Abstract: Stone monuments and buildings are susceptible to weathering. Carbonate-based stones are especially vulnerable in acidic environments, whereas magmatic acidic stones are more susceptible to chemical weathering in basic environments. To slow down surface corrosion of limestone and marble artworks/buildings, protective coatings which inhibit calcite dissolution have been proposed. In this work, samples from two stone types with different porosity were treated with ammonium oxalate (AmOx) to create a protective layer of calcium oxalate (CaOx) using the previously developed brushing method. Two different synchrotron microscopy experiments were performed to determine its protective capability. X-ray powder diffraction (SR-mu-XRPD) in transmission geometry allowed visualization of the distributions of calcium carbonate and oxalates along the sample depths. In a second step, X-ray fluorescence (SR-mu-XRF) was used to check the efficiency/integrity of the protective surface coating layer. This was done by measuring the sulfur distribution on the stone surface after exposing the protected stones to sulfuric acid. XRPD showed the formation of a protective oxalate layer with a thickness of 5-15 mu m on the less porous stone, while a 20-30 mu m thick layer formed on the more porous stone. The XRF study showed that the optimal treatment time depends on the stone porosity. Increasing the treatment time from 1 to 3 h resulted in a decreased efficiency of the protective layer for the low porosity stone. We assume that this is due to the formation of vertical channels (cracks) in the protective layer.

Abstract: In electron microscopy, the maximum a posteriori (MAP) probability rule has been introduced as a tool to determine the most probable atomic structure from high-resolution annular dark-field (ADF) scanning transmission electron microscopy (STEM) images exhibiting low contrast-to-noise ratio (CNR). Besides ADF imaging, STEM can also be applied in the annular bright-field (ABF) regime. The ABF STEM mode allows to directly visualize light-element atomic columns in the presence of heavy columns. Typically, light-element nanomaterials are sensitive to the electron beam, limiting the incoming electron dose in order to avoid beam damage and leading to images exhibiting low CNR. Therefore, it is of interest to apply the MAP probability rule not only to ADF STEM images, but to ABF STEM images as well. In this work, the methodology of the MAP rule, which combines statistical parameter estimation theory and model-order selection, is extended to be applied to simultaneously acquired ABF and ADF STEM images. For this, an extension of the commonly used parametric models in STEM is proposed. Hereby, the effect of specimen tilt has been taken into account, since small tilts from the crystal zone axis affect, especially, ABF STEM intensities. Using simulations as well as experimental data, it is shown that the proposed methodology can be successfully used to detect light elements in the presence of heavy elements.

Abstract: We present a quantitative method which allows us to reliably measure dynamic changes in the atomic structure of monatomic crystalline nanomaterials from a time series of atomic resolution annular dark field scanning transmission electron microscopy images. The approach is based on the so-called hidden Markov model and estimates the number of atoms in each atomic column of the nanomaterial in each frame of the time series. We discuss the origin of the improved performance for time series atom-counting as compared to the current state-of-the-art atom-counting procedures, and show that the so-called transition probabilities that describe the probability for an atomic column to lose or gain one or more atoms from frame to frame are particularly important. Using these transition probabilities, we show that the method can also be used to estimate the probability and cross section related to structural changes. Furthermore, we explore the possibilities for applying the method to time series recorded under variable environmental conditions. The method is shown to be promising for a reliable quantitative analysis of dynamic processes such as surface diffusion, adatom dynamics, beam effects, or in situ experiments.

Abstract: The highly energetic electrons in a transmission electron microscope (TEM) can alter or even completely destroy the structure of samples before sufficient information can be obtained. This is especially problematic in the case of zeolites, organic and biological materials. As this effect depends on both the electron beam and the sample and can involve multiple damage pathways, its study remained difficult and is plagued with irreproducibility issues, circumstantial evidence, rumors, and a general lack of solid data. Here we take on the experimental challenge to investigate the role of the STEM scan pattern on the damage behavior of a commercially available zeolite sample with the clear aim to make our observations as reproducible as possible. We make use of a freely programmable scan engine that gives full control over the tempospatial distribution of the electron probe on the sample and we use its flexibility to obtain multiple repeated experiments under identical conditions comparing the difference in beam damage between a conventional raster scan pattern and a newly proposed interleaved scan pattern that provides exactly the same dose and dose rate and visits exactly the same scan points. We observe a significant difference in beam damage for both patterns with up to 11 % reduction in damage (measured from mass loss). These observations demonstrate without doubt that electron dose, dose rate and acceleration voltage are not the only parameters affecting beam damage in (S)TEM experiments and invite the community to rethink beam damage as an unavoidable consequence of applied electron dose.

Abstract: Electron ptychography provides highly sensitive, dose efficient phase images which can be corrected for aberrations after the data has been acquired. This is crucial when very precise quantification is required, such as with sensitivity to charge transfer due to bonding. Drift can now be essentially eliminated as a major impediment to focused probe ptychography, which benefits from the availability of easily interpretable simultaneous Z-contrast imaging. However challenges have remained when quantifying the ptychographic phases of atomic sites. The phase response of a single atom has a negative halo which can cause atoms to reduce in phase when brought closer together. When unaccounted for, as in integrating methods of quantification, this effect can completely obscure the effects of charge transfer. Here we provide a new method of quantification that overcomes this challenge, at least for 2D materials, and is robust to experimental parameters such as noise, sample tilt.

Abstract: We report a study of scattering dynamics in crystals employing momentum-resolved scanning transmission
electron microscopy under varying illumination conditions. As we perform successive changes of the probe
focus, multiple real-space signals are obtained in dependence of the shape of the incident electron wave.
With support from extensive simulations, each signal is shown to be characterised by an optimum focus for
which the contrast is maximum and which differs among different signals. For instance, a systematic focus
mismatch is found between images formed by high-angle scattering, being sensitive to thickness and chemical
composition, and the first moment in diffraction space, being sensitive to electric fields. It follows that a single
recording at one specific probe focus is usually insufficient to characterise materials comprehensively. Most
importantly, we demonstrate in experiment and simulation that the second moment (

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.