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.

Abstract: The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and structural biology. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and fairly accurate, especially for scanning TEM (STEM) annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory, which was previously mainly required for holography. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We argue that a physically better justified ab initio description of the scattering potential is both useful and viable for an increasing number of systems, and we expect such simulations to steadily gain in popularity and importance.

Abstract: We introduce a facile approach to transfer thin films and other mechanically sensitive TEM samples inside a FIB with minimal introduction of stress and bending. The method is making use of a pre-synthetized flexible freestanding Ag nanowire attached to the tip of a typical tungsten micromanipulator inside the FIB. The main advantages of this approach are the significantly reduced stress-induced bending during transfer and attachment of the TEM sample, the very short time required to attach and cut the nanowire, the operation at very low dose and ion current, and only using the e-beam for Pt deposition during the transfer of sensitive TEM samples. This results in a reduced sample preparation time and reduced exposure to the ion beam or e-beam for Pt deposition during the sample preparation and thus also reduced contamination and beam damage. The method was applied to a number of thin films and different TEM samples in order to illustrate the advantageous benefits of the concept. In particular, the technique has been successfully tested for the transfer of a thin film onto a MEMS heating chip for in situ TEM experiments.

Abstract: In this second part of a series we attempt to construct an empirical model that can mimick all experimental observations made regarding the role of an alternative interleaved scan pattern in STEM imaging on the beam damage in a specific zeolite sample. We make use of a 2D diffusion model that describes the dissipation of the deposited beam energy in the sequence of probe positions that are visited during the scan pattern. The diffusion process allows for the concept of trying to ‘outrun’ the beam damage by carefully tuning the dwell time and distance between consecutively visited probe positions. We add a non linear function to include a threshold effect and evaluate the accumulated damage in each part of the image as a function of scan pattern details. Together, these ingredients are able to describe qualitatively all aspects of the experimental data and provide us with a model that could guide a further optimisation towards even lower beam damage without lowering the applied electron dose. We deliberately remain vague on what is diffusing here which avoids introducing too many sample specific details. This provides hope that the model can be applied also in sample classes that were not yet studied in such great detail by adjusting higher level parameters: a sample dependent diffusion constant and damage threshold.

Abstract: This paper investigates the possible benefits for counting atoms of different chemical nature when analysing multiple 2D scanning transmission electron microscopy (STEM) images resulting from independent annular dark field (ADF) detector regimes. To reach this goal, the principles of statistical detection theory are used to quantify the probability of error when determining the number of atoms in atomic columns consisting of multiple types of elements. In order to apply this theory, atom-counting is formulated as a statistical hypothesis test, where each hypothesis corresponds to a specific number of atoms of each atom type in an atomic column. The probability of error, which is limited by the unavoidable presence of electron counting noise, can then be computed from scattering-cross sections extracted from multiple ADF STEM images. Minimisation of the probability of error as a function of the inner and outer angles of a specified number of independent ADF collection regimes results in optimal experimental designs. Based on simulations of spherical Au@Ag and Au@Pt core–shell nanoparticles, we investigate how the combination of two non-overlapping detector regimes helps to improve the probability of error when unscrambling two types of atoms. In particular, the combination of a narrow low angle ADF detector with a detector formed by the remaining annular collection regime is found to be optimal. The benefit is more significant if the atomic number Z difference becomes larger. In
addition, we show the benefit of subdividing the detector regime into three collection areas for heterogeneous nanostructures based on a structure consisting of three types of elements, e.g., a mixture of Au, Ag and Al atoms. Finally, these results are compared with the probability of error resulting when one would ultimately use a pixelated 4D STEM detector and how this could help to further reduce the incident electron dose.

Abstract: Advanced materials often consist of multiple elements which are arranged in a complicated structure. Quantitative scanning transmission electron microscopy is useful to determine the composition and thickness of nanostructures at the atomic scale. However, significant difficulties remain to quantify mixed columns by comparing the resulting atomic resolution images and spectroscopy data with multislice simulations where dynamic scattering needs to be taken into account. The combination of the computationally intensive nature of these simulations and the enormous amount of possible mixed column configurations for a given composition indeed severely hamper the quantification process. To overcome these challenges, we here report the development of an incoherent non-linear method for the fast prediction of ADF-EDX scattering cross-sections of mixed columns under channelling conditions. We first explain the origin of the ADF and EDX incoherence from scattering physics suggesting a linear dependence between those two signals in the case of a high-angle ADF detector. Taking EDX as a perfect incoherent reference mode, we quantitatively examine the ADF longitudinal incoherence under different microscope conditions using multislice simulations. Based on incoherent imaging, the atomic lensing model previously developed for ADF is now expanded to EDX, which yields ADF-EDX scattering cross-section predictions in good agreement with multislice simulations for mixed columns in a core–shell nanoparticle and a high entropy alloy. The fast and accurate prediction of ADF-EDX scattering cross-sections opens up new opportunities to explore the wide range of ordering possibilities of heterogeneous materials with multiple elements.

Abstract: Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15–30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.

Abstract: In this paper convexity constraints are derived for a background model of electron energy loss spectra (EELS) that is linear in the fitting parameters. The model outperforms a power-law both on experimental and simulated backgrounds, especially for wide energy ranges, and thus improves elemental quantification results. Owing to the model’s linearity, the constraints can be imposed through fitting by quadratic programming. This has important advantages over conventional nonlinear power-law fitting such as high speed and a guaranteed unique solution without need for initial parameters. As such, the need for user input is significantly reduced, which is essential for unsupervised treatment of large datasets. This is demonstrated on a demanding spectrum image of a semiconductor device sample with a high number of elements over a wide energy range.

Abstract: Ptychography provides high dose efficiency images that can reveal light elements next to heavy atoms. However, despite ptychography having an otherwise single signed contrast transfer function, contrast reversals can occur when the projected potential becomes strong for both direct and iterative inversion ptychography methods. It has recently been shown that these reversals can often be counteracted in direct ptychography methods by adapting the focus. Here we provide an explanation of why the best contrast is often found with the probe focused to the middle of the sample. The phase contribution due to defocus at each sample slice above and below the central plane in this configuration effectively cancels out, which can prevent contrast reversals when dynamical scattering effects are not overly strong. In addition we show that the convergence angle can be an important consideration for removal of contrast reversals in relatively thin samples.

Abstract: Epicuticular wax (EW) protects the plant’s integrity and acts as a barrier against biotic and abiotic stresses. The micro-structured three-dimensional EW’s and presence of leaf trichomes influence the wettability of a leaf surface. In this study, leaves of 96 perennial urban plant species were examined to determine an association between epicuticular wax structure (EWS) types and leaf wettability and investigate their seasonal variation. The EWS types were identified using Scanning Electron Microscopy (SEM), while leaf wettability was analyzed by measuring the drop contact angle (DCA) on both the abaxial and the adaxial sides of leaves collected from a common garden in June and September 2016. Four distinct EWS types namely thin film, platelets, crusts, and tubules were observed on leaves of investigated plant species in both June and September. The EWS types varied significantly between functional plant types and plant families in both June and September. In June, the abaxial DCA ranged from 56° to 147°, and the adaxial DCA ranged from 56° to 136°. In September, the abaxial DCA ranged from 54° to 130°, and the adaxial DCA ranged from 51° to 125°. The effect of time, leaf side, and EWS type on leaf wettability were significant. Plant species which showed a change in EWS type or clustering from June to September did not show a more pronounced reduction in DCA compared to those species which exhibited a constant EWS type. Findings from our study illustrate that DCA is not a good indicator in determining the different EWS types due to overlapping DCA intervals between the identified EWS types. However, the identified EWS types remained fairly stable throughout the in-leaf season and do not require repeated measurements for characterization.

Abstract: Air pollution caused by particulate matter (PM) is a well-known health issue in urban environments. Urban green infrastructure offers opportunities as a nature-based solution to urban PM pollution. Green walls have advantages over other types of urban green infrastructure, since they can be applied to the enormous available wall area in cities and since they do not interfere with the prevailing ventilation resulting in elevated PM levels. However, this has raised questions about the effectiveness of GW in removing PM and this could explain the limited applicability of green walls to tackle PM pollution. Nevertheless, it is suggested that green walls have a significant unexploited potential and this review article aims to address current knowledge gaps and to propose future research requirements for the implementation of green walls to mitigate urban PM pollution. An in-depth analysis is given of the mechanisms behind PM deposition and the influence of vegetation properties on this process, as well as the practices followed to model PM dispersion and deposition. It was suggested that particle deposition on green walls depends on the green wall species, pollution level, and the residence time of PM in a street (canyon). Rainfall plays an important role in the PM pathway, although it is not a necessary requirement to sustain PM deposition on plant leaves. There are still some discrepancies in the literature about the ideal plant characteristics for PM deposition in terms of the macro- and microstructures that require further investigation, especially in comparison with tree and shrub species. In addition, extensively validated models are required to accurately calculate the impact of green walls on air flow and the PM concentration on site.

Abstract: Fourier transform laser microprobe mass spectrometry (FT LMMS) has been developed for the molecular analysis of both organic and inorganic components at the surface of microobjects with the ultimate specificity of high-mass resolution. These capabilities are needed in numerous applications of practical material analysis, such as tracing back anomalies in microobjects. The purpose of this paper is to address representative example from industrial trouble shooting, in which organic and inorganic analytes in a single microparticle have been identified unambiguously. This motivates the research to extend the methodology towards quantification. This paper deals with the fundamental aspect of information depth, specifically for inorganic molecular adduct ions. Finally, data will show the quantitative capabilities of FT LMMS. A suitable methodology for the preparation of reference specimens has allowed the empirical calibration of the response as a function of the local concentration to be achieved.

Abstract: Results are discussed of a transmission electron microscopy study of high-dose oxygen implanted silicon. In addition to the general high temperature (> 1200-degrees-C) annealing treatments also annealings at 'low' temperatures (1000-1100-degrees-C) were performed in order to slow down the precipitate and defect reactions. The observed dissolution of the oxide precipitates during prolonged high temperature annealing is explained by critical radius considerations. Threading dislocations are the remaining lattice defects in the silicon overlayer and cannot be removed by further annealing. Low temperature annealing results in the formation and subsequent unfaulting of extrinsic stacking fault loops below the buried oxide layer.

Abstract: In een context van stijgende waterschaarste verkennen wij, naar ons weten voor het eerst in Vlaanderen, publieke steun voor de behandeling en het hergebruik van afvalwater als drinkwater. Vlaanderen is vandaag een van de weinige regio’s waar afvalwater reeds gerecycleerd wordt voor drinkwaterdoeleinden. Dit gebeurt op kleinschalig niveau en de uitbreiding hiervan is vandaag een van de Vlaamse beleidsdoelstellingen. Internationale voorbeelden toonden echter dat een gebrek aan publieke steun een aanzienlijk obstakel kan zijn. Vaak worden gezondheids- en veiligheidsbezorgdheden aangehaald als oorzaak voor het beperkte draagvlak. Minder is geweten over de socio-demografische distributie van dit draagvlak. Daarbovenop blijft er onduidelijkheid over de samenhang tussen socio-demografische kenmerken en gezondheids- en veiligheidsbezorgdheden. Met behulp van een enquête uitgevoerd in Vlaanderen (N=2309), bestudeerden wij ten eerste deze socio-demografische verschillen op basis van bivariate associaties (gender, opleidingsniveau, leeftijd en woonplaats). Ten tweede construeerden we een padmodel om te onderzoeken of deze verschillen verklaard kunnen worden aan de hand van gezondheids- en veiligheidsbezorgdheden. Onze resultaten toonden dat publieke steun voor afvalwaterhergebruik voor drinkwaterdoeleinden in Vlaanderen beperkt is. Het draagvlak was het laagst bij oudere mensen, vrouwen, lager geschoolde groepen en mensen die niet in de Provincie Antwerpen wonen. Voor een groot deel konden socio-demografische verschillen verklaard worden door hogere gezondheids- en veiligheidsbezorgdheden bij vrouwen, lager geschoolden en mensen uit West- en Oost-Vlaanderen. Dit suggereert een gebrek aan vertrouwen in waterexperts en -technologie bij bepaalde socio-demografische groepen, wat zich vertaalt in een verminderde publieke steun voor afvalwaterhergebruik. Op basis van deze bevindingen bespreken we een aantal potentiële actiestrategieën om publieke oppositie te anticiperen en proactief publieke steun te verwerven via doelgerichte (risico)communicatie.

Abstract: Both landfill taxes and Enhanced Waste Management (EWM) practices can mitigate the scarcity issue of landfill capacity by respectively reducing landfilled waste volumes and valorising future waste streams. However, high landfill taxes might erode incentives for EWM, even though EWM creates value by valorising waste. Concentrating on Flanders (Belgium), the paper applies dynamic optimisation modelling techniques to analyse how landfill taxation and EWM can reinforce each other and how taxation schemes can be adjusted in order to foster sustainable and welfare maximising ways of processing future waste streams. Based on the Flemish simulation results, insights are offered that are generally applicable in international waste and resource management policy. As shown, the optimal Flemish landfill tax that optimises welfare in the no EWM scenario is higher than the one in the EWM scenario (93 against (sic)50/ton). This difference should create incentives for applying EWM and is driven by the positive external effects that are generated by EWM practices. In Flanders, as the current landfill tax is slightly lower than these optimal levels, the choice that can be made is to further increase taxation levels or show complete commitment to EWM. A first generally applicable insight that was found points to the fact that it is not necessarily the case that the higher the landfill tax, the more effective waste management improvements can be realised. Other insights are about providing sufficient incentives for applying EMW practices and formulating appropriate pleas in support of technological development. By these insights, this paper should provide relevant information that can assist in triggering the transition towards a resource efficient, circular economy in Europe. (C) 2016 Elsevier Ltd. All rights reserved.