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Author van den Broek, W.; Rosenauer, A.; Goris, B.; Martinez, G.T.; Bals, S.; Van Aert, S.; van Dyck, D. pdf  doi
openurl 
  Title Correction of non-linear thickness effects in HAADF STEM electron tomography Type A1 Journal article
  Year 2012 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 116 Issue Pages 8-12  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab  
  Abstract In materials science, high angle annular dark field scanning transmission electron microscopy is often used for tomography at the nanometer scale. In this work, it is shown that a thickness dependent, non-linear damping of the recorded intensities occurs. This results in an underestimated intensity in the interior of reconstructions of homogeneous particles, which is known as the cupping artifact. In this paper, this non-linear effect is demonstrated in experimental images taken under common conditions and is reproduced with a numerical simulation. Furthermore, an analytical derivation shows that these non-linearities can be inverted if the imaging is done quantitatively, thus preventing cupping in the reconstruction.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000304473700002 Publication Date 2012-03-09  
  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 (down) 2.843 Times cited 67 Open Access  
  Notes Fwo Approved Most recent IF: 2.843; 2012 IF: 2.470  
  Call Number UA @ lucian @ c:irua:96558 Serial 518  
Permanent link to this record
 
 
Author Van Aert, S.; Chang, L.Y.; Bals, S.; Kirkland, A.I.; Van Tendeloo, G. pdf  doi
openurl 
  Title Effect of amorphous layers on the interpretation of restored exit waves Type A1 Journal article
  Year 2009 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 109 Issue 3 Pages 237-246  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract The effects of amorphous layers on the quality of exit wave restorations have been investigated. Two independently developed software implementations for exit wave restoration have been used to simulated focal series of images of SrTiO3 with amorphous carbon layers incorporated. The restored exit waves have been compared both qualitatively and quantitatively. We have shown that amorphous layers have a strong impact on the quantitative measurements of atomic column positions, however, the error in the position measurements is still in the picometer range.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000264280200005 Publication Date 2008-11-15  
  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 (down) 2.843 Times cited 10 Open Access  
  Notes Fwo; Esteem 026019 Approved Most recent IF: 2.843; 2009 IF: 2.067  
  Call Number UA @ lucian @ c:irua:76421 Serial 796  
Permanent link to this record
 
 
Author Croitoru, M.D.; van Dyck, D.; Van Aert, S.; Bals, S.; Verbeeck, J. pdf  doi
openurl 
  Title An efficient way of including thermal diffuse scattering in simulation of scanning transmission electron microscopic images Type A1 Journal article
  Year 2006 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 106 Issue 10 Pages 933-940  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT); Condensed Matter Theory (CMT); Vision lab  
  Abstract We propose an improved image simulation procedure for atomic-resolution annular dark-field scanning transmission electron microscopy (STEM) based on the multislice formulation, which takes thermal diffuse scattering fully into account. The improvement with regard to the classical frozen phonon approach is realized by separating the lattice configuration statistics from the dynamical scattering so as to avoid repetitive calculations. As an example, the influence of phonon scattering on the image contrast is calculated and investigated. STEM image simulation of crystals can be applied with reasonable computing times to problems involving a large number of atoms and thick or large supercells.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Amsterdam Editor  
  Language Wos 000240397200006 Publication Date 2006-05-10  
  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 (down) 2.843 Times cited 18 Open Access  
  Notes Fwo; Fwo-V Approved Most recent IF: 2.843; 2006 IF: 1.706  
  Call Number UA @ lucian @ c:irua:87604UA @ admin @ c:irua:87604 Serial 876  
Permanent link to this record
 
 
Author Goris, B.; van den Broek, W.; Batenburg, K.J.; Heidari Mezerji, H.; Bals, S. pdf  doi
openurl 
  Title Electron tomography based on a total variation minimization reconstruction technique Type A1 Journal article
  Year 2012 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Bladt, E.; Pelt, D.M.; Bals, S.; Batenburg, K.J. pdf  url
doi  openurl
  Title Electron tomography based on highly limited data using a neural network reconstruction technique Type A1 Journal article
  Year 2015 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Goris, B.; Bals, S.; van den Broek, W.; Verbeeck, J.; Van Tendeloo, G. pdf  doi
openurl 
  Title Exploring different inelastic projection mechanisms for electron tomography Type A1 Journal article
  Year 2011 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Bals, S.; Kilaas, R.; Kisielowski, C. pdf  doi
openurl 
  Title Nonlinear imaging using annular dark field TEM Type A1 Journal article
  Year 2005 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Van Eyndhoven, G.; Kurttepeli, M.; van Oers, C.J.; Cool, P.; Bals, S.; Batenburg, K.J.; Sijbers, J. pdf  url
doi  openurl
  Title Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials Type A1 Journal article
  Year 2015 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Heidari Mezerji, H.; van den Broek, W.; Bals, S. pdf  doi
openurl 
  Title A practical method to determine the effective resolution in incoherent experimental electron tomography Type A1 Journal article
  Year 2011 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Chen, D.; Goris, B.; Bleichrodt, F.; Heidari Mezerji, H.; Bals, S.; Batenburg, K.J.; de With, G.; Friedrich, H. pdf  url
doi  openurl
  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 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 (down) 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  
Permanent link to this record
 
 
Author Van Aert, S.; Verbeeck, J.; Erni, R.; Bals, S.; Luysberg, M.; van Dyck, D.; Van Tendeloo, G. pdf  doi
openurl 
  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 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 (down) 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. pdf  url
doi  openurl
  Title Quantitative electron tomography : the effect of the three-dimensional point spread function Type A1 Journal article
  Year 2013 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Ke, X.; Bals, S.; Romo Negreira, A.; Hantschel, T.; Bender, H.; Van Tendeloo, G. pdf  doi
openurl 
  Title TEM sample preparation by FIB for carbon nanotube interconnects Type A1 Journal article
  Year 2009 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author van Aarle, W.; Palenstijn, W.J.; De Beenhouwer, J.; Altantzis, T.; Bals, S.; Batenburg, K.J.; Sijbers, J. pdf  url
doi  openurl
  Title The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography Type A1 Journal article
  Year 2015 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Zanaga, D.; Altantzis, T.; Sanctorum, J.; Freitag, B.; Bals, S. pdf  url
doi  openurl
  Title An alternative approach for ζ-factor measurement using pure element nanoparticles Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Goris, B.; Meledina, M.; Turner, S.; Zhong, Z.; Batenburg, K.J.; Bals, S. pdf  url
doi  openurl
  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 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 (down) 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  
Permanent link to this record
 
 
Author Alania, M.; Altantzis, T.; De Backer, A.; Lobato, I.; Bals, S.; Van Aert, S. pdf  url
doi  openurl
  Title Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal Ultramicroscopy  
  Volume 177 Issue 177 Pages 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 (down) 2.843 Times cited 13 Open Access OpenAccess  
  Notes The authors acknowledge financial support from the European Union under the Seventh Framework Program under a contract for an Integrated Infrastructure Initiative. Reference No. 312483-ESTEEM2. S. Bals acknowledges funding from the European Research Council (Starting Grant No. COLOURATOMS 335078). The authors acknowledge financial support from the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0374.13N, G.0369.15N and G.0368.15N) and a post-doctoral grant to A. De Backer and T. Altantzis. The authors are grateful to Professor Luis M. Liz-Marzán for providing the sample.; ECAS_Sara; (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); Approved Most recent IF: 2.843  
  Call Number EMAT @ emat @ c:irua:138015UA @ admin @ c:irua:138015 Serial 4316  
Permanent link to this record
 
 
Author Zanaga, D.; Altantzis, T.; Sanctorum, J.; Freitag, B.; Bals, S. pdf  url
doi  openurl
  Title An alternative approach for \zeta-factor measurement using pure element nanoparticles Type A1 Journal article
  Year 2016 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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. pdf  url
doi  openurl
  Title A bimodal tomographic reconstruction technique combining EDS-STEM and HAADF-STEM Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal 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 (down) 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  
Permanent link to this record
 
 
Author Zhuge, X.; Jinnai, H.; Dunin-Borkowski, R.E.; Migunov, V.; Bals, S.; Cool, P.; Bons, A.-J.; Batenburg, K.J. pdf  url
doi  openurl
  Title Automated discrete electron tomography – Towards routine high-fidelity reconstruction of nanomaterials Type A1 Journal article
  Year 2017 Publication Ultramicroscopy Abbreviated Journal 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.		  
  Address  
  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 (down) 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  
Permanent link to this record
 
 
Author Zhong, Z.; Aveyard, R.; Rieger, B.; Bals, S.; Palenstijn, W.J.; Batenburg, K.J. pdf  url
doi  openurl
  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 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.'));  
  Address  
  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 (down) 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  
Permanent link to this record
 
 
Author Vanrompay, H.; Skorikov, A.; Bladt, E.; Béché, A.; Freitag, B.; Verbeeck, J.; Bals, S. url  doi
openurl 
  Title Fast versus conventional HAADF-STEM tomography of nanoparticles: advantages and challenges Type A1 Journal article
  Year 2021 Publication Ultramicroscopy Abbreviated Journal 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.  
  Address  
  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 (down) 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  
Permanent link to this record
 
 
Author Li, C.; Tardajos, A.P.; Wang, D.; Choukroun, D.; Van Daele, K.; Breugelmans, T.; Bals, S. url  doi
openurl 
  Title A simple method to clean ligand contamination on TEM grids Type A1 Journal article
  Year 2021 Publication Ultramicroscopy Abbreviated Journal 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.  
  Address  
  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 (down) 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  
Permanent link to this record
 
 
Author Koo, J.; Dahl, A.B.; Bærentzen, J.A.; Chen, Q.; Bals, S.; Dahl, V.A. pdf  url
doi  openurl
  Title Shape from projections via differentiable forward projector for computed tomography Type A1 Journal article
  Year 2021 Publication Ultramicroscopy Abbreviated Journal 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.  
  Address  
  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 (down) 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  
Permanent link to this record
 
 
Author Bals, S.; Verbeeck, J.; Van Tendeloo, G.; Liu, Y.-L.; Grivel, J.-C. pdf  doi
openurl 
  Title Quantitative electron microscopy of (Bi,Pb)2Sr2Ca2Cu3O10+\delta/Ag multifilament tapes during initial stages of annealing Type A1 Journal article
  Year 2005 Publication Journal of the American Ceramic Society Abbreviated Journal J Am Ceram Soc  
  Volume 88 Issue 2 Pages 431-436  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract The microstructural and compositional evolution during initial annealing of a superconducting (Bi,Pb)(2)Sr2Ca2Cu3O10+delta/Ag tape is studied using quantitative transmission electron microscopy. Special attention is devoted to the occurrence of Pb-rich liquids, which are crucial for the Bi2Sr2CaCu2O8+delta to (Bi,Pb)(2)Sr2Ca2Cu3O10+delta transformation. Ca and/or Pb-rich (Bi,Pb)(2)Sr2CaCu2O8+delta grains dissolve into a liquid, which reacts with Ca-rich phases to increase the liquid's Ca-content. This leads to (Bi,Pb)(2)Sr2Ca2Cu3O10+delta formation. Apparently, a Ca/Sr ratio of around I is sufficient to keep (Bi,Pb)(2)Sr2Ca2Cu3O10+delta nucleation going. It is confirmed that Ag particles are transported from the Ag-sheath into the oxide core by the liquid and not by mechanical treatment of the tape.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Columbus, Ohio Editor  
  Language Wos 000227510200030 Publication Date 2005-02-16  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0002-7820;1551-2916; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (down) 2.841 Times cited 1 Open Access  
  Notes Approved Most recent IF: 2.841; 2005 IF: 1.586  
  Call Number UA @ lucian @ c:irua:54876UA @ admin @ c:irua:54876 Serial 2754  
Permanent link to this record
 
 
Author Vanrompay, H.; Buurlage, J.‐W.; Pelt, D.M.; Kumar, V.; Zhuo, X.; Liz‐Marzán, L.M.; Bals, S.; Batenburg, K.J. pdf  url
doi  openurl
  Title Real‐Time Reconstruction of Arbitrary Slices for Quantitative and In Situ 3D Characterization of Nanoparticles Type A1 Journal article
  Year 2020 Publication Particle & Particle Systems Characterization Abbreviated Journal Part Part Syst Char  
  Volume 37 Issue 37 Pages 2000073  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract A detailed 3D investigation of nanoparticles at a local scale is of great importance to connect their structure and composition to their properties. Electron tomography has therefore become an important tool for the 3D characterization of nanomaterials. 3D investigations typically comprise multiple steps, including acquisition, reconstruction, and analysis/quantification. Usually, the latter two steps are performed offline, at a dedicated workstation. This sequential workflow prevents on-the-fly control of experimental parameters to improve the quality of the 3D reconstruction, to select a relevant nanoparticle for further characterization or to steer an in-situ tomography experiment. Here, we present an efficient approach to overcome these limitations, based on the real-time reconstruction of arbitrary 2D reconstructed slices through a 3D object. Implementation of this method may lead to generalized implementation of electron tomography for routine nanoparticle characterization in 3D.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000536357100001 Publication Date 2020-05-29  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0934-0866 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (down) 2.7 Times cited 10 Open Access OpenAccess  
  Notes Fonds Wetenschappelijk Onderzoek, 1S32617N ; Fonds Wetenschappelijk Onderzoek, G026718N ; Nederlandse Organisatie voor Wetenschappelijk Onderzoek, 639.073.506 016.Veni.192.235 ; 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 G026718N). Financial support was provided by The Netherlands Organization for Scientific Research (NWO), project numbers 639.073.506 and 016.Veni.192.235. 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). H.V. and J.-W.B contributed equally to this work.; sygma Approved Most recent IF: 2.7; 2020 IF: 4.474  
  Call Number EMAT @ emat @c:irua:169704 Serial 6371  
Permanent link to this record
 
 
Author Chen, Q.; Skorikov, A.; van der Hoeven, J.E.S.; van Blaaderen, A.; Albrecht, W.; Perez-Garza, H.H.; Bals, S. pdf  doi
openurl 
  Title Estimation of temperature homogeneity in MEMS-based heating nanochips via quantitative HAADF-STEM tomography Type A1 Journal article
  Year 2023 Publication Particle and particle systems characterization Abbreviated Journal  
  Volume 41 Issue 2 Pages 1-8  
  Keywords A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)  
  Abstract Sample holders for transmission electron microscopy (TEM) based on micro-electro-mechanical systems (MEMS) have recently become popular for investigating the behavior of nanomaterials under in situ or environmental conditions. The accuracy and reproducibility of these in situ holders are essential to ensure the reliability of experimental results. In addition, the uniformity of an applied temperature trigger across the MEMS chip is a crucial parameter. In this work, it is measured the temperature homogeneity of MEMS-based heating sample supports by locally analyzing the dynamics of heat-induced alloying of Au@Ag nanoparticles located in different regions of the support through quantitative fast high-angle annular dark-field scanning TEM tomography. These results demonstrate the superior temperature homogeneity of a microheater design based on a heating element shaped as a circular spiral with a width decreasing outwards compared to a double spiral-shaped designed microheater. The proposed approach to measure the local temperature homogeneity based on the thermal properties of bimetallic nanoparticles will support the future development of MEMS-based heating supports with improved thermal properties and in situ studies where high precision in the temperature at a certain position is required. This schematic delineates an approach to quantifying potential localized temperature deviation within a nanochip. Employing two comparable nanoparticles as thermal probes in discrete nanochip regions, the alloying kinetics of these nanoparticles are monitorable using in situ quantitative high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) tomography, thus enabling the precise estimation of local temperature deviations.image  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 001060394600001 Publication Date 2023-09-08  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0934-0866 ISBN Additional Links UA library record; WoS full record  
  Impact Factor (down) 2.7 Times cited Open Access Not_Open_Access  
  Notes This project was funded from the European Commission and The Marie Sklodowska-Curie Innovative Training Network MUMMERING (Grant Agreement no. 765604) Approved Most recent IF: 2.7; 2023 IF: 4.474  
  Call Number UA @ admin @ c:irua:199219 Serial 8863  
Permanent link to this record
 
 
Author Guzzinati, G.; Altantzis, T.; Batuk, M.; De Backer, A.; Lumbeeck, G.; Samaee, V.; Batuk, D.; Idrissi, H.; Hadermann, J.; Van Aert, S.; Schryvers, D.; Verbeeck, J.; Bals, S. url  doi
openurl 
  Title Recent Advances in Transmission Electron Microscopy for Materials Science at the EMAT Lab of the University of Antwerp Type A1 Journal article
  Year 2018 Publication Materials Abbreviated Journal Materials  
  Volume 11 Issue 11 Pages 1304  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract The rapid progress in materials science that enables the design of materials down to the nanoscale also demands characterization techniques able to analyze the materials down to the same scale, such as transmission electron microscopy. As Belgium’s foremost electron microscopy group, among the largest in the world, EMAT is continuously contributing to the development of TEM techniques, such as high-resolution imaging, diffraction, electron tomography, and spectroscopies, with an emphasis on quantification and reproducibility, as well as employing TEM methodology at the highest level to solve real-world materials science problems. The lab’s recent contributions are presented here together with specific case studies in order to highlight the usefulness of TEM to the advancement of materials science.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000444112800041 Publication Date 2018-07-28  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 1996-1944 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (down) 2.654 Times cited 15 Open Access OpenAccess  
  Notes Fonds Wetenschappelijk Onderzoek, G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N AUHA13009 ; European Research Council, COLOURATOM 335078 ; Universiteit Antwerpen, GOA Solarpaint ; G. Guzzinati, T. Altantzis and A. De Backer have been supported by postdoctoral fellowship grants from the Research Foundation Flanders (FWO). Funding was also received from the European Research Council (starting grant no. COLOURATOM 335078), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 770887), the Research Foundation Flanders (FWO, Belgium) through project fundings (G.0502.18N, G.0267.18N, G.0120.12N, G.0365.15N, G.0934.17N, S.0100.18N, G.0401.16N) and from the University of Antwerp through GOA project Solarpaint. Funding for the TopSPIN precession system under grant AUHA13009, as well as for the Qu-Ant-EM microscope, is acknowledged from the HERCULES Foundation. H. Idrissi is mandated by the Belgian National Fund for Scientific Research (F.R.S.-FNRS). (ROMEO:green; preprint:; postprint:can ; pdfversion:can); saraecas; ECAS_Sara; Approved Most recent IF: 2.654  
  Call Number EMAT @ emat @c:irua:153737UA @ admin @ c:irua:153737 Serial 5064  
Permanent link to this record
 
 
Author Cremers, V.; Rampelberg, G.; Barhoum, A.; Walters, P.; Claes, N.; Oliveira, T.M. de; Assche, G.V.; Bals, S.; Dendooven, J.; Detavernier, C. pdf  url
doi  openurl
  Title Oxidation barrier of Cu and Fe powder by Atomic Layer Deposition Type A1 Journal article
  Year 2018 Publication Surface and coatings technology Abbreviated Journal Surf Coat Tech  
  Volume 349 Issue 349 Pages 1032-1041  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract Atomic layer deposition (ALD) is a vapor based technique which allows to deposit uniform, conformal films with a thickness control at the atomic scale. In this research, Al 2 O 3 coatings were deposited on micrometer-sized Fe and Cu powder (particles) using the thermal trimethylaluminum (TMA)/ water (H 2 O) process in a rotary pump-type ALD reactor. Rotation of the powder during deposition was required to obtain a pinhole-free ALD coating. The protective nature of the coating was evaluated by quantifying its effectiveness in protecting the metal particles during oxidative annealing treatments. The Al 2 O 3 coated powders were annealed in ambient air while in-situ thermogravimetric analysis (TGA) and in-situ x-ray diffraction (XRD) data were acquired. The thermal stability of a series of Cu and Fe powder with different Al 2 O 3 thicknesses were determined with TGA. In both samples a clear shift in oxidation temperature is visible. For Cu and Fe powder coated with 25 nm Al 2 O 3 , we observed an increase of the oxidation temperature with 300-400°C. For the Cu powder a thin film of only 8 nm is required to obtain an initial increase in oxidation temperature of 200°C. In contrast, for Fe powder a thicker coating of 25 nm is required. In both cases, the oxidation temperature increases with increasing thickness of the Al 2 O 3 coating. These results illustrate that the Al 2 O 3 thin film, deposited by the thermal ALD process (TMA/H 2 O) can be an efficient and pinhole-free barrier layer for micrometer-sized powder particles, provided that the powder is properly agitated during the process to ensure sufficient vapour-solid interaction.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication Editor  
  Language Wos 000441492600108 Publication Date 2018-06-25  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0257-8972 ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (down) 2.589 Times cited 10 Open Access OpenAccess  
  Notes The authors acknowledge financial support from the Strategic Initiative Materials in Flanders (SIM, SBO-FUNC project) and the Special Research Fund BOF of Ghent University (GOA 01G01513). J. D. acknowledges the Research Foundation Flanders (FWO-Vlaanderen) for a postdoctoral fellowship. N.C. and S.B. acknowledge financial support from European Research Council (ERC Starting Grant 335078-COLOURATOMS). The authors acknowledge S. Goeteyn for the assistance in preliminary depositions. (ROMEO:green; preprint:; postprint:can ; pdfversion:cannot); ecas_sara Approved Most recent IF: 2.589  
  Call Number EMAT @ emat @c:irua:152174UA @ admin @ c:irua:152174 Serial 4994  
Permanent link to this record
 
 
Author Boschker, H.; Huijben, M.; Vailinois, A.; Verbeeck, J.; Van Aert, S.; Luysberg, M.; Bals, S.; Van Tendeloo, G.; Houwman, E.P.; Koster, G.; Blank, D.H.A.; Rijnders, G. pdf  doi
openurl 
  Title Optimized fabrication of high-quality La0.67Sr0.33MnO3 thin films considering all essential characteristics Type A1 Journal article
  Year 2011 Publication Journal of physics: D: applied physics Abbreviated Journal J Phys D Appl Phys  
  Volume 44 Issue 20 Pages 205001-205001,9  
  Keywords A1 Journal article; Electron microscopy for materials research (EMAT)  
  Abstract In this paper, an overview of the fabrication and properties of high-quality La0.67Sr0.33MnO3 (LSMO) thin films is given. A high-quality LSMO film combines a smooth surface morphology with a large magnetization and a small residual resistivity, while avoiding precipitates and surface segregation. In the literature, typically only a few of these issues are adressed. We therefore present a thorough characterization of our films, which were grown by pulsed laser deposition. The films were characterized with reflection high energy electron diffraction, atomic force microscopy, x-ray diffraction, magnetization and transport measurements, x-ray photoelectron spectroscopy and scanning transmission electron microscopy. The films have a saturation magnetization of 4.0 µB/Mn, a Curie temperature of 350 K and a residual resistivity of 60 µΩ cm. These results indicate that high-quality films, combining both large magnetization and small residual resistivity, were realized. A comparison between different samples presented in the literature shows that focussing on a single property is insufficient for the optimization of the deposition process. For high-quality films, all properties have to be adressed. For LSMO devices, the thin-film quality is crucial for the device performance. Therefore, this research is important for the application of LSMO in devices.  
  Address  
  Corporate Author Thesis  
  Publisher Place of Publication London Editor  
  Language Wos 000290150900001 Publication Date 2011-04-29  
  Series Editor Series Title Abbreviated Series Title  
  Series Volume Series Issue Edition  
  ISSN 0022-3727;1361-6463; ISBN Additional Links UA library record; WoS full record; WoS citing articles  
  Impact Factor (down) 2.588 Times cited 99 Open Access  
  Notes This research was financially supported by the Dutch Science Foundation, by NanoNed, a nanotechnology program of the Dutch Ministry of Economic Affairs, and by the NanOxide program of the European Science Foundation. This work is supported in part by the Department of Energy, Office of Basic Energy Sciences, Division of Materials Sciences and Engineering, under contract DE-AC02-76SF00515. Approved Most recent IF: 2.588; 2011 IF: 2.544  
  Call Number UA @ lucian @ c:irua:89557UA @ admin @ c:irua:89557 Serial 2491  
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