Using Your Beam Efficiently: Reducing Electron Dose in the STEM via Flyback Compensation

In the scanning transmission electron microscope, fast-scanning and frame-averaging are two widely used approaches for reducing electron-beam damage and increasing image signal noise ratio which require no additional specialized hardware. Unfortunately, for scans with short pixel dwell-times (less than 5 μs), line flyback time represents an increasingly wasteful overhead. Although beam exposure during flyback causes damage while yielding no useful information, scan coil hysteresis means that eliminating it entirely leads to unacceptably distorted images. In this work, we reduce this flyback to an absolute minimum by calibrating and correcting for this hysteresis in postprocessing. Substantial improvements in dose efficiency can be realized (up to 20%), while crystallographic and spatial fidelity is maintained for displacement/strain measurement.

Improving the reliability of Fe- and S-XANES measurements in silicate glasses: correcting beam damage and identifying Fe-oxide nanolites in hydrous and anhydrous melt inclusions

The redox state of silicate melts influences crystallization, element partitioning, and degassing behavior. Synchrotron-based micro-X-ray absorption near edge structure (μXANES) spectroscopy has emerged as a powerful tool for determining redox conditions through the direct measurement of speciation of multivalent elements such as iron and sulfur in silicate glasses. In particular, the high spatial resolution afforded by synchrotron μXANES makes it one of the few techniques available for determining redox conditions in melt inclusions, which can provide insights into pre-eruptive melt properties. However, the small size of melt inclusions, the deep penetration of X-rays, and irradiation-induced beam damage make μXANES measurements in melt inclusions challenging. Here we present data that show rapid Fe- and S-μXANES beam damage in experimental glasses, mid-ocean ridge basalt glasses, and olivine-hosted melt inclusions from the southern Cascade arc and Kīlauea Volcano and develop approaches to recognize and correct for beam damage through repeated rapid analyses. By applying a time-dependent correction to a series of rapid measurements (~82 s/scan) of Fe-μXANES pre-edge centroid positions, irradiation-induced photo-oxidation (Fe2+ to Fe3+) can be corrected back to undamaged initial Fe3+/ΣFe even in damage-susceptible hydrous glasses. Using this beam damage correction technique, hydrous basaltic melt inclusions from the southern Cascades have Fe3+/ΣFe that is ~0.036 lower (corresponding to -0.5 log units lower oxygen fugacity) than would have been indicated by standard Fe-μXANES measurements. Repeated, rapid analyses (150 – 300 s/scan) were used to identify S-μXANES beam damage (photo-reduction of S6+ to S4+), which was corrected with a peak fitting method to restore initial S6+/ΣS. We observe that S-μXANES beam damage can occur rapidly even in low-H2O mid-ocean ridge basaltic glasses and melt inclusions from Kīlauea Volcano, which are otherwise stable during even prolonged Fe-μXANES analyses. By mitigating and correcting for sulfur photo-reduction, we conclude that some mid-ocean ridge basaltic glasses contain 0.08 – 0.09 S6+/ΣS, which is more sulfate than might be expected based on the reduced oxidation state of these glasses (near the fayalite-magnetite-quartz oxygen buffer). Using beam damage identification and correction techniques, the valence states of iron and sulfur can be accurately measured even in beam damage-susceptible glasses and melt inclusions. Finally, using Fe-μXANES, we demonstrate the presence of Fe-oxide nanolites within otherwise glassy, naturally quenched melt inclusions, which can complicate determination of iron valence state in affected glasses.

High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams

Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.