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Scanning transmission electron microscopy (STEM) is widely used for imaging, diffraction, and spectroscopy of materials down to atomic resolution. Recent advances in detector technology and computational methods have enabled many experiments that record a full image of the STEM probe for many probe positions, either in diffraction space or real space. In this paper, we review the use of these four-dimensional STEM experiments for virtual diffraction imaging, phase, orientation and strain mapping, measurements of medium-range order, thickness and tilt of samples, and phase contrast imaging methods, including differential phase contrast, ptychography, and others.

The demand for high-throughput data collection in electron microscopy is increasing for applications in structural and cellular biology. Here we present a combination of software tools that enable automated acquisition guided by image analysis for a variety of transmission electron microscopy acquisition schemes. SerialEM controls microscopes and detectors and can trigger automated tasks at multiple positions with high flexibility. Py-EM interfaces with SerialEM to enact specimen-specific image-analysis pipelines that enable feedback microscopy. As example applications, we demonstrate dose reduction in cryo-electron microscopy experiments, fully automated acquisition of every cell in a plastic section and automated targeting on serial sections for 3D volume imaging across multiple grids.Py-EM and SerialEM enable automated microscope control for high-throughput data acquisition in diverse transmission electron microscopy imaging experiments.

The biological identity of nanoparticles (NPs) is established by their interactions with a wide range of biomolecules around their surfaces after exposure to biological media. Understanding the true nature of the biomolecular corona (BC) in its native state is, therefore, essential for its safe and efficient application in clinical settings. The fundamental challenge is to visualize the biomolecules within the corona and their relationship/association to the surface of the NPs. Using a synergistic application of cryo-electron microscopy, cryo-electron tomography, and three-dimensional reconstruction, we revealed the unique morphological details of the biomolecules and their distribution/association with the surface of polystyrene NPs at a nanoscale resolution. The analysis of the BC at a single NP level and its variability among NPs in the same sample, and the discovery of the presence of nonspecific biomolecules in plasma residues, enable more precise characterization of NPs, improving predictions of their safety and efficacies. Understanding the biomolecular corona is of key importance to nanomedicine. Here, the authors report on cryo-electron and tomographic imaging of the corona formed on model nanoparticles and the 3D reconstruction of the corona to study the distribution and association of the biomolecules with the nanoparticle.

Crystalline materials used in technological applications are often complex assemblies composed of multiple phases and differently oriented grains. Robust identification of the phases and orientation relationships from these samples is crucial, but the information extracted from the diffraction condition probed by an electron beam is often incomplete. We have developed an automated crystal orientation mapping (ACOM) procedure which uses a converged electron probe to collect diffraction patterns from multiple locations across a complex sample. We provide an algorithm to determine the orientation of each diffraction pattern based on a fast sparse correlation method. We demonstrate the speed and accuracy of our method by indexing diffraction patterns generated using both kinematical and dynamical simulations. We have also measured orientation maps from an experimental dataset consisting of a complex polycrystalline twisted helical AuAgPd nanowire. From these maps we identify twin planes between adjacent grains, which may be responsible for the twisted helical structure. All of our methods are made freely available as open source code, including tutorials which can be easily adapted to perform ACOM measurements on diffraction pattern datasets.

Corrosion is a ubiquitous failure mode of materials. Often, the progression of localized corrosion is accompanied by the evolution of porosity in materials previously reported to be either three-dimensional or two-dimensional. However, using new tools and analysis techniques, we have realized that a more localized form of corrosion, which we call 1D wormhole corrosion, has previously been miscategorized in some situations. Using electron tomography, we show multiple examples of this 1D and percolating morphology. To understand the origin of this mechanism in a Ni-Cr alloy corroded by molten salt, we combined energy-filtered four-dimensional scanning transmission electron microscopy and ab initio density functional theory calculations to develop a vacancy mapping method with nanometer-resolution, identifying a remarkably high vacancy concentration in the diffusion-induced grain boundary migration zone, up to 100 times the equilibrium value at the melting point. Deciphering the origins of 1D corrosion is an important step towards designing structural materials with enhanced corrosion resistance. Corrosion is a ubiquitous failure mode in materials. Here the authors report a percolating 1D wormhole corrosion morphology using advanced electron microscopy and theoretical simulations. The work presents a vacancy mapping method with nm-resolution, identifying the incubation sites of the wormholes.

In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC–STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC–STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules. This paper explores the use of scanning transmission electron microscopy (STEM) to vitrified biological samples for biomolecular structure elucidation. Integrated differential phase contrast (iDPC)–STEM imaging of keyhole limpet hemocyanin and tobacco mosaic virus enabled cryo-EM structure determination at 6.5 and 3.5 Å resolution, respectively.

Crystallization of biomacromolecules-metal-organic frameworks (BMOFs) allows for orderly assemble of symbiotic hybrids with desirable biological and chemical functions in one voxel. The structure-activity relationship of this symbiotic crystal, however, is still blurred. Here, we directly identify the atomic-level structure of BMOFs, using the integrated differential phase contrast-scanning transmission electron microscopy, cryo-electron microscopy and x-ray absorption fine structure techniques. We discover an obvious difference in the nanoarchitecture of BMOFs under different crystallization pathways that was previously not seen. In addition, we find the nanoarchitecture significantly affects the bioactivity of the BMOFs. This work gives an important insight into the structure-activity relationship of BMOFs synthesized in different scenarios, and may act as a guide to engineer next-generation materials with excellent biological and chemical functions. Biomolecule-metal-organic-frameworks allow for the creation of hybrid materials with desired biological and chemical function. Here, the authors refine the structure-function relationship by identifying the atomic-layer structure of the hybrids and show differences in structure upon different crystallisation pathways.

The bacterium Sporosarcina pasteurii (SP) is known for its ability to cause the phenomenon of microbially induced calcium carbonate precipitation (MICP). We explored bacterial participation in the initial stages of the MICP process at the cellular length scale under two different growth environments (a) liquid culture (b) MICP in a soft agar (0.5%) column. In the liquid culture, ex-situ imaging of the cellular environment indicated that S. pasteurii was facilitating nucleation of nanoscale crystals of calcium carbonate on bacterial cell surface and its growth via ureolysis. During the same period, the meso-scale environment (bulk medium) was found to have overgrown calcium carbonate crystals. The effect of media components (urea, CaCl2), presence of live and dead in the growth medium were explored. The agar column method allows for in-situ visualization of the phenomena, and using this platform, we found conclusive evidence of the bacterial cell surface facilitating formation of nanoscale crystals in the microenvironment. Here also the bulk environment or the meso-scale environment was found to possess overgrown calcium carbonate crystals. Extensive elemental analysis using Energy dispersive X-ray spectroscopy (EDS) and X-ray powder diffraction (XRD), confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified. Active participation of S. pasteurii cell surface as the site of calcium carbonate precipitation has been shown using EDS elemental mapping with Scanning transmission electron microscopy (STEM) and scanning electron microscopy (SEM).

The recent development of electron-sensitive and pixelated detectors has attracted the use of four-dimensional scanning transmission electron microscopy (4D-STEM). Here, we present a precession electron diffraction-assisted 4D-STEM technique for automated orientation mapping using diffraction spot patterns directly captured by an in-column scintillator-based complementary metal-oxide-semiconductor (CMOS) detector. We compare the results to a conventional approach, which utilizes a fluorescent screen filmed by an external charge charge-coupled device camera. The high-dynamic range and signal-to-noise characteristics of the detector greatly improve the image quality of the diffraction patterns, especially the visibility of diffraction spots at high scattering angles. In the orientation maps reconstructed via the template matching process, the CMOS data yield a significant reduction of false indexing and higher reliability compared to the conventional approach. The angular resolution of misorientation measurement could also be improved by masking reflections close to the direct beam. This is because the orientation sensitive, weak, and small diffraction spots at high scattering angles are more significant. The results show that fine details, such as nanograins, nanotwins, and sub-grain boundaries, can be resolved with a sub-degree angular resolution which is comparable to orientation mapping using Kikuchi diffraction patterns.

Clearly, (1Ē2), (112) planes exist in the electron diffraction pattern. [...]П2), (112) planes are also present in HRTEM images under low electron dose2, selected-area electron diffraction (SAED)3,4 and X-ray diffraction (XRD)5-7 characterizations. Owing to lack of the corresponding in situ high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) image in the original paper, it is impossible to prove that the higher-contrast spots are PbS quantum dots rather than PbI2 particles. If possible, it would also be better if they compared the particle size and size distribution of colloidal quantum dots and quantum dots in perovskite in the original paper. [...]a low dose10-15 and low temperature2,13 can reduce the damage of electron-beam irradiation to perovskite, and may help to obtain the real structure of the quantum dots in perovskite solids.