Imaging biological samples by integrated differential phase contrast (iDPC) STEM technique

An introduction to scanning transmission electron microscopy for the study of protozoans

Since its inception in the 1930s, transmission electron microscopy (TEM) has been a powerful method to explore the cellular structure of parasites. TEM usually requires samples of <100 nm thick and with protozoans being larger than 1 μm, their study requires resin embedding and ultrathin sectioning. During the past decade, several new methods have been developed to improve, facilitate, and speed up the structural characterisation of biological samples, offering new imaging modalities for the study of protozoans. In particular, scanning transmission electron microscopy (STEM) can be used to observe sample sections as thick as 1 μm thus becoming an alternative to conventional TEM. STEM can also be performed under cryogenic conditions in combination with cryo-electron tomography providing access to the study of thicker samples in their native hydrated states in 3D. This method, called cryo-scanning transmission electron tomography (cryo-STET), was first developed in 2014. This review presents the basic concepts and benefits of STEM methods and provides examples to illustrate the potential for new insights into the structure and ultrastructure of protozoans.

GoldDigger and Checkers, computational developments in cryo-scanning transmission electron tomography to improve the quality of reconstructed volumes

In this work, we present a pair of tools to improve the fiducial tracking and reconstruction quality of cryo-scanning transmission electron tomography (STET) datasets. We then demonstrate the effectiveness of these two tools on experimental cryo-STET data. The first tool, GoldDigger, improves the tracking of fiducials in cryo-STET by accommodating the changed appearance of highly defocussed fiducial markers. Since defocus effects are much stronger in scanning transmission electron microscopy than in conventional transmission electron microscopy, existing alignment tools do not perform well without manual intervention. The second tool, Checkers, combines image inpainting and unsupervised deep learning for denoising tomograms. Existing tools for denoising cryo-tomography often rely on paired noisy image frames, which are unavailable in cryo-STET datasets, necessitating a new approach. Finally, we make the two software tools freely available for the cryo-STET community.

Imaging built-in electric fields and light matter by Fourier-precession TEM

We report the precise measurement of electric fields in nanostructures, and high-contrast imaging of soft matter at ultralow electron doses by transmission electron microscopy (TEM). In particular, a versatile method based on the theorem of reciprocity is introduced to enable differential phase contrast imaging and ptychography in conventional, plane-wave illumination TEM. This is realised by a series of TEM images acquired under different tilts, thereby introducing the sampling rate in reciprocal space as a tuneable parameter, in contrast to momentum-resolved scanning techniques. First, the electric field of a p-n junction in GaAs is imaged. Second, low-dose, in-focus ptychographic and DPC characterisation of Kagome pores in weakly scattering covalent organic frameworks is demonstrated by using a precessing electron beam in combination with a direct electron detector. The approach offers utmost flexibility to record relevant spatial frequencies selectively, while acquisition times and dose requirements are significantly reduced compared to the 4D-STEM counterpart.

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.

A Review of the Current State of Magnetic Force Microscopy to Unravel the Magnetic Properties of Nanomaterials Applied in Biological Systems and Future Directions for Quantum Technologies

Magnetism plays a pivotal role in many biological systems. However, the intensity of the magnetic forces exerted between magnetic bodies is usually low, which demands the development of ultra-sensitivity tools for proper sensing. In this framework, magnetic force microscopy (MFM) offers excellent lateral resolution and the possibility of conducting single-molecule studies like other single-probe microscopy (SPM) techniques. This comprehensive review attempts to describe the paramount importance of magnetic forces for biological applications by highlighting MFM's main advantages but also intrinsic limitations. While the working principles are described in depth, the article also focuses on novel micro- and nanofabrication procedures for MFM tips, which enhance the magnetic response signal of tested biomaterials compared to commercial nanoprobes. This work also depicts some relevant examples where MFM can quantitatively assess the magnetic performance of nanomaterials involved in biological systems, including magnetotactic bacteria, cryptochrome flavoproteins, and magnetic nanoparticles that can interact with animal tissues. Additionally, the most promising perspectives in this field are highlighted to make the reader aware of upcoming challenges when aiming toward quantum technologies.

Direct imaging of local atomic structures in zeolite using optimum bright-field scanning transmission electron microscopy

Zeolites are used in industries as catalysts, ion exchangers, and molecular sieves because of their unique porous atomic structures. However, direct observation of zeolitic local atomic structures via electron microscopy is difficult owing to low electron irradiation resistance. Subsequently, their fundamental structure-property relationships remain unclear. A low-electron-dose imaging technique, optimum bright-field scanning transmission electron microscopy (OBF STEM), has recently been developed. It reconstructs images with a high signal-to-noise ratio and a dose efficiency approximately two orders of magnitude higher than that of conventional methods. Here, we performed low-dose atomic-resolution OBF STEM observations of two types of zeolite, effectively visualizing all atomic sites in their frameworks. In addition, we visualized the complex local atomic structure of the twin boundaries in a faujasite (FAU)-type zeolite and Na+ ions with low occupancy in eight-membered rings in a Na-Linde Type A (LTA) zeolite. The results of this study facilitate the characterization of local atomic structures in many electron beam-sensitive materials.

Transmission electron microscopy of thick polymer and biological specimens

We explore the properties of elastic and inelastic scattering in a thick organic specimen, together with the mechanisms that provide contrast in a transmission electron microscope (TEM) and scanning-transmission electron microscope (STEM). Experimental data recorded from amorphous carbon are used to predict the bright-field image intensity, mass-thickness contrast and dose-limited resolution as a function of thickness, objective-aperture size, and primary-electron energy E₀. Combining this information with estimates of chromatic aberration, objective-aperture diffraction and beam broadening in the specimen, we calculate the achievable TEM and STEM resolution to be around 4 nm at E₀ = 300 keV (or below 3 nm at MeV energies) for a 10 µm-diameter objective aperture and 1 - 2 µm thickness of hydrated biological tissue. The 3 MeV resolution for a 10-μm tissue sample is probably closer to 10 nm. We also comment on the error involved in quadrature addition of resolution factors, when one or more of the point-spread functions are non-Gaussian.

Optimizing experimental parameters of integrated differential phase contrast (iDPC) for atomic resolution imaging

Integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM) technique has been well developed for studying atomic structures at sub-Å resolution with the capability of simultaneously imaging heavy and light atoms even at an extremely low electron dose. As a direct phase contrast imaging technique, atomic resolution iDPC-STEM is sensitive to the imaging conditions. Although great achievements have been made both in aspect of theory and experiments, the influence of experimental parameters on the contrast of atomic resolution iDPC-STEM images has not been systematically investigated. Here, we perform the iDPC-STEM simulations on the prototypical example of SrTiO₃ with respect to the routine experimental factors, including the defocus, specimen thickness, accelerating voltage, convergence angle, collection angle, sample tilt and electron dose. Through the evaluation of image contrast and atom column intensity, the parameters are discussed to improve the image contrast and the visibility of light elements. Moreover, the dose-dependent simulations demonstrate the advantage of low dose iDPC-STEM imaging over other conventional STEM modes. Our results provide a practical guideline to experimentally obtain accessible atomic resolution iDPC-STEM images.

Real-Space Imaging of the Node-Linker Coordination on the Interfaces between Self-Assembled Metal-Organic Frameworks

Surface and interface, with unique local characteristics different from bulk structure, are of great significance in various applications of metal-organic frameworks (MOFs), which should be studied by real-space imaging methods, such as electron microscopy. However, it is still challenging to atomically resolve these local structures in MOFs, because they are even more sensitive to electron irradiation. Here, we use integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM) to achieve the atomic imaging of both the metal nodes and organic linkers in UiO-66 (Zr) nanocrystals and their assembly. After adding acetic acid, we modulate the whole process of MOF assembly and observe the organic linkers at both the surfaces and twin interfaces in the chemically assembled UiO-66 (Zr) crystals by the iDPC-STEM. These results bring us a deeper understanding on the role of acid modulators that promote the MOF assembly by generating the missing-linker defects on the crystal surface.

Single-particle cryo-EM structures from iDPC-STEM at near-atomic resolution

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.