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“Electron tomography based on highly limited data using a neural network reconstruction technique”. Bladt E, Pelt DM, Bals S, Batenburg KJ, Ultramicroscopy 158, 81 (2015). http://doi.org/10.1016/j.ultramic.2015.07.001
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 25
DOI: 10.1016/j.ultramic.2015.07.001
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“Exploring different inelastic projection mechanisms for electron tomography”. Goris B, Bals S, van den Broek W, Verbeeck J, Van Tendeloo G, Ultramicroscopy 111, 1262 (2011). http://doi.org/10.1016/j.ultramic.2011.02.007
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 21
DOI: 10.1016/j.ultramic.2011.02.007
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“Nonlinear imaging using annular dark field TEM”. Bals S, Kilaas R, Kisielowski C, Ultramicroscopy 104, 281 (2005). http://doi.org/10.1016/j.ultramic.2005.05.004
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 15
DOI: 10.1016/j.ultramic.2005.05.004
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“Pore REconstruction and Segmentation (PORES) method for improved porosity quantification of nanoporous materials”. Van Eyndhoven G, Kurttepeli M, van Oers CJ, Cool P, Bals S, Batenburg KJ, Sijbers J, Ultramicroscopy 148, 10 (2015). http://doi.org/10.1016/j.ultramic.2014.08.008
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab; Laboratory of adsorption and catalysis (LADCA)
Impact Factor: 2.843
Times cited: 7
DOI: 10.1016/j.ultramic.2014.08.008
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“A practical method to determine the effective resolution in incoherent experimental electron tomography”. Heidari Mezerji H, van den Broek W, Bals S, Ultramicroscopy 111, 330 (2011). http://doi.org/10.1016/j.ultramic.2011.01.021
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 26
DOI: 10.1016/j.ultramic.2011.01.021
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“The properties of SIRT, TVM, and DART for 3D imaging of tubular domains in nanocomposite thin-films and sections”. Chen D, Goris B, Bleichrodt F, Heidari Mezerji H, Bals S, Batenburg KJ, de With G, Friedrich H, Ultramicroscopy 147, 137 (2014). http://doi.org/10.1016/j.ultramic.2014.08.005
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 42
DOI: 10.1016/j.ultramic.2014.08.005
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“Quantitative atomic resolution mapping using high-angle annular dark field scanning transmission electron microscopy”. Van Aert S, Verbeeck J, Erni R, Bals S, Luysberg M, van Dyck D, Van Tendeloo G, Ultramicroscopy 109, 1236 (2009). http://doi.org/10.1016/j.ultramic.2009.05.010
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 166
DOI: 10.1016/j.ultramic.2009.05.010
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“Quantitative electron tomography : the effect of the three-dimensional point spread function”. Heidari H, van den Broek W, Bals S, Ultramicroscopy 135, 1 (2013). http://doi.org/10.1016/j.ultramic.2013.06.005
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 6
DOI: 10.1016/j.ultramic.2013.06.005
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“TEM sample preparation by FIB for carbon nanotube interconnects”. Ke X, Bals S, Romo Negreira A, Hantschel T, Bender H, Van Tendeloo G, Ultramicroscopy 109, 1353 (2009). http://doi.org/10.1016/j.ultramic.2009.06.011
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 21
DOI: 10.1016/j.ultramic.2009.06.011
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“The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography”. van Aarle W, Palenstijn WJ, De Beenhouwer J, Altantzis T, Bals S, Batenburg KJ, Sijbers J, Ultramicroscopy 157, 35 (2015). http://doi.org/10.1016/j.ultramic.2015.05.002
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Vision lab
Impact Factor: 2.843
Times cited: 562
DOI: 10.1016/j.ultramic.2015.05.002
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“An alternative approach for ζ-factor measurement using pure element nanoparticles”. Zanaga D, Altantzis T, Sanctorum J, Freitag B, Bals S, Ultramicroscopy 164, 11 (2016). http://doi.org/10.1016/j.ultramic.2016.03.002
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 19
DOI: 10.1016/j.ultramic.2016.03.002
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“Three dimensional mapping of Fe dopants in ceria nanocrystals using direct spectroscopic electron tomography”. Goris B, Meledina M, Turner S, Zhong Z, Batenburg KJ, Bals S, Ultramicroscopy 171, 55 (2016). http://doi.org/10.1016/j.ultramic.2016.08.017
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 13
DOI: 10.1016/j.ultramic.2016.08.017
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“Depth sectioning combined with atom-counting in HAADF STEM to retrieve the 3D atomic structure”. Alania M, Altantzis T, De Backer A, Lobato I, Bals S, Van Aert S, Ultramicroscopy 177, 36 (2016). http://doi.org/10.1016/j.ultramic.2016.11.002
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 13
DOI: 10.1016/j.ultramic.2016.11.002
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“An alternative approach for \zeta-factor measurement using pure element nanoparticles”. Zanaga D, Altantzis T, Sanctorum J, Freitag B, Bals S, Ultramicroscopy 164, 11 (2016). http://doi.org/10.1016/J.ULTRAMIC.2016.03.002
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 19
DOI: 10.1016/J.ULTRAMIC.2016.03.002
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“A bimodal tomographic reconstruction technique combining EDS-STEM and HAADF-STEM”. Zhong Z, Goris B, Schoenmakers R, Bals S, Batenburg KJ, Ultramicroscopy 174, 35 (2017). http://doi.org/10.1016/j.ultramic.2016.12.008
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 26
DOI: 10.1016/j.ultramic.2016.12.008
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“Automated discrete electron tomography &ndash, Towards routine high-fidelity reconstruction of nanomaterials”. Zhuge X, Jinnai H, Dunin-Borkowski RE, Migunov V, Bals S, Cool P, Bons A-J, Batenburg KJ, Ultramicroscopy 175, 87 (2017). http://doi.org/10.1016/j.ultramic.2017.01.009
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Laboratory of adsorption and catalysis (LADCA)
Impact Factor: 2.843
Times cited: 22
DOI: 10.1016/j.ultramic.2017.01.009
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“Automatic correction of nonlinear damping effects in HAADF-STEM tomography for nanomaterials of discrete compositions”. Zhong Z, Aveyard R, Rieger B, Bals S, Palenstijn WJ, Batenburg KJ, Ultramicroscopy 184, 57 (2018). http://doi.org/10.1016/J.ULTRAMIC.2017.10.013
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.'));
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 8
DOI: 10.1016/J.ULTRAMIC.2017.10.013
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“Fast versus conventional HAADF-STEM tomography of nanoparticles: advantages and challenges”. Vanrompay H, Skorikov A, Bladt E, Béché, A, Freitag B, Verbeeck J, Bals S, Ultramicroscopy 221, 113191 (2021). http://doi.org/10.1016/j.ultramic.2020.113191
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.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 15
DOI: 10.1016/j.ultramic.2020.113191
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“A simple method to clean ligand contamination on TEM grids”. Li C, Tardajos AP, Wang D, Choukroun D, Van Daele K, Breugelmans T, Bals S, Ultramicroscopy 221, 113195 (2021). http://doi.org/10.1016/j.ultramic.2020.113195
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT); Applied Electrochemistry & Catalysis (ELCAT)
Impact Factor: 2.843
Times cited: 10
DOI: 10.1016/j.ultramic.2020.113195
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“Shape from projections via differentiable forward projector for computed tomography”. Koo J, Dahl AB, Bærentzen JA, Chen Q, Bals S, Dahl VA, Ultramicroscopy 224, 113239 (2021). http://doi.org/10.1016/j.ultramic.2021.113239
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.
Keywords: A1 Journal article; Engineering sciences. Technology; Electron microscopy for materials research (EMAT)
Impact Factor: 2.843
Times cited: 3
DOI: 10.1016/j.ultramic.2021.113239
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“A decade of atom-counting in STEM: From the first results toward reliable 3D atomic models from a single projection”. De Backer A, Bals S, Van Aert S, Ultramicroscopy , 113702 (2023). http://doi.org/10.1016/j.ultramic.2023.113702
Abstract: Quantitative structure determination is needed in order to study and understand nanomaterials at the atomic scale. Materials characterisation resulting in precise structural information is a crucial point to understand the structure–property relation of materials. Counting the number of atoms and retrieving the 3D atomic structure of nanoparticles plays an important role here. In this paper, an overview will be given of the atom-counting methodology and its applications over the past decade. The procedure to count the number of atoms will be discussed in detail and it will be shown how the performance of the method can be further improved. Furthermore, advances toward mixed element nanostructures, 3D atomic modelling based on the atom-counting results, and quantifying the nanoparticle dynamics will be highlighted.
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT)
Impact Factor: 2.2
Times cited: 3
DOI: 10.1016/j.ultramic.2023.113702
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“The uptake and elimination of ZnO and CuO nanoparticles in Daphnia magna under chronic exposure scenarios”. Adam N, Leroux F, Knapen D, Bals S, Blust R, Water research 68, 249 (2015). http://doi.org/10.1016/j.watres.2014.10.001
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
Keywords: A1 Journal article; Electron microscopy for materials research (EMAT); Veterinary physiology and biochemistry
Impact Factor: 6.942
Times cited: 51
DOI: 10.1016/j.watres.2014.10.001
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