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Author Goris, B.; van den Broek, W.; Batenburg, K.J.; Heidari Mezerji, H.; Bals, S.
Title Electron tomography based on a total variation minimization reconstruction technique Type A1 Journal article
Year 2012 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 113 Issue Pages 120-130
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract The 3D reconstruction of a tilt series for electron tomography is mostly carried out using the weighted backprojection (WBP) algorithm or using one of the iterative algorithms such as the simultaneous iterative reconstruction technique (SIRT). However, it is known that these reconstruction algorithms cannot compensate for the missing wedge. Here, we apply a new reconstruction algorithm for electron tomography, which is based on compressive sensing. This is a field in image processing specialized in finding a sparse solution or a solution with a sparse gradient to a set of ill-posed linear equations. Therefore, it can be applied to electron tomography where the reconstructed objects often have a sparse gradient at the nanoscale. Using a combination of different simulated and experimental datasets, it is shown that missing wedge artefacts are reduced in the final reconstruction. Moreover, it seems that the reconstructed datasets have a higher fidelity and are easier to segment in comparison to reconstructions obtained by more conventional iterative algorithms.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000300554400006 Publication Date 2011-11-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 171 Open Access
Notes Fwo Approved Most recent IF: 2.843; 2012 IF: 2.470
Call Number UA @ lucian @ c:irua:93637 Serial 987
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Author Bladt, E.; Pelt, D.M.; Bals, S.; Batenburg, K.J.
Title Electron tomography based on highly limited data using a neural network reconstruction technique Type A1 Journal article
Year 2015 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 158 Issue 158 Pages 81-88
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract Gold nanoparticles are studied extensively due to their unique optical and catalytical properties. Their exact shape determines the properties and thereby the possible applications. Electron tomography is therefore often used to examine the three-dimensional (3D) shape of nanoparticles. However, since the acquisition of the experimental tilt series and the 3D reconstructions are very time consuming, it is difficult to obtain statistical results concerning the 3D shape of nanoparticles. Here, we propose a new approach for electron tomography that is based on artificial neural networks. The use of a new reconstruction approach enables us to reduce the number of projection images with a factor of 5 or more. The decrease in acquisition time of the tilt series and use of an efficient reconstruction algorithm allows us to examine a large amount of nanoparticles in order to retrieve statistical results concerning the 3D shape.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000361574800011 Publication Date 2015-07-10
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 25 Open Access OpenAccess
Notes 335078 COLOURATOM; FWO; COST Action MP1207; 312483 ESTEEM2; esteem2jra4; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843; 2015 IF: 2.436
Call Number c:irua:126675 c:irua:126675 Serial 988
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Author Goris, B.; Bals, S.; van den Broek, W.; Verbeeck, J.; Van Tendeloo, G.
Title Exploring different inelastic projection mechanisms for electron tomography Type A1 Journal article
Year 2011 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 111 Issue 8 Pages 1262-1267
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract Several different projection mechanisms that all make use of inelastically scattered electrons are used for electron tomography. The advantages and the disadvantages of these methods are compared to HAADFSTEM tomography, which is considered as the standard electron tomography technique in materials science. The different inelastic setups used are energy filtered transmission electron microscopy (EFTEM), thickness mapping based on the log-ratio method and bulk plasmon mapping. We present a comparison that can be used to select the best inelastic signal for tomography, depending on different parameters such as the beam stability and nature of the sample. The appropriate signal will obviously also depend on the exact information which is requested.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000300461100039 Publication Date 2011-03-07
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 21 Open Access
Notes Fwo; Iap; Esteem 026019 Approved Most recent IF: 2.843; 2011 IF: 2.471
Call Number UA @ lucian @ c:irua:91260UA @ admin @ c:irua:91260 Serial 1151
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Author Bals, S.; Kilaas, R.; Kisielowski, C.
Title Nonlinear imaging using annular dark field TEM Type A1 Journal article
Year 2005 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 104 Issue 3/4 Pages 281-289
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract Annular dark field TEM images exhibit a dominant mass-thickness contrast that can be quantified to extract single atom scattering cross sections. On top of this incoherent background, additional lattice fringes appear with a nonlinear information limit of 1.2 angstrom at 150 kV. The formation of these fringes is described by coherent nonlinear imaging theory and good agreement is found between experimental and simulated images. Calculations furthermore predict that the use of aberration corrected microscopes will improve the image quality dramatically. (c) 2005 Elsevier B.V. All rights reserved.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000231297100012 Publication Date 2005-06-16
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 15 Open Access
Notes Approved Most recent IF: 2.843; 2005 IF: 2.490
Call Number UA @ lucian @ c:irua:64685 Serial 2352
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Author Van Eyndhoven, G.; Kurttepeli, M.; van Oers, C.J.; Cool, P.; Bals, S.; Batenburg, K.J.; Sijbers, J.
Title Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials Type A1 Journal article
Year 2015 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 148 Issue 148 Pages 10-19
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab; Laboratory of adsorption and catalysis (LADCA)
Abstract Electron tomography is currently a versatile tool to investigate the connection between the structure and properties of nanomaterials. However, a quantitative interpretation of electron tomography results is still far from straightforward. Especially accurate quantification of pore-space is hampered by artifacts introduced in all steps of the processing chain, i.e., acquisition, reconstruction, segmentation and quantification. Furthermore, most common approaches require subjective manual user input. In this paper, the PORES algorithm POre REconstruction and Segmentation is introduced; it is a tailor-made, integral approach, for the reconstruction, segmentation, and quantification of porous nanomaterials. The PORES processing chain starts by calculating a reconstruction with a nanoporous-specific reconstruction algorithm: the Simultaneous Update of Pore Pixels by iterative REconstruction and Simple Segmentation algorithm (SUPPRESS). It classifies the interior region to the pores during reconstruction, while reconstructing the remaining region by reducing the error with respect to the acquired electron microscopy data. The SUPPRESS reconstruction can be directly plugged into the remaining processing chain of the PORES algorithm, resulting in accurate individual pore quantification and full sample pore statistics. The proposed approach was extensively validated on both simulated and experimental data, indicating its ability to generate accurate statistics of nanoporous materials.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000345973000002 Publication Date 2014-08-23
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 2.843 Times cited 7 Open Access OpenAccess
Notes Colouratom; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843; 2015 IF: 2.436
Call Number c:irua:119083 Serial 2672
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Author Heidari Mezerji, H.; van den Broek, W.; Bals, S.
Title A practical method to determine the effective resolution in incoherent experimental electron tomography Type A1 Journal article
Year 2011 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 111 Issue 5 Pages 330-336
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract It is not straightforward to determine resolution for a 3D reconstruction when performing an electron tomography experiment. Different contributions such as missing wedge and misalignment add up and often influence the final resolution in an anisotropic manner. The conventional resolution measures can not be used for all of the reconstruction techniques, especially for iterative techniques which are more commonly used for electron tomography in materials science. Here we define a quantitative resolution measure that determines the resolution in three orthogonal directions of the reconstruction. As an application we use this measure to determine the optimum number of simultaneous iterative reconstruction technique (SIRT) iterations to reconstruct the gold nanoparticles, based on a high angle annular dark field STEM (HAADF-STEM) tilt series.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000289396900005 Publication Date 2011-01-24
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 26 Open Access
Notes Esteem 026019; Fwo Approved Most recent IF: 2.843; 2011 IF: 2.471
Call Number UA @ lucian @ c:irua:87606 Serial 2688
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Author Chen, D.; Goris, B.; Bleichrodt, F.; Heidari Mezerji, H.; Bals, S.; Batenburg, K.J.; de With, G.; Friedrich, H.
Title The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections Type A1 Journal article
Year 2014 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 147 Issue Pages 137-148
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract In electron tomography, the fidelity of the 3D reconstruction strongly depends on the employed reconstruction algorithm. In this paper, the properties of SIRT, TVM and DART reconstructions are studied with respect to having only a limited number of electrons available for imaging and applying different angular sampling schemes. A well-defined realistic model is generated, which consists of tubular domains within a matrix having slab-geometry. Subsequently, the electron tomography workflow is simulated from calculated tilt-series over experimental effects to reconstruction. In comparison with the model, the fidelity of each reconstruction method is evaluated qualitatively and quantitatively based on global and local edge profiles and resolvable distance between particles. Results show that the performance of all reconstruction methods declines with the total electron dose. Overall, SIRT algorithm is the most stable method and insensitive to changes in angular sampling. TVM algorithm yields significantly sharper edges in the reconstruction, but the edge positions are strongly influenced by the tilt scheme and the tubular objects become thinned. The DART algorithm markedly suppresses the elongation artifacts along the beam direction and moreover segments the reconstruction which can be considered a significant advantage for quantification. Finally, no advantage of TVM and DART to deal better with fewer projections was observed.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000343157400015 Publication Date 2014-08-19
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 42 Open Access OpenAccess
Notes Fwo Approved Most recent IF: 2.843; 2014 IF: 2.436
Call Number UA @ lucian @ c:irua:119073 Serial 2729
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Author Van Aert, S.; Verbeeck, J.; Erni, R.; Bals, S.; Luysberg, M.; van Dyck, D.; Van Tendeloo, G.
Title Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy Type A1 Journal article
Year 2009 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 109 Issue 10 Pages 1236-1244
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract A model-based method is proposed to relatively quantify the chemical composition of atomic columns using high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) images. The method is based on a quantification of the total intensity of the scattered electrons for the individual atomic columns using statistical parameter estimation theory. In order to apply this theory, a model is required describing the image contrast of the HAADF STEM images. Therefore, a simple, effective incoherent model has been assumed which takes the probe intensity profile into account. The scattered intensities can then be estimated by fitting this model to an experimental HAADF STEM image. These estimates are used as a performance measure to distinguish between different atomic column types and to identify the nature of unknown columns with good accuracy and precision using statistical hypothesis testing. The reliability of the method is supported by means of simulated HAADF STEM images as well as a combination of experimental images and electron energy-loss spectra. It is experimentally shown that statistically meaningful information on the composition of individual columns can be obtained even if the difference in averaged atomic number Z is only 3. Using this method, quantitative mapping at atomic resolution using HAADF STEM images only has become possible without the need of simultaneously recorded electron energy loss spectra.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000270015200004 Publication Date 2009-05-28
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 2.843 Times cited 166 Open Access
Notes Fwo; Esteem 026019 Approved Most recent IF: 2.843; 2009 IF: 2.067
Call Number UA @ lucian @ c:irua:78585UA @ admin @ c:irua:78585 Serial 2748
Permanent link to this record
 

 
Author Heidari, H.; van den Broek, W.; Bals, S.
Title Quantitative electron tomography : the effect of the three-dimensional point spread function Type A1 Journal article
Year 2013 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 135 Issue Pages 1-5
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract The intensity levels in a three-dimensional (3D) reconstruction, obtained by electron tomography, can be influenced by several experimental imperfections. Such artifacts will hamper a quantitative interpretation of the results. In this paper, we will correct for artificial intensity variations by determining the 3D point spread function (PSF) of a tomographic reconstruction based on high angle annular dark field scanning transmission electron microscopy. The large tails of the PSF cause an underestimation of the intensity of smaller particles, which in turn hampers an accurate radius estimate. Here, the error introduced by the PSF is quantified and corrected a posteriori.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000326941500001 Publication Date 2013-06-21
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 6 Open Access
Notes Esteem2; Sunflower; esteem2_jra4 Approved Most recent IF: 2.843; 2013 IF: 2.745
Call Number UA @ lucian @ c:irua:111397 Serial 2756
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Author Ke, X.; Bals, S.; Romo Negreira, A.; Hantschel, T.; Bender, H.; Van Tendeloo, G.
Title TEM sample preparation by FIB for carbon nanotube interconnects Type A1 Journal article
Year 2009 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 109 Issue 11 Pages 1353-1359
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract A powerful method to study carbon nanotubes (CNTs) grown in patterned substrates for potential interconnects applications is transmission electron microscopy (TEM). However, high-quality TEM samples are necessary for such a study. Here, TEM specimen preparation by focused ion beam (FIB) has been used to obtain lamellae of patterned samples containing CNTs grown inside contact holes. A dual-cap Pt protection layer and an extensive 5 kV cleaning procedure are applied in order to preserve the CNTs and avoid deterioration during milling. TEM results show that the inner shell structure of the carbon nanotubes has been preserved, which proves that focused ion beam is a useful technique to prepare TEM samples of CNT interconnects.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000270765800006 Publication Date 2009-07-11
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 21 Open Access
Notes Esteem 026019; Iap Approved Most recent IF: 2.843; 2009 IF: 2.067
Call Number UA @ lucian @ c:irua:79074 Serial 3485
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Author van Aarle, W.; Palenstijn, W.J.; De Beenhouwer, J.; Altantzis, T.; Bals, S.; Batenburg, K.J.; Sijbers, J.
Title The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography Type A1 Journal article
Year 2015 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 157 Issue 157 Pages 35-47
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Abstract We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language English Wos 000361002400005 Publication Date 2015-05-06
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 562 Open Access OpenAccess
Notes The authors acknowledge financial support from the iMinds ICONMetroCT project,the IWT SBO Tom Food project and from the Netherlands Organisation for Scientific Research (NWO),Project no. 639.072.005. Networking support was provided by the EXTREMA COST Action MP 1207. Sara Bals acknowledges financial support from the European Research Council (ERC Starting Grant #335078 COLOURATOMS).; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843; 2015 IF: 2.436
Call Number c:irua:127834 Serial 3974
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Author Zanaga, D.; Altantzis, T.; Sanctorum, J.; Freitag, B.; Bals, S.
Title An alternative approach for ζ-factor measurement using pure element nanoparticles Type A1 Journal article
Year 2016 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 164 Issue 164 Pages 11-16
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract It is very challenging to measure the chemical composition of hetero nanostructures in a reliable and quantitative manner. Here, we propose a novel and straightforward approach that can be used to quantify energy dispersive X-ray spectra acquired in a transmission electron microscope. Our method is based on a combination of electron tomography and the so-called ζ-factor technique. We will demonstrate the reliability of our approach as well as its applicability by investigating Au-Ag and Au-Pt hetero nanostructures. Given its simplicity, we expect that the method could become a new standard in the field of chemical characterization using electron microscopy.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000373526200002 Publication Date 2016-03-10
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 19 Open Access OpenAccess
Notes The authors acknowledge financial support from the European Research Council (ERC Starting Grant # 335078-COLOURATOMS) and the European Union under the FP7 (Integrated Infrastructure Initiative N. 312483 – ESTEEM2). The authors would also like to thank Luis M. Liz-Marzán, Ana Sánchez-Iglesias, Stefanos Mourdikoudis and Cristina Fernández-López for sample provision and useful discussions.; esteem2jra4; ECASSara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843
Call Number EMAT @ emat @ Serial 4019
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Author Goris, B.; Meledina, M.; Turner, S.; Zhong, Z.; Batenburg, K.J.; Bals, S.
Title Three dimensional mapping of Fe dopants in ceria nanocrystals using direct spectroscopic electron tomography Type A1 Journal article
Year 2016 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 171 Issue 171 Pages 55-62
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract Electron tomography is a powerful technique for the 3D characterization of the morphology of nanostructures. Nevertheless, resolving the chemical composition of complex nanostructures in 3D remains challenging and the number of studies in which electron energy loss spectroscopy (EELS) is combined with tomography is limited. During the last decade, dedicated reconstruction algorithms have been developed for HAADF-STEM tomography using prior knowledge about the investigated sample. Here, we will use the prior knowledge that the experimental spectrum of each reconstructed voxel is a linear combination of a well-known set of references spectra in a so-called direct spectroscopic tomography technique. Based on a simulation experiment, it is shown that this technique provides superior results in comparison to conventional reconstruction methods for spectroscopic data, especially for spectrum images containing a relatively low signal to noise ratio. Next, this technique is used to investigate the spatial distribution of Fe dopants in Fe:Ceria nanoparticles in 3D. It is shown that the presence of the Fe2+ dopants is correlated with a reduction of the Ce atoms from Ce4+ towards Ce3+. In addition, it is demonstrated that most of the Fe dopants are located near the voids inside the nanoparticle.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000389106200007 Publication Date 2016-09-06
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 13 Open Access OpenAccess
Notes The work was supported by the Research Foundation Flanders (FWO Vlaanderen) by project funding (G038116N, 3G004613) and by a post-doctoral research grants to B.G. S.B. acknowledges funding from the European Research Council (Starting Grant no. COLOURATOMS 335078). K.J.B. acknowledges funding from The Netherlands Organization for Scientific Research (NWO) (program 639.072.005.). We would like to thank Dr. Hilde Poelman, Dr. Vladimir Galvita and Prof. Dr. Guy B. Marin for the synthesis of the investigated sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843
Call Number c:irua:135185 c:irua:135185 Serial 4123
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Author Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S.
Title Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure Type A1 Journal article
Year 2016 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 177 Issue 177 Pages 36-42
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract Aberration correction in scanning transmission electron microscopy (STEM) has greatly improved the lateral and depth resolution. When using depth sectioning, a technique during which a series of images is recorded at different defocus values, single impurity atoms can be visualised in three dimensions. In this paper, we investigate new possibilities emerging when combining depth sectioning and precise atom-counting in order to reconstruct nanosized particles in three dimensions. Although the depth resolution does not allow one to precisely locate each atom within an atomic column, it will be shown that the depth location of an atomic column as a whole can be measured precisely. In this manner, the morphology of a nanoparticle can be reconstructed in three dimensions. This will be demonstrated using simulations and experimental data of a gold nanorod.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000401219800006 Publication Date 2016-11-09
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 13 Open Access OpenAccess
Notes The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843
Call Number EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 Serial 4316
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Author Zanaga, D.; Altantzis, T.; Sanctorum, J.; Freitag, B.; Bals, S.
Title An alternative approach for \zeta-factor measurement using pure element nanoparticles Type A1 Journal article
Year 2016 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 164 Issue Pages 11-16
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract It is very challenging to measure the chemical composition of hetero nanostructures in a reliable and quantitative manner. Here, we propose a novel and straightforward approach that can be used to quantify energy dispersive X-ray spectra acquired in a transmission electron microscope. Our method is based on a combination of electron tomography and the so-called zeta-factor technique. We will demonstrate the reliability of our approach as well as its applicability by investigating Au-Ag and Au-Pt hetero nanostructures. Given its simplicity, we expect that the method could become a new standard in the field of chemical characterization using electron microscopy. (C) 2016 Elsevier B.V. All rights reserved.
Address
Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000373526200002 Publication Date 2016-03-10
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 19 Open Access OpenAccess
Notes ; The authors acknowledge financial support from the European Research Council (ERC Starting Grant # 335078-COLOURATOMS) and the European Union under the FP7 (Integrated Infrastructure Initiative N. 312483 – ESTEEM2). ; ecas_Sara Approved Most recent IF: 2.843
Call Number UA @ lucian @ c:irua:133259 Serial 4439
Permanent link to this record
 

 
Author Zhong, Z.; Goris, B.; Schoenmakers, R.; Bals, S.; Batenburg, K.J.
Title A bimodal tomographic reconstruction technique combining EDS-STEM and HAADF-STEM Type A1 Journal article
Year 2017 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 174 Issue 174 Pages 35-45
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract A three-dimensional (3D) chemical characterization of nanomaterials can be obtained using tomography based on high angle annular dark field (HAADF) scanning transmission electron microscopy (STEM) or energy dispersive X-ray spectroscopy (EDS) STEM. These two complementary techniques have both advantages and disadvantages. The Z-contrast images have good image quality but lack robustness in the compositional analysis, while the elemental maps give more element-specific information, but at a low signal-to-noise ratio and a longer exposure time. Our aim is to combine these two types of complementary information in one single tomographic reconstruction process. Therefore, an imaging model is proposed combining both HAADF-STEM

and EDS-STEM. Based on this model, the elemental distributions can be reconstructed using both types of information simultaneously during the reconstruction process. The performance of the new technique is evaluated using simulated data and real experimental data. The results demonstrate that combining two imaging modalities leads to tomographic reconstructions with suppressed noise and enhanced contrast.
Address
Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000403342200005 Publication Date 2016-12-11
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 26 Open Access OpenAccess
Notes This research is supported by the Dutch Technology Foundation STW (http://www.stw.nl/), which is part of the Netherlands Organization for Scientific Research (NWO), and which is partly funded by the Ministry of Economic Affairs, Agriculture and Innovation under project number 13314. It is also supported by the Flemish research foundation (FWO Vlaanderen) by project funding (G038116N) and a postdoctoral research grant to B.G. Funding from the European Research Council (Starting Grant No. COLOURATOMS 335078) is acknowledged by S.B. The authors would like to thank Dr. Bernd Rieger and Dr. Richard Aveyard for useful discussions, and Prof. Dr. Luis M. Liz-Marzan for providing the investigated samples. We also acknowledge COST Action MP1207 for networking support. (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); saraecas; ECAS_Sara; Approved Most recent IF: 2.843
Call Number EMAT @ emat @ c:irua:141719UA @ admin @ c:irua:141719 Serial 4484
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Author Zhuge, X.; Jinnai, H.; Dunin-Borkowski, R.E.; Migunov, V.; Bals, S.; Cool, P.; Bons, A.-J.; Batenburg, K.J.
Title Automated discrete electron tomography – Towards routine high-fidelity reconstruction of nanomaterials Type A1 Journal article
Year 2017 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 175 Issue 175 Pages 87-96
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Laboratory of adsorption and catalysis (LADCA)
Abstract Electron tomography is an essential imaging technique for the investigation of morphology and 3D structure of nanomaterials. This method, however, suffers from well-known missing wedge artifacts due to a restricted tilt range, which limits the objectiveness, repeatability and efficiency of quantitative structural analysis. Discrete tomography represents one of the promising reconstruction techniques for materials science, potentially capable of delivering higher fidelity reconstructions by exploiting the prior knowledge of the limited number of material compositions in a specimen. However, the application of discrete tomography to practical datasets remains a difficult task due to the underlying challenging mathematical problem. In practice, it is often hard to obtain consistent reconstructions from experimental datasets. In addition, numerous parameters need to be tuned manually, which can lead to bias and non-repeatability. In this paper, we present the application of a new

iterative reconstruction technique, named TVR-DART, for discrete electron tomography. The technique is capable of consistently delivering reconstructions with significantly reduced missing wedge artifacts for a variety of challenging data and imaging conditions, and can automatically estimate its key parameters. We describe the principles of the technique and apply it to datasets from three different types of samples acquired under diverse imaging modes. By further reducing the available tilt range and number of projections, we show that the

proposed technique can still produce consistent reconstructions with minimized missing wedge artifacts. This new development promises to provide the electron microscopy community with an easy-to-use and robust tool for high-fidelity 3D characterization of nanomaterials.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000403342500008 Publication Date 2017-01-24
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 22 Open Access OpenAccess
Notes This work has been supported in part by the Stichting voor de Technische Wetenschappen (STW) through a personal grant (Veni,13610), and was in part by ExxonMobil Chemical Europe Inc. The authors further acknowledge financial support from the University of Antwerp through BOF GOA funding. S.B. acknowledges financial support from the European Research Council (ERC Starting Grant #335078-COLOURATOMS). R.D.B. is grateful for funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ ERC grant agreement number 320832. Thomas Altantzis is gratefully acknowledged for acquiring the Anatase nanosheets dataset. (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); saraecas; ECAS_Sara; Approved Most recent IF: 2.843
Call Number EMAT @ emat @ c:irua:141218UA @ admin @ c:irua:141218 Serial 4485
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Author Zhong, Z.; Aveyard, R.; Rieger, B.; Bals, S.; Palenstijn, W.J.; Batenburg, K.J.
Title Automatic correction of nonlinear damping effects in HAADF-STEM tomography for nanomaterials of discrete compositions Type A1 Journal article
Year 2018 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 184 Issue 184 Pages 57-65
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract <script type='text/javascript'>document.write(unpmarked('HAADF-STEM tomography is a common technique for characterizing the three-dimensional morphology of nanomaterials. In conventional tomographic reconstruction algorithms, the image intensity is assumed to be a linear projection of a physical property of the specimen. However, this assumption of linearity is not completely valid due to the nonlinear damping of signal intensities. The nonlinear damping effects increase w.r.t the specimen thickness and lead to so-called \u0022cupping artifacts\u0022, due to a mismatch with the linear model used in the reconstruction algorithm. Moreover, nonlinear damping effects can strongly limit the applicability of advanced reconstruction approaches such as Total Variation Minimization and discrete tomography. In this paper, we propose an algorithm for automatically correcting the nonlinear effects and the subsequent cupping artifacts. It is applicable to samples in which chemical compositions can be segmented based on image gray levels. The correction is realized by iteratively estimating the nonlinear relationship between projection intensity and sample thickness, based on which the projections are linearized. The correction and reconstruction algorithms are tested on simulated and experimental data. (C) 2017 Elsevier B.V. All rights reserved.'));
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Corporate Author Thesis
Publisher Place of Publication Amsterdam Editor
Language Wos 000417779800008 Publication Date 2017-10-31
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 8 Open Access OpenAccess
Notes ; This research is supported by the Dutch Technology Foundation STW (http:// www.stw.nl/), which is part of the Netherlands Organization for Scientific Research (NWO), and which is partly funded by the Ministry of Economic Affairs, Agriculture and Innovation under project number 13314. Funding from the European Research Council (Starting grant no. COLOURATOMS 335078) is acknowledged by S. Bals. The authors would like to thank Dr. Thomas Altantzis and Dr. Bart Goris for providing the experimental data, and Prof. Dr. Luis M. Liz-Marzan for providing the investigated samples. ; ecas_sara Approved Most recent IF: 2.843
Call Number UA @ lucian @ c:irua:148501UA @ admin @ c:irua:148501 Serial 4867
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Author Vanrompay, H.; Skorikov, A.; Bladt, E.; Béché, A.; Freitag, B.; Verbeeck, J.; Bals, S.
Title Fast versus conventional HAADF-STEM tomography of nanoparticles: advantages and challenges Type A1 Journal article
Year 2021 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 221 Issue Pages 113191
Keywords A1 Journal article; Electron microscopy for materials research (EMAT)
Abstract HAADF-STEM tomography is a widely used experimental technique for analyzing nanometer-scale crystalline structures of a large variety of materials in three dimensions. Unfortunately, the acquisition of conventional HAADF-STEM tilt series can easily take up one hour or more, depending on the complexity of the experiment. It is therefore far from straightforward to investigate samples that do not withstand long acquisition or to acquire large amounts of tilt series during a single TEM experiment. The latter would lead to the ability to obtain statistically meaningful 3D data, or to perform in situ 3D characterizations with a much shorter time resolution. Various HAADF-STEM acquisition strategies have been proposed to accelerate the tomographic acquisition and reduce the required electron dose. These methods include tilting the holder continuously while acquiring a projection “movie” and a hybrid, incremental, methodology which combines the benefits of the conventional and continuous technique. However, until now an experimental evaluation has been lacking. In this paper, the different acquisition strategies will be experimentally compared in terms of speed, resolution and electron dose. This evaluation will be performed based on experimental tilt series acquired for various metallic nanoparticles with different shapes and sizes. We discuss the data processing involved with the fast HAADF-STEM tilt series and provide a general guideline when which acquisition strategy should be preferentially used.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000612539600003 Publication Date 2020-12-08
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 15 Open Access OpenAccess
Notes We acknowledge Prof. Luis M. Liz-Marzán and co-workers of the Bionanoplasmonics Laboratory, CIC biomaGUNE, Spain for providing the Au@Ag nanoparticles, Prof. Sara. E. Skrabalak and co-workers of Indiana University, United States for the provision of the Au octopods and Prof. Teri W. Odom of Northwestern University, United States for the provision of the Au nanostars. H.V. acknowledges financial support by the Research Foundation Flanders (FWO grant 1S32617N). S.B acknowledges financial support by the Research Foundation Flanders (FWO grant G.0381.16N). This project received funding as well from the European Union’s Horizon 2020 research and innovation program under grant agreement No 731019 (EUSMI) and No 815128 (REALNANO). The authors acknowledge the entire EMAT technical staff for their support.; sygma Approved Most recent IF: 2.843
Call Number EMAT @ emat @c:irua:174551 Serial 6660
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Author Li, C.; Tardajos, A.P.; Wang, D.; Choukroun, D.; Van Daele, K.; Breugelmans, T.; Bals, S.
Title A simple method to clean ligand contamination on TEM grids Type A1 Journal article
Year 2021 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 221 Issue Pages 113195
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
Abstract Colloidal nanoparticles (NPs) including nanowires and nanosheets made by chemical methods involve many organic ligands. When the structure of NPs is investigated via transmission electron microscopy (TEM), the organic ligands act as a source for e-beam induced deposition and this causes substantial build-up of carbon layers in the investigated areas, which is typically referred to as “contamination” in the eld of electron mi- croscopy. This contamination is often more severe for scanning TEM, a technique that is based on a focused electron beam and hence higher electron dose rate. In this paper, we report a simple and effective method to clean drop-cast TEM grids that contain NPs with ligands. Using a combination of activated carbon and ethanol, this method effectively reduces the amount of ligands on TEM grids, and therefore greatly improves the quality of electron microscopy images and subsequent analytical measurements. This ef cient and facile method can be helpful during electron microscopy investigation of different kinds of nanomaterials that suffer from ligand- induced contamination.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000612539600002 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 2.843 Times cited 10 Open Access OpenAccess
Notes This research was funded by the University Antwerp GOA project (ID 33928). DW acknowledges an Individual Fellowship funded by the Marie Sklodowska-Curie Actions (MSCA) in Horizon 2020 program (grant 894254 SuprAtom). Approved Most recent IF: 2.843
Call Number EMAT @ emat @c:irua:174947 Serial 6666
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Author Koo, J.; Dahl, A.B.; Bærentzen, J.A.; Chen, Q.; Bals, S.; Dahl, V.A.
Title Shape from projections via differentiable forward projector for computed tomography Type A1 Journal article
Year 2021 Publication Ultramicroscopy Abbreviated Journal (up) Ultramicroscopy
Volume 224 Issue Pages 113239
Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Abstract In computed tomography, the reconstruction is typically obtained on a voxel grid. In this work, however, we propose a mesh-based reconstruction method. For tomographic problems, 3D meshes have mostly been studied to simulate data acquisition, but not for reconstruction, for which a 3D mesh means the inverse process of estimating shapes from projections. In this paper, we propose a differentiable forward model for 3D meshes that bridge the gap between the forward model for 3D surfaces and optimization. We view the forward projection as a rendering process, and make it differentiable by extending recent work in differentiable rendering. We use the proposed forward model to reconstruct 3D shapes directly from projections. Experimental results for single-object problems show that the proposed method outperforms traditional voxel-based methods on noisy simulated data. We also apply the proposed method on electron tomography images of nanoparticles to demonstrate the applicability of the method on real data.
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Corporate Author Thesis
Publisher Place of Publication Editor
Language Wos 000744576800008 Publication Date 2021-03-11
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0304-3991 ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 2.843 Times cited 3 Open Access OpenAccess
Notes EU Horizon 2020 MSCA Innovative Training Network MUMMERING Grant Number 765604. Approved Most recent IF: 2.843
Call Number EMAT @ emat @c:irua:183267 Serial 6825
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Author Adam, N.; Leroux, F.; Knapen, D.; Bals, S.; Blust, R.
Title The uptake and elimination of ZnO and CuO nanoparticles in Daphnia magna under chronic exposure scenarios Type A1 Journal article
Year 2015 Publication Water research Abbreviated Journal (up) Water Res
Volume 68 Issue 68 Pages 249-261
Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Veterinary physiology and biochemistry
Abstract In this study, the uptake and elimination of ZnO and CuO nanoparticles in Daphnia magna was tested. Daphnids were exposed during 10 days to sublethal concentrations of ZnO and CuO nanoparticles and corresponding metal salts (ZnCl2 and CuCl2.2H2O), after which they were transferred to unexposed medium for another 10 days. At different times during the exposure and none-exposure, the total and internal zinc or copper concentration of the daphnids was determined and the nanoparticles were localized in the organism using electron microscopy. The exposure concentrations were characterized by measuring the dissolved, nanoparticle and aggregated fraction in the medium. The results showed that the ZnO nanoparticles quickly dissolved after addition to the medium. Contrarily, only a small fraction (corresponding to the dissolved metal salt) of the CuO nanoparticles dissolved, while most of these nanoparticles formed large aggregates. Despite an initial increase in zinc and copper concentration during the first 48 hour to 5 day exposure, the body concentration reached a plateau level that was comparable for the ZnO nanoparticles and ZnCl2, but much higher for the CuO nanoparticles (with visible aggregates accumulating in the gut) than CuCl2.2H2O. During the remaining exposure and subsequent none-exposure phase, the zinc and copper concentration decreased fast to concentrations comparable with the unexposed daphnids. The results indicate that D. magna can regulate its internal zinc and copper concentration after exposure to ZnO and CuO nanoparticles, similar as after exposure to metal salts. The combined dissolution, accumulation and toxicity results confirm that the toxicity of ZnO and CuO nanoparticles is caused by the dissolved fraction. Keywords nano; zinc; copper; dissolution; aggregation; electron microscopy
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Corporate Author Thesis
Publisher Place of Publication Oxford Editor
Language Wos 000347756900022 Publication Date 2014-10-14
Series Editor Series Title Abbreviated Series Title
Series Volume Series Issue Edition
ISSN 0043-1354; ISBN Additional Links UA library record; WoS full record; WoS citing articles
Impact Factor 6.942 Times cited 51 Open Access OpenAccess
Notes ; The authors would like to thank Valentine Mubiana and Steven Joosen (Sphere, UA) for performing the ICP-MS and ICP-OES measurements and Prof. Dr. Gustaaf Van Tendeloo for making the collaboration between the EMAT and Sphere group possible. This study is part of the ENNSATOX-project, which was funded by the EU (NMP4-SL-2009-229244). The authors report no conflicts of interest. ; Approved Most recent IF: 6.942; 2015 IF: 5.528
Call Number c:irua:119366 c:irua:119366 Serial 3822
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