887). | Approved | Most recent IF: 2.843 | ||
Call Number | EMAT @ emat @UA @ admin @ c:irua:155721 | Serial | 5074 | ||
Permanent link to this record | |||||
Author | Attri, P.; Kaushik, N.K.; Kaushik, N.; Hammerschmid, D.; Privat-Maldonado, A.; De Backer, J.; Shiratani, M.; Choi, E.H.; Bogaerts, A. | ||||
Title | Plasma treatment causes structural modifications in lysozyme, and increases cytotoxicity towards cancer cells | Type | A1 Journal Article | ||
Year | 2021 | Publication | International Journal Of Biological Macromolecules | Abbreviated Journal | Int J Biol Macromol |
Volume ![]() |
182 | Issue | Pages | 1724-1736 | |
Keywords | A1 Journal Article; Lysozyme; Cold atmospheric plasma; Cancer cell death; Plasma, laser ablation and surface modeling Antwerp (PLASMANT) ; | ||||
Abstract | Bacterial and mammalian proteins, such as lysozyme, are gaining increasing interest as anticancer drugs. This study aims to modify the lysozyme structure using cold atmospheric plasma to boost its cancer cell killing effect. We investigated the structure at acidic and neutral pH using various experimental techniques (circular dichroism, fluorescence, and mass spectrometry) and molecular dynamics simulations. The controlled structural modification of lysozyme at neutral pH enhances its activity, while the activity was lost at acidic pH at the same treatment conditions. Indeed, a larger number of amino acids were oxidized at acidic pH after plasma treatment, which results in a greater distortion of the lysozyme structure, whereas only limited structural changes were observed in lysozyme after plasma treatment at neutral pH. We found that the plasma-treated lysozyme significantly induced apoptosis to the cancer cells. Our results reveal that plasma-treated lysozyme could have potential as a new cancer cell killing drug. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000675794700005 | Publication Date | 2021-05-27 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0141-8130 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 3.671 | Times cited | Open Access | OpenAccess | |
Notes | Japan Society for the Promotion of Science; We gratefully acknowledge the European H2020 Marie SkłodowskaCurie Actions Individual Fellowship “Anticancer-PAM” within Horizon2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. NK thanks to National Research Foundation of Korea under Ministry of Science and ICT (NRF2021R1C1C1013875) of Korean Government. The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. | Approved | Most recent IF: 3.671 | ||
Call Number | PLASMANT @ plasmant @c:irua:178813 | Serial | 6792 | ||
Permanent link to this record | |||||
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 | 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 | 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 | ||
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 | 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 | Schryvers, D.; Salje, E.K.H.; Nishida, M.; De Backer, A.; Idrissi, H.; Van Aert, S. | ||||
Title | Quantification by aberration corrected (S)TEM of boundaries formed by symmetry breaking phase transformations | Type | A1 Journal article | ||
Year | 2017 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
176 | Issue | Pages | 194-199 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT) | ||||
Abstract | The present contribution gives a review of recent quantification work of atom displacements, atom site occupations and level of crystallinity in various systems and based on aberration corrected HR(S)TEM images. Depending on the case studied, picometer range precisions for individual distances can be obtained, boundary widths at the unit cell level determined or statistical evolutions of fractions of the ordered areas calculated. In all of these cases, these quantitative measures imply new routes for the applications of the respective materials. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000403992200026 | Publication Date | 2017-01-09 | |
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 | 1 | Open Access | OpenAccess |
Notes | The authors acknowledge financial support from the Fund for Scientific Research-Flanders (G.0064.10N, G.0393.11N, G.0374.13N, G.0368.15N, G.0369.15N) and the Flemish Hercules 3 program for large infrastructure as well as financial support from the European Union Seventh Framework Programme (FP7/2007 – 2013) under Grant agreement no. 312483 (ESTEEM2). EKHS thanks EPSRC (EP/ K009702/1) and the Leverhulme trust (EM-2016-004) for support. DS and MN acknowledge financial support from the Japan Society for the Promotion of Science (JSPS, Japan) through the Grant-in-Aid for Scientific Research (A: No. 26249090) and the Strategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation (R2408). | Approved | Most recent IF: 2.843 | ||
Call Number | EMAT @ emat @c:irua:149654 | Serial | 4914 | ||
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 | 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 | 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 | 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 | Attri, P.; Park, J.-H.; De Backer, J.; Kim, M.; Yun, J.-H.; Heo, Y.; Dewilde, S.; Shiratani, M.; Choi, E.H.; Lee, W.; Bogaerts, A. | ||||
Title | Structural modification of NADPH oxidase activator (Noxa 1) by oxidative stress: An experimental and computational study | Type | A1 Journal article | ||
Year | 2020 | Publication | International Journal Of Biological Macromolecules | Abbreviated Journal | Int J Biol Macromol |
Volume ![]() |
163 | Issue | Pages | 2405-2414 | |
Keywords | A1 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT) | ||||
Abstract | NADPH oxidases 1 (NOX1) derived reactive oxygen species (ROS) play an important role in the progression of cancer through signaling pathways. Therefore, in this paper, we demonstrate the effect of cold atmospheric plasma (CAP) on the structural changes of Noxa1 SH3 protein, one of the regulatory subunits of NOX1. For this purpose, firstly we purified the Noxa1 SH3 protein and analyzed the structure using X-ray crystallography, and subsequently, we treated the protein with two types of CAP reactors such as pulsed dielectric barrier discharge (DBD) and Soft Jet for different time intervals. The structural deformation of Noxa1 SH3 protein was analyzed by various experimental methods (circular dichroism, fluorescence, and NMR spectroscopy) and by MD simulations. Additionally, we demonstrate the effect of CAP (DBD and Soft Jet) on the viability and expression of NOX1 in A375 cancer cells. Our results are useful to understand the structural modification/oxidation occur in protein due to reactive oxygen and nitrogen (RONS) species generated by CAP. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Editor | |||
Language | Wos | 000579839600233 | Publication Date | 2020-09-19 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0141-8130 | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 8.2 | Times cited | Open Access | ||
Notes | European Marie Skłodowska-Curie Individual Fellowship, 743546 ; JSPS, 20K14454 ; National Research Foundation of Korea, 2019M3A9F6021810 NRF-2017M3A9F6029753 NRF-2019M3E5D6063903 NRF-2016R1A6A3A04010213 ; Brain Korea 21; MSIT, NRF-2016K1A4A3914113 ; Hercules Foundation; Flemish Government; UA; We gratefully acknowledge the European Marie SkłodowskaCurie Individual Fellowship “Anticancer-PAM” within Horizon 2020 (grant number 743546). This work was also supported by JSPS-KAKENHI grant number 20K14454. Additionally, work was supported by several grants (2019M3A9F6021810, NRF2017M3A9F6029753, NRF-2019M3E5D6063903 to W. Lee), Basic Science Research Program (NRF-2016R1A6A3A04010213 to J.H. Yun) through the National Research Foundation of Korea and in part by the Brain Korea 21 (BK21) PLUS program (J.H.P.). EHC is thankful to National Research Foundation (NRF) of Korea, funded by the Korea government (MSIT) under the grant number (NRF2016K1A4A3914113). The computational work was carried out using the Turing HPC infrastructure at the CalcUA core facility of the Universiteit Antwerpen (UA), a division of the Flemish Supercomputer Center VSC, funded by the Hercules Foundation, the Flemish Government (department EWI) and the UA. | Approved | Most recent IF: 8.2; 2020 IF: 3.671 | ||
Call Number | PLASMANT @ plasmant @c:irua:172451 | Serial | 6419 | ||
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 | |||||
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.; 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 | 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 | 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 | den Dekker, A.J.; Gonnissen, J.; de Backer, A.; Sijbers, J.; Van Aert, S. | ||||
Title | Estimation of unknown structure parameters from high-resolution (S)TEM images : what are the limits? | Type | A1 Journal article | ||
Year | 2013 | Publication | Ultramicroscopy | Abbreviated Journal | Ultramicroscopy |
Volume ![]() |
134 | Issue | Pages | 34-43 | |
Keywords | A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab | ||||
Abstract | Statistical parameter estimation theory is proposed as a quantitative method to measure unknown structure parameters from electron microscopy images. Images are then purely considered as data planes from which structure parameters have to be determined as accurately and precisely as possible using a parametric statistical model of the observations. For this purpose, an efficient algorithm is proposed for the estimation of atomic column positions and intensities from high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. Furthermore, the so-called CramérRao lower bound (CRLB) is reviewed to determine the limits to the precision with which continuous parameters such as atomic column positions and intensities can be estimated. Since this lower bound can only be derived for continuous parameters, alternative measures using the principles of detection theory are introduced for problems concerning the estimation of discrete parameters such as atomic numbers. An experimental case study is presented to show the practical use of these measures for the optimization of the experiment design if the purpose is to decide between the presence of specific atom types using STEM images. | ||||
Address | |||||
Corporate Author | Thesis | ||||
Publisher | Place of Publication | Amsterdam | Editor | ||
Language | Wos | 000324474900006 | Publication Date | 2013-06-01 | |
Series Editor | Series Title | Abbreviated Series Title | |||
Series Volume | Series Issue | Edition | |||
ISSN | 0304-3991; | ISBN | Additional Links | UA library record; WoS full record; WoS citing articles | |
Impact Factor | 2.843 | Times cited | 31 | Open Access | |
Notes | FWO; FP 2007-2013; Esteem2; esteem2_jra2 | Approved | Most recent IF: 2.843; 2013 IF: 2.745 | ||
Call Number | UA @ lucian @ c:irua:109240 | Serial | 1083 | ||
Permanent link to this record | |||||
Author | 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. | ||||
Address | |||||
Corporate Author | Thesis | ||||
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 | ||
Permanent link to this record |