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	Author	Şentürk, DG.; Yu, CP.; De Backer, A.; Van Aert, S.
	Title	Atom counting from a combination of two ADF STEM images			Type	A1 Journal article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	255	Issue		Pages	113859
	Keywords	A1 Journal article; Electron microscopy for materials research (EMAT)
	Abstract	To understand the structure–property relationship of nanostructures, reliably quantifying parameters, such as the number of atoms along the projection direction, is important. Advanced statistical methodologies have made it possible to count the number of atoms for monotype crystalline nanoparticles from a single ADF STEM image. Recent developments enable one to simultaneously acquire multiple ADF STEM images. Here, we present an extended statistics-based method for atom counting from a combination of multiple statistically independent ADF STEM images reconstructed from non-overlapping annular detector collection regions which improves the accuracy and allows one to retrieve precise atom-counts, especially for images acquired with low electron doses and multiple element structures.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos	001089064200001	Publication Date	2023-09-23
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record; WoS full record; WoS citing articles
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G034621N, G0A7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).			Approved	Most recent IF: 2.2; 2024 IF: 2.843
	Call Number	EMAT @ emat @c:irua:201008			Serial	8964
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	Author	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
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	Author	Şentürk, D.G.; De Backer, A.; Van Aert, S.
	Title	Element specific atom counting for heterogeneous nanostructures: Combining multiple ADF STEM images for simultaneous thickness and composition determination			Type	A1 Journal Article
	Year	2024	Publication	Ultramicroscopy	Abbreviated Journal	Ultramicroscopy
	Volume	259	Issue		Pages	113941
	Keywords	A1 Journal Article; Electron Microscopy for Materials Science (EMAT) ;
	Abstract	In this paper, a methodology is presented to count the number of atoms in heterogeneous nanoparticles based on the combination of multiple annular dark field scanning transmission electron microscopy (ADF STEM) images. The different non-overlapping annular detector collection regions are selected based on the principles of optimal statistical experiment design for the atom-counting problem. To count the number of atoms, the total intensities of scattered electrons for each atomic column, the so-called scattering cross-sections, are simultaneously compared with simulated library values for the different detector regions by minimising the squared differences. The performance of the method is evaluated for simulated Ni@Pt and Au@Ag core-shell nanoparticles. Our approach turns out to be a dose efficient alternative for the investigation of beam-sensitive heterogeneous materials as compared to the combination of ADF STEM and energy dispersive X-ray spectroscopy.
	Address
	Corporate Author				Thesis
	Publisher		Place of Publication		Editor
	Language		Wos		Publication Date	2024-02-19
	Series Editor		Series Title		Abbreviated Series Title
	Series Volume		Series Issue		Edition
	ISSN	0304-3991	ISBN		Additional Links	UA library record
	Impact Factor	2.2	Times cited		Open Access	OpenAccess
	Notes	This work was supported by the European Research Council (Grant 770887 PICOMETRICS to S. Van Aert). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0346.21N, GOA7723N, and EOS 40007495) and a postdoctoral grant to A. De Backer. S. Van Aert acknowledges funding from the University of Antwerp Research fund (BOF).			Approved	Most recent IF: 2.2; 2024 IF: 2.843
	Call Number	EMAT @ emat @c:irua:204353			Serial	8996
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	Author	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
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	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
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	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
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	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
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	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
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	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