Cryo-Electron Ptychography: Applications and Potential in Biological Characterisation

There is a clear need for developments in characterisation techniques that provide detailed information about structure-function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterisation of biological systems under low fluence conditions. Using this method with increased information content from multiple sampled regions of interest, potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution for systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations and potential areas for future development of this approach for both single particle analysis and in applications to heterogeneous large objects

Cryo-electron ptychography: applications and potential in biological characterisation

There is a clear need for developments in characterisation techniques that provide detailed information about structure–function relationships in biology. Using electron microscopy to achieve high resolution while maintaining a broad field of view remains a challenge, particularly for radiation-sensitive specimens where the signal-to-noise ratio required to maintain structural integrity is limited by low electron fluence. In this review, we explore the potential of cryogenic electron ptychography as an alternative method for characterising biological systems under low-fluence conditions. Using this method with increased information content from multiple sampled regions of interest potentially allows 3D reconstruction with far fewer particles than required in conventional cryo-electron microscopy. This is important for achieving higher resolution in systems where distributions of homogeneous single particles are difficult to obtain. We discuss the progress, limitations, and potential areas for future development of this approach for both single particle analysis and applications to heterogeneous large objects

Direct detection of electron backscatter diffraction patterns.

We report the first use of direct detection for recording electron backscatter diffraction patterns. We demonstrate the following advantages of direct detection: the resolution in the patterns is such that higher order features are visible; patterns can be recorded at beam energies below those at which conventional detectors usefully operate; high precision in cross-correlation based pattern shift measurements needed for high resolution electron backscatter diffraction strain mapping can be obtained. We also show that the physics underlying direct detection is sufficiently well understood at low primary electron energies such that simulated patterns can be generated to verify our experimental data

Detectors—The ongoing revolution in scanning transmission electron microscopy and why this important to material characterization

Detectors are revolutionizing possibilities in scanning transmission electron microscopy because of the advent of direct electron detectors that record at a high quantum efficiency and with a high frame rate. This allows the whole back focal plane to be captured for each pixel in a scan and the dataset to be processed to reveal whichever features are of interest. There are many possible uses for this advance of direct relevance to understanding the nano- and atomic-scale structure of materials and heterostructures. This article gives our perspective of the current state of the field and some of the directions where it is likely to go next. First, a wider overview of the recent work in this area is given before two specific examples of its application are given: one is imaging strain in thin films and the other one is imaging changes in periodicity along the beam direction as a result of the formation of an ordered structure in an epitaxial thin film. This is followed by an outlook that presents future possible directions in this rapidly expanding field

SIM-STEM Lab: Incorporating Compressed Sensing Theory for Fast STEM Simulation

Recently it has been shown that precise dose control and an increase in the overall acquisition speed of atomic resolution scanning transmission electron microscope (STEM) images can be achieved by acquiring only a small fraction of the pixels in the image experimentally and then reconstructing the full image using an inpainting algorithm. In this paper, we apply the same inpainting approach (a form of compressed sensing) to simulated, sub-sampled atomic resolution STEM images. We find that it is possible to significantly sub-sample the area that is simulated, the number of g-vectors contributing the image, and the number of frozen phonon configurations contributing to the final image while still producing an acceptable fit to a fully sampled simulation. Here we discuss the parameters that we use and how the resulting simulations can be quantifiably compared to the full simulations. As with any Compressed Sensing methodology, care must be taken to ensure that isolated events are not excluded from the process, but the observed increase in simulation speed provides significant opportunities for real time simulations, image classification and analytics to be performed as a supplement to experiments on a microscope to be developed in the future.Comment: 20 pages (includes 3 supplementary pages), 15 figures (includes 5 supplementary figures), submitted to Ultramicroscop

Influence of precession electron diffraction parameters and energy filtering on reduced density function analysis of thin amorphous silica films—implications for structural studies

We investigated the influence of precession angle, energy filtering and sample thickness on the structural parameters of amorphous SiO2 thin films from the electron reduced density functions obtained by applying precession electron diffraction. The results demonstrate that the peak positions in the electron reduced density functions are generally insensitive to the studied experimental conditions, while both precession angle and energy filtering influence peak heights considerably. It is also shown that introducing precession with small angles of up to 2 degrees and energy filtering results in higher coordination numbers that are closer to the expected theoretical values of 4 and 2 for Si and O, respectively, for data obtained from a thicker sample

High‐speed 4‐dimensional scanning transmission electron microscopy using compressive sensing techniques

Here we show that compressive sensing allows 4‐dimensional (4‐D) STEM data to be obtained and accurately reconstructed with both high‐speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4‐D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide dataset shows that it is possible to recover over 25 dB peak signal‐to‐noise ratio in the recovered phase using 0.3% of the total data. Lay abstract: Four‐dimensional scanning transmission electron microscopy (4‐D STEM) is a powerful technique for characterizing complex nanoscale structures. In this method, a convergent beam electron diffraction pattern (CBED) is acquired at each probe location during the scan of the sample. This means that a 2‐dimensional signal is acquired at each 2‐D probe location, equating to a 4‐D dataset. Despite the recent development of fast direct electron detectors, some capable of 100kHz frame rates, the limiting factor for 4‐D STEM is acquisition times in the majority of cases, where cameras will typically operate on the order of 2kHz. This means that a raster scan containing 256^2 probe locations can take on the order of 30s, approximately 100‐1000 times longer than a conventional STEM imaging technique using monolithic radial detectors. As a result, 4‐D STEM acquisitions can be subject to adverse effects such as drift, beam damage, and sample contamination. Recent advances in computational imaging techniques for STEM have allowed for faster acquisition speeds by way of acquiring only a random subset of probe locations from the field of view. By doing this, the acquisition time is significantly reduced, in some cases by a factor of 10‐100 times. The acquired data is then processed to fill‐in or inpaint the missing data, taking advantage of the inherently low‐complex signals which can be linearly combined to recover the information. In this work, similar methods are demonstrated for the acquisition of 4‐D STEM data, where only a random subset of CBED patterns are acquired over the raster scan. We simulate the compressive sensing acquisition method for 4‐D STEM and present our findings for a variety of analysis techniques such as ptychography and differential phase contrast. Our results show that acquisition times can be significantly reduced on the order of 100‐300 times, therefore improving existing frame rates, as well as further reducing the electron fluence beyond just using a faster camera