The standard technique for sub-pixel estimation of atom positions from atomic resolution scanning transmission electron microscopy images relies on fitting intensity maxima or minima with a two-dimensional Gaussian function. While this is a widespread method of measurement, it can be error prone in images with non-zero aberrations, strong intensity differences between adjacent atoms or in situations where the neighboring atom positions approach the resolution limit of the microscope. Here we demonstrate mpfit, an atom finding algorithm that iteratively calculates a series of overlapping two-dimensional Gaussian functions to fit the experimental dataset and then subsequently uses a subset of the calculated Gaussian functions to perform sub-pixel refinement of atom positions. Based on both simulated and experimental datasets presented in this work, this approach gives lower errors when compared to the commonly used single Gaussian peak fitting approach and demonstrates increased robustness over a wider range of experimental conditions.

Scanning precession electron diffraction involves the acquisition of a two-dimensional precession electron diffraction pattern at every probe position in a two-dimensional scan. The data typically comprise many more diffraction patterns than the number of distinct microstructural volume elements (e.g. crystals) in the region sampled. A dimensionality reduction, ideally to one representative diffraction pattern per distinct element, may then be sought. Further, some diffraction patterns will contain contributions from multiple crystals sampled along the beam path, which may be unmixed by harnessing this oversampling. Here, we report on the application of unsupervised machine learning methods to achieve both dimensionality reduction and signal unmixing. Potential artefacts are discussed and precession electron diffraction is demonstrated to improve results by reducing the impact of bending and dynamical diffraction so that the data better approximate the case in which each crystal yields a given diffraction pattern.

Dislocations and stacking faults are important crystal defects, because they strongly influence material properties. As of now, transmission electron microscopy (TEM) is the most frequently used technique to study the properties of single dislocations and stacking faults. Specifically, the Burgers vector b of dislocations or displacement vector R of stacking faults can be determined on the basis of the g·b = n (g·R = n) criterion by setting up different two-beam diffraction conditions with an imaging vector g. Based on the reciprocity theorem, scanning transmission electron microscopy (STEM) can also be applied for defect characterization, but has been less frequently used up to now. In this work, we demonstrate g·b = n (g·R = n) analyses of dislocations and stacking faults in GaN by STEM imaging in a scanning electron microscope. The instrument is equipped with a STEM detector, double-tilt TEM specimen holder, and a charge-coupled-device camera for the acquisition of on-axis diffraction patterns. The latter two accessories are mandatory to control the specimen orientation, which has not been possible before in a scanning electron microscope.

Micro-Extinction Spectroscopy (MExS), a flexible, optical, and spatial-scanning hyperspectral technique, has been developed and is described with examples. Software and hardware capabilities are described in detail, including transmission, reflectance, and scattering measurements. Each capability is demonstrated through a case study of nanomaterial characterization, i.e., transmission of transition metal dichalcogenides revealing transition energy and efficiency, reflectance of transition metal dichalcogenides grown on nontransparent substrates identifying the presence of monolayer following electrochemical ablation, and scattering to study single plasmonic nanoparticles and obtain values for the refractive index sensitivity and sensing figure of merit of over a hundred single particles with various shapes and sizes. With the growing integration of nanotechnology in many areas, MExS can be a powerful tool to both characterize and test nanomaterials.

One of the biggest bottlenecks for structural analysis of proteins remains the creation of high-yield and high-purity samples of the target protein. Cell-free protein synthesis technologies are powerful and customizable platforms for obtaining functional proteins of interest in short timeframes, while avoiding potential toxicity issues and permitting high-throughput screening. These methods have benefited many areas of genomic and proteomics research, therapeutics, vaccine development and protein chip constructions. In this work, we demonstrate a versatile and multiscale eukaryotic wheat germ cell-free protein expression pipeline to generate functional proteins of different sizes from multiple host organism and DNA source origins. We also report on a robust purification procedure, which can produce highly pure (> 98%) proteins with no specialized equipment required and minimal time invested. This pipeline successfully produced and analyzed proteins in all three major geometry formats used for structural biology including single particle analysis with electron microscopy, and both two-dimensional and three-dimensional protein crystallography. The flexibility of the wheat germ system in combination with the multiscale pipeline described here provides a new workflow for rapid production and purification of samples that may not be amenable to other recombinant approaches for structural characterization.

Image simulation for scanning transmission electron microscopy at atomic resolution for samples with realistic dimensions can require very large computation times using existing simulation algorithms. We present a new algorithm named PRISM that combines features of the two most commonly used algorithms, namely the Bloch wave and multislice methods. PRISM uses a Fourier interpolation factor f that has typical values of 4–20 for atomic resolution simulations. We show that in many cases PRISM can provide a speedup that scales with f4 compared to multislice simulations, with a negligible loss of accuracy. We demonstrate the usefulness of this method with large-scale scanning transmission electron microscopy image simulations of a crystalline nanoparticle on an amorphous carbon substrate.

It is now established that the 3D structure of homogeneous nanocrystals can be recovered from in-line hologram of single projections. The method builds on a quantitative contrast interpretation of electron exit wave functions. Since simulated exit wave functions of single and bilayers of graphene reveal the atomic structure of carbon-based materials with sufficient resolution, we explore theoretically how the approach can be expanded beyond periodic carbon-based materials to include non-periodic molecular structures. We show here theoretically that the 3D atomic structure of randomly oriented oleic acid molecules can be recovered from a single projection.

The MAX IV Laboratory is currently the synchrotron X-ray source with the beam of highest brilliance. Four imaging beamlines are in construction or in the project phase. Their common characteristic will be the high acquisition rates of phase-enhanced images. This high data flow will be managed at the local computing cluster jointly with the Swedish National Computing Infrastructure. A common image reconstruction and analysis platform is being designed to offer reliable quantification of the multidimensional images acquired at all the imaging beamlines at MAX IV.

Abstract Although magnetism originates at the atomic scale, the existing spectroscopic techniques sensitive to magnetic signals only produce spectra with spatial resolution on a larger scale. However, recently, it has been theoretically argued that atomic size electron probes with customized phase distributions can detect magnetic circular dichroism. Here, we report a direct experimental real-space detection of magnetic circular dichroism in aberration-corrected scanning transmission electron microscopy (STEM). Using an atomic size-aberrated electron probe with a customized phase distribution, we reveal the checkerboard antiferromagnetic ordering of Mn moments in LaMnAsO by observing a dichroic signal in the Mn L-edge. The novel experimental setup presented here, which can easily be implemented in aberration-corrected STEM, opens new paths for probing dichroic signals in materials with unprecedented spatial resolution.

Abstract The introduction of gaseous atmospheres in transmission electron microscopy offers the possibility of studying materials in situ under chemically relevant environments. The presence of a gas environment can degrade the resolution. Surprisingly, this phenomenon has been shown to depend on the electron-dose-rate. In this article, we demonstrate that both the total and areal electron-dose-rates work as descriptors for the dose-rate-dependent resolution and are related through the illumination area. Furthermore, the resolution degradation was observed to occur gradually over time after initializing the illumination of the sample and gas by the electron beam. The resolution was also observed to be sensitive to the electrical conductivity of the sample. These observations can be explained by a charge buildup over the electron-illuminated sample area, caused by the beam–gas–sample interaction, and by a subsequent sample motion induced by electrical capacitance in the sample.