Active pixel sensor array as a detector for electron microscopy

Atomic-level imaging of beam-sensitive COFs and MOFs by low-dose electron microscopy

Electron microscopy, an important technique that allows for the precise determination of structural information with high spatiotemporal resolution, has become indispensable in unravelling the complex relationships between material structure and properties ranging from mesoscale morphology to atomic arrangement. However, beam-sensitive materials, particularly those comprising organic components such as metal-organic frameworks (MOFs) and covalent organic frameworks (COFs), would suffer catastrophic damage from the high energy electrons, hindering the determination of atomic structures. A low-dose approach has arisen as a possible solution to this problem based on the integration of advancements in several aspects: electron optical system, detector, image processing, and specimen preservation. This article summarizes the transmission electron microscopy characterization of MOFs and COFs, including local structures, host-guest interactions, and interfaces at the atomic level. Revolutions in advanced direct electron detectors, algorithms in image acquisition and processing, and emerging methodology for high quality low-dose imaging are also reviewed. Finally, perspectives on the future development of electron microscopy methodology with the support of computer science are presented.

Accurate magnification determination for cryoEM using gold

Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.

Characterization of a Timepix detector for use in SEM acceleration voltage range

Hybrid pixel direct electron detectors are gaining popularity in electron microscopy due to their excellent properties. Some commercial cameras based on this technology are relatively affordable which makes them attractive tools for experimentation especially in combination with an SEM setup. To support this, a detector characterization (Modulation Transfer Function, Detective Quantum Efficiency) of an Advacam Minipix and Advacam Advapix detector in the 15-30 keV range was made. In the current work we present images of Point Spread Function, plots of MTF/DQE curves and values of DQE(0) for these detectors. At low beam currents, the silicon detector layer behaviour should be dominant, which could make these findings transferable to any other available detector based on either Medipix2, Timepix or Timepix3 provided the same detector layer is used.

Evaluating direct detection detectors for short-range order characterization of amorphous materials by electron scattering

The introduction of direct electron detectors (DEDs) to transmission electron microscopy has set off the 'resolution revolution', especially for cryoTEM low-dose imaging of soft matter. In comparison to traditional indirect electron detectors such as Charged-Coupled Devices (CCD), DEDs show an improved modulation transfer function (MTF) and detective quantum efficiency (DQE) across all spatial frequencies, as well as faster frame rates which enable single electron counting. The benefits of such characteristics for imaging, spectroscopy and electron holography have been demonstrated previously. However, studies are lacking on the application of DEDs for localized characterization of short- to medium- range-order (SRO, MRO) in amorphous materials using electron scattering. Therefore, we evaluate the performance of a Monolithic Active Pixel Sensor DED for the characterization of SRO and MRO in nanoscale volumes of amorphous materials, using SiO₂ and Ta₂O₅ thin films as test cases. The performance of the detector is compared systematically to electron scattering measurements recorded on an indirect detector (CCD) using 200 keV electrons and electron doses starting at approximately 500e^-Ų . In addition, the effects of sample cooling and energy-filtering on the measured SRO of the oxides were investigated. We demonstrate that the performance of the DED resulted in improved SRO characterization in comparison to that obtained from the CCD measurements. The DED enabled to achieve a larger measured maximal scattering vector, ∼16.51Å compared to ∼151Å, for the CCD. Furthermore, an improved signal-to-noise ratio of approximately two-fold was observed across all spatial frequencies for both 200 keV and 80 keV electrons. These improvements are shown to result from the superior DQE of the DED. Consequently, the DED measurements enabled to determine the coordination numbers of atomic bonds more accurately. We expect that further benefits of the DED for S/MRO characterization will be highlighted for ultra- sensitive materials that cannot withstand electron doses above several e^-Ų .

Characterizing the resolution and throughput of the Apollo direct electron detector

Advances in electron detection have been essential to the success of high-resolution cryo-EM structure determination. A new generation of direct electron detector called the Apollo, has been developed by Direct Electron. The Apollo uses a novel event-based MAPS detector custom designed for ultra-fast electron counting. We have evaluated this new camera, finding that it delivers high detective quantum efficiency (DQE) and low coincidence loss, enabling high-quality electron counting data acquisition at up to nearly 80 input electrons per pixel per second. We further characterized the performance of Apollo for single particle cryo-EM on real biological samples. Using mouse apoferritin, Apollo yielded better than 1.9 Å resolution reconstructions at all three tested dose rates from a half-day data collection session each. With longer collection time and improved specimen preparation, mouse apoferritin was reconstructed to 1.66 Å resolution. Applied to a more challenging small protein aldolase, we obtained a 2.24 Å resolution reconstruction. The high quality of the map indicates that the Apollo has sufficiently high DQE to reconstruct smaller proteins and complexes with high-fidelity. Our results demonstrate that the Apollo camera performs well across a broad range of dose rates and is capable of capturing high quality data that produce high-resolution reconstructions for large and small single particle samples.

A feature-guided, focused 3D signal permutation method for subtomogram averaging

Advances in electron microscope instrumentation, cryo-electron tomography data collection, and subtomogram averaging have allowed for the in-situ visualization of molecules and their complexes in their native environment. Current data processing pipelines commonly extract subtomograms as a cubic subvolume with the key assumption that the selected object of interest is discrete from its surroundings. However, in instances when the object is in its native environment, surrounding densities may negatively affect the subsequent alignment and refinement processes, leading to loss of information due to misalignment. For example, the strong densities from surrounding membranes may dominate the alignment process for membrane proteins. Here, we developed methods for feature-guided subtomogram alignment and 3D signal permutation for subtomogram averaging. Our 3D signal permutation method randomizes and filters voxels outside a mask of any shape and blurs the boundary of the mask that encapsulates the object of interest. The randomization preserves global statistical properties such as mean density and standard deviation of voxel density values, effectively producing a featureless background surrounding the object of interest. This signal permutation process can be repeatedly applied with intervening alignments of the 3D signal-permuted subvolumes, recentering of the mask, and optional adjustments of the shape of the mask. We have implemented these methods in a new processing pipeline which starts from tomograms, contains feature-guided subtomogram extraction and alignment, 3D signal-permutation, and subtomogram visualization tools. As an example, feature-guided alignment and 3D signal permutation leads to improved subtomogram average maps for a dataset of synaptic protein complexes in their native environment.

Photonics enabled intelligence system to identify SARS-CoV 2 mutations

Abstract

The COVID-19, MERS-CoV, and SARS-CoV are hazardous epidemics that have resulted in many deaths which caused a worldwide debate. Despite control efforts, SARS-CoV-2 continues to spread, and the fast spread of this highly infectious illness has posed a grave threat to global health. The effect of the SARS-CoV-2 mutation, on the other hand, has been characterized by worrying variations that modify viral characteristics in response to the changing resistance profile of the human population. The repeated transmission of virus mutation indicates that epidemics are likely to occur. Therefore, an early identification system of ongoing mutations of SARS-CoV-2 will provide essential insights for planning and avoiding future outbreaks. This article discussed the following highlights: First, comparing the omicron mutation with other variants; second, analysis and evaluation of the spread rate of the SARS-CoV 2 variations in the countries; third, identification of mutation areas in spike protein; and fourth, it discussed the photonics approaches enabled with artificial intelligence. Therefore, our goal is to identify the SARS-CoV 2 virus directly without the need for sample preparation or molecular amplification procedures. Furthermore, by connecting through the optical network, the COVID-19 test becomes a component of the Internet of healthcare things to improve precision, service efficiency, and flexibility and provide greater availability for the evaluation of the general population.

Key points

• A proposed framework of photonics based on AI for identifying and sorting SARS-CoV 2 mutations.

• Comparative scatter rates Omicron variant and other SARS-CoV 2 variations per country.

• Evaluating mutation areas in spike protein and AI enabled by photonic technologies for SARS-CoV 2 virus detection.

Plasmon-assisted polarization-sensitive photodetection with tunable polarity for integrated silicon photonic communication systems

To establish high-bandwidth chip-to-chip interconnects in optoelectronic integrated circuits, requires high-performance photon emitters and signal receiving components. Regarding the photodetector, fast device concepts like Schottky junction devices, large carrier mobility materials and shrinking the channel length will enable higher operation speed. However, integrating photodetectors in highly scaled ICs technologies is challenging due to the efficiency-speed trade-off. Here, we report a scalable and CMOS-compatible approach for an ultra-scaled germanium (Ge) based photodetector with tunable polarity. The photodetector is composed of a Ge Schottky barrier field effect transistor with monolithic aluminum (Al) source/drain contacts, offering plasmon assisted and polarization-resolved photodetection. The ultra-scaled Ge photodetector with a channel length of only 200 nm shows high responsivity of aboutR = 424 A W^-1and a maximum polarization sensitivity ratio of TM/TE = 11.

An overview of the recent advances in cryo-electron microscopy for life sciences

Cryo-electron microscopy (CryoEM) has superseded X-ray crystallography and NMR to emerge as a popular and effective tool for structure determination in recent times. It has become indispensable for the characterization of large macromolecular assemblies, membrane proteins, or samples that are limited, conformationally heterogeneous, and recalcitrant to crystallization. Besides, it is the only tool capable of elucidating high-resolution structures of macromolecules and biological assemblies in situ. A state-of-the-art electron microscope operable at cryo-temperature helps preserve high-resolution details of the biological sample. The structures can be determined, either in isolation via single-particle analysis (SPA) or helical reconstruction, electron diffraction (ED) or within the cellular environment via cryo-electron tomography (cryoET). All the three streams of SPA, ED, and cryoET (along with subtomogram averaging) have undergone significant advancements in recent times. This has resulted in breaking the boundaries with respect to both the size of the macromolecules/assemblies whose structures could be determined along with the visualization of atomic details at resolutions unprecedented for cryoEM. In addition, the collection of larger datasets combined with the ability to sort and process multiple conformational states from the same sample are providing the much-needed link between the protein structures and their functions. In overview, these developments are helping scientists decipher the molecular mechanism of critical cellular processes, solve structures of macromolecules that were challenging targets for structure determination until now, propelling forward the fields of biology and biomedicine. Here, we summarize recent advances and key contributions of the three cryo-electron microscopy streams of SPA, ED, and cryoET.

Quantifying the performance of a hybrid pixel detector with GaAs:Cr sensor for transmission electron microscopy

Hybrid pixel detectors (HPDs) have been shown to be highly effective for diffraction-based and time-resolved studies in transmission electron microscopy, but their performance is limited by the fact that high-energy electrons scatter over long distances in their thick Si sensors. An advantage of HPDs compared to monolithic active pixel sensors is that their sensors do not need to be fabricated from Si. We have compared the performance of the Medipix3 HPD with a Si sensor and a GaAs:Cr sensor using primary electrons in the energy range of 60-300 keV. We describe the measurement and calculation of the detectors' modulation transfer function (MTF) and detective quantum efficiency (DQE), which show that the performance of the GaAs:Cr device is markedly superior to that of the Si device for high-energy electrons.

Elemental mapping of labelled biological specimens at intermediate energy loss in an energy-filtered TEM acquired using a direct detection device

The technique of colour EM that was recently developed enabled localisation of specific macromolecules/proteins of interest by the targeted deposition of diaminobenzidine (DAB) conjugated to lanthanide chelates. By acquiring lanthanide elemental maps by energy‐filtered transmission electron microscopy (EFTEM) and overlaying them in pseudo‐colour over the conventional greyscale TEM image, a colour EM image is generated. This provides a powerful tool for visualising subcellular component/s, by the ability to clearly distinguish them from the general staining of the endogenous cellular material. Previously, the lanthanide elemental maps were acquired at the high‐loss M_4,5 edge (excitation of 3d electrons), where the characteristic signal is extremely low and required considerably long exposures. In this paper, we explore the possibility of acquiring the elemental maps of lanthanides at their N_4,5 edge (excitation of 4d electrons), which occurring at a much lower energy‐loss regime, thereby contains significantly greater total characteristic signal owing to the higher inelastic scattering cross‐sections at the N_4,5 edge. Acquiring EFTEM lanthanide elemental maps at the N_4,5 edge instead of the M_4,5 edge, provides ∼4× increase in signal‐to‐noise and ∼2× increase in resolution. However, the interpretation of the lanthanide maps acquired at the N_4,5 edge by the traditional 3‐window method, is complicated due to the broad shape of the edge profile and the lower signal‐above‐background ratio. Most of these problems can be circumvented by the acquisition of elemental maps with the more sophisticated technique of EFTEM Spectrum Imaging (EFTEM SI). Here, we also report the chemical synthesis of novel second‐generation DAB lanthanide metal chelate conjugates that contain 2 lanthanide ions per DAB molecule in comparison with 0.5 lanthanide ion per DAB in the first generation. Thereby, fourfold more Ln³⁺ per oxidised DAB would be deposited providing significant amplification of signal. This paper applies the colour EM technique at the intermediate‐loss energy‐loss regime to three different cellular targets, namely using mitochondrial matrix‐directed APEX2, histone H2B‐Nucleosome and EdU‐DNA. All the examples shown in the paper are single colour EM images only.

Icosahedral virus structures and the protein data bank

The structural study of icosahedral viruses has a long and impactful history in both crystallographic methodology and molecular biology. The evolution of the Protein Data Bank has paralleled and supported these studies providing readily accessible formats dealing with novel features associated with viral particle symmetries and subunit interactions. This overview describes the growth in size and complexity of icosahedral viruses from the first early studies of small RNA plant viruses and human picornaviruses up to the larger and more complex bacterial phage, insect, and human disease viruses such as Zika, hepatitis B, Adeno and Polyoma virus. The analysis of icosahedral viral capsid protein domain folds has shown striking similarities, with the beta jelly roll motif observed across multiple evolutionarily divergent species. The icosahedral symmetry of viruses drove the development of noncrystallographic symmetry averaging as a powerful phasing method, and the constraints of maintaining this symmetry resulted in the concept of quasi-equivalence in viral structures. Symmetry also played an important early role in demonstrating the power of cryo-electron microscopy as an alternative to crystallography in generating atomic resolution structures of these viruses. The Protein Data Bank has been a critical resource for assembling and disseminating these structures to a wide community, and the virus particle explorer (VIPER) was developed to enable users to easily generate and view complete viral capsid structures from their asymmetric building blocks. Finally, we share a personal perspective on the early use of computer graphics to communicate the intricacies, interactions, and beauty of these virus structures.

CERES: a cryo-EM re-refinement system for continuous improvement of deposited models

The field of electron cryomicroscopy (cryo-EM) has advanced quickly in recent years as the result of numerous technological and methodological developments. This has led to an increase in the number of atomic structures determined using this method. Recently, several tools for the analysis of cryo-EM data and models have been developed within the Phenix software package, such as phenix.real_space_refine for the refinement of atomic models against real-space maps. Also, new validation metrics have been developed for low-resolution cryo-EM models. To understand the quality of deposited cryo-EM structures and how they might be improved, models deposited in the Protein Data Bank that have map resolutions of better than 5 Å were automatically re-refined using current versions of Phenix tools. The results are available on a publicly accessible web page (https://cci.lbl.gov/ceres). The implementation of a Cryo-EM Re-refinement System (CERES) for the improvement of models deposited in the wwPDB, and the results of the re-refinements, are described. Based on these results, contents are proposed for a `cryo-EM Table 1', which summarizes experimental details and validation metrics in a similar way to `Table 1' in crystallography. The consistent use of robust metrics for the evaluation of cryo-EM models and data should accompany every structure deposition and be reported in scientific publications.

Electron backscattered diffraction using a new monolithic direct detector: High resolution and fast acquisition

A monolithic active pixel sensor based direct detector that is optimized for the primary beam energies in scanning electron microscopes is implemented for electron back-scattered diffraction (EBSD) applications. The high detection efficiency of the detector and its large array of pixels allow sensitive and accurate detection of Kikuchi bands arising from primary electron beam excitation energies of 4 keV to 28 keV, with the optimal contrast occurring in the range of 8-16 keV. The diffraction pattern acquisition speed is substantially improved via a sparse sampling mode, resulting from the acquisition of a reduced number of pixels on the detector. Standard inpainting algorithms are implemented to effectively estimate the information in the skipped regions in the acquired diffraction pattern. For EBSD mapping, an acquisition speed as high as 5988 scan points per second is demonstrated, with a tolerable fraction of indexed points and accuracy. The collective capabilities spanning from high angular resolution EBSD patterns to high speed pattern acquisition are achieved on the same detector, facilitating simultaneous detection modalities that enable a multitude of advanced EBSD applications, including lattice strain mapping, structural refinement, low-dose characterization, 3D-EBSD and dynamic in situ EBSD.

Bulk and local structures of metal-organic frameworks unravelled by high-resolution electron microscopy

The periodic bulk structures of metal-organic frameworks (MOFs) can be solved by diffraction-based techniques; however, their non-periodic local structures-such as crystal surfaces, grain boundaries, defects, and guest molecules-have long been elusive due to a lack of suitable characterization tools. Recent advances in (scanning) transmission electron microscopy ((S)TEM) has made it possible to probe the local structures of MOFs at atomic resolution. In this article, we discuss why high-resolution (S)TEM of MOFs is challenging and how the new low-dose techniques overcome this challenge, and we review various MOF structural features observed by (S)TEM and important insights gained from these observations. Our discussions focus on real-space imaging, excluding other TEM-related characterization techniques (e.g. electron diffraction and spectroscopy).

Electrochemical and Structural Analysis in All-Solid-State Lithium Batteries by Analytical Electron Microscopy: Progress and Perspectives

Advanced scanning transmission electron microscopy (STEM) and its associated instruments have made significant contributions to the characterization of all-solid-state (ASS) Li batteries, as these tools provide localized information on the structure, morphology, chemistry, and electronic state of electrodes, electrolytes, and their interfaces at the nano- and atomic scale. Furthermore, the rapid development of in situ techniques has enabled a deep understanding of interfacial dynamic behavior and heterogeneous characteristics during the cycling process. However, due to the beam-sensitive nature of light elements in the interphases, e.g., Li and O, thorough and reliable studies of the interfacial structure and chemistry at an ultrahigh spatial resolution without beam damage is still a formidable challenge. Herein, the following points are discussed: (1) the recent contributions of advanced STEM to the study of ASS Li batteries; (2) current challenges associated with using this method; and (3) potential opportunities for combining cryo-electron microscopy and the STEM phase contrast imaging techniques.

Laser-free GHz stroboscopic transmission electron microscope: Components, system integration, and practical considerations for pump-probe measurements

A 300 keV transmission electron microscope was modified to produce broadband pulsed beams that can be, in principle, between 40 MHz and 12 GHz, corresponding to temporal resolution in the nanosecond to picosecond range without an excitation laser. The key enabling technology is a pair of phase-matched modulating and de-modulating traveling wave metallic comb striplines (pulsers). An initial temporal resolution of 30 ps was achieved with a strobe frequency of 6.0 GHz. The placement of the pulsers, mounted immediately below the gun, allows for preservation of all optical configurations, otherwise available to the unmodified instrument, and therefore makes such a post-modified instrument for dual-use, i.e., both pulsed-beam mode (i.e., stroboscopic time-resolved) and conventional continuous waveform mode. In this article, we describe the elements inserted into the beam path, challenges encountered during integration with an in-service microscope, and early results from an electric-field-driven pump-probe experiment. We conclude with ideas for making this class of instruments broadly applicable for examining cyclical and repeatable phenomena.

A Visualization Tool for Cryo-EM Protein Validation with an Unsupervised Machine Learning Model in Chimera Platform

Background: Cryo-electron microscopy (cryo-EM) has become a major technique for protein structure determination. However, due to the low quality of cryo-EM density maps, many protein structures derived from cryo-EM contain outliers introduced during the modeling process. The current protein model validation system lacks identification features for cryo-EM proteins making it not enough to identify outliers in cryo-EM proteins. Methods: This study introduces an efficient unsupervised outlier detection model for validating protein models built from cryo-EM technique. The current model uses a high-resolution X-ray dataset (<1.5 Å) as the reference dataset. The distal block distance, side-chain length, phi, psi, and first chi angle of the residues in the reference dataset are collected and saved as a database of the histogram-based outlier score (HBOS). The HBOS value of the residues in target cryo-EM proteins can be read from this HBOS database. Results: Protein residues with a HBOS value greater than ten are labeled as outliers by default. Four datasets containing proteins derived from cryo-EM density maps were tested with this probabilistic anomaly detection model. Conclusions: According to the proposed model, a visualization assistant tool was designed for Chimera, a protein visualization platform.

Four-Dimensional Scanning Transmission Electron Microscopy (4D-STEM): From Scanning Nanodiffraction to Ptychography and Beyond

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.

New tools for the analysis and validation of cryo-EM maps and atomic models

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d99 to estimate resolution, phenix.auto_sharpen to improve maps and phenix.mtriage to analyze cryo-EM maps. It is suggested that cryo-EM half-maps and masks should be deposited to facilitate the evaluation and validation of cryo-EM-derived atomic models and maps. The application of these tools to deposited cryo-EM atomic models and maps is also presented.

From Electron Crystallography to Single Particle CryoEM (Nobel Lecture)

Pictures are a key to knowledge: The development of electron microscopy from its beginnings to modern single particle cryo-EM is described by R. Henderson in his Nobel lecture. Shown is the first projection structure at 7 Å resolution of the purple membrane from October 1974.

Validating Resolution Revolution

Recent advances in instrumentation and image-processing software have resulted in a resolution revolution in cryo-electron microscopy (cryo-EM) and a surge in the popularity of this technique. However, despite technical progress and hundreds of structures determined so far, development of standards assessing the agreement between the cryo-EM map and the respective model has fallen behind. Here we establish a validation procedure evaluating this agreement and applied it to a set of 565 cryo-EM structures. Analysis of the results revealed that three-quarters of the validated structures exhibit moderate or low agreement between the map and the corresponding model, mostly due to limited structural features possessed by these maps. Model re-refinement significantly improved the agreement for only one-fifth of the structures, reaffirming the necessity to re-evaluate map resolution. The presented procedure provides an approach to re-estimate the resolution of cryo-EM map areas interpreted by the model.

Dynamics of Transformation from Platinum Icosahedral Nanoparticles to Larger FCC Crystal at Millisecond Time Resolution

Atomic motion at grain boundaries is essential to microstructure development, growth and stability of catalysts and other nanostructured materials. However, boundary atomic motion is often too fast to observe in a conventional transmission electron microscope (TEM) and too slow for ultrafast electron microscopy. Here, we report on the entire transformation process of strained Pt icosahedral nanoparticles (ICNPs) into larger FCC crystals, captured at 2.5 ms time resolution using a fast electron camera. Results show slow diffusive dislocation motion at nm/s inside ICNPs and fast surface transformation at μm/s. By characterizing nanoparticle strain, we show that the fast transformation is driven by inhomogeneous surface stress. And interaction with pre-existing defects led to the slowdown of the transformation front inside the nanoparticles. Particle coalescence, assisted by oxygen-induced surface migration at T ≥ 300 °C, also played a critical role. Thus by studying transformation in the Pt ICNPs at high time and spatial resolution, we obtain critical insights into the transformation mechanisms in strained Pt nanoparticles.

Single-particle cryo-EM using alignment by classification (ABC): the structure of Lumbricus terrestris haemoglobin

Single-particle cryogenic electron microscopy (cryo-EM) can now yield near-atomic resolution structures of biological complexes. However, the reference-based alignment algorithms commonly used in cryo-EM suffer from reference bias, limiting their applicability (also known as the 'Einstein from random noise' problem). Low-dose cryo-EM therefore requires robust and objective approaches to reveal the structural information contained in the extremely noisy data, especially when dealing with small structures. A reference-free pipeline is presented for obtaining near-atomic resolution three-dimensional reconstructions from heterogeneous ('four-dimensional') cryo-EM data sets. The methodologies integrated in this pipeline include a posteriori camera correction, movie-based full-data-set contrast transfer function determination, movie-alignment algorithms, (Fourier-space) multivariate statistical data compression and unsupervised classification, 'random-startup' three-dimensional reconstructions, four-dimensional structural refinements and Fourier shell correlation criteria for evaluating anisotropic resolution. The procedures exclusively use information emerging from the data set itself, without external 'starting models'. Euler-angle assignments are performed by angular reconstitution rather than by the inherently slower projection-matching approaches. The comprehensive 'ABC-4D' pipeline is based on the two-dimensional reference-free 'alignment by classification' (ABC) approach, where similar images in similar orientations are grouped by unsupervised classification. Some fundamental differences between X-ray crystallography versus single-particle cryo-EM data collection and data processing are discussed. The structure of the giant haemoglobin from Lumbricus terrestris at a global resolution of ∼3.8 Å is presented as an example of the use of the ABC-4D procedure.

Direct Detection Electron Energy-Loss Spectroscopy: A Method to Push the Limits of Resolution and Sensitivity

In many cases, electron counting with direct detection sensors offers improved resolution, lower noise, and higher pixel density compared to conventional, indirect detection sensors for electron microscopy applications. Direct detection technology has previously been utilized, with great success, for imaging and diffraction, but potential advantages for spectroscopy remain unexplored. Here we compare the performance of a direct detection sensor operated in counting mode and an indirect detection sensor (scintillator/fiber-optic/CCD) for electron energy-loss spectroscopy. Clear improvements in measured detective quantum efficiency and combined energy resolution/energy field-of-view are offered by counting mode direct detection, showing promise for efficient spectrum imaging, low-dose mapping of beam-sensitive specimens, trace element analysis, and time-resolved spectroscopy. Despite the limited counting rate imposed by the readout electronics, we show that both core-loss and low-loss spectral acquisition are practical. These developments will benefit biologists, chemists, physicists, and materials scientists alike.

Measurement of atomic electric fields and charge densities from average momentum transfers using scanning transmission electron microscopy

This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory. A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10×10 available pixels.

The advent of structural biology in situ by single particle cryo-electron tomography

Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.

Electron Cryo-microscopy as a Tool for Structure-Based Drug Development

For decades, X-ray crystallography and NMR have been the most important techniques for studying the atomic structure of macromolecules. However, as a result of size, instability, low yield, and other factors, many macromolecules are difficult to crystallize or unsuitable for NMR studies. Electron cryo-microscopy (cryo-EM) does not depend on crystals and has therefore been the method of choice for many macromolecular complexes that cannot be crystallized, but atomic resolution has mostly been beyond its reach. A new generation of detectors that are capable of sensing directly the incident electrons has recently revolutionized the field, with structures of macromolecules now routinely being solved to near-atomic resolution. In this review, we summarize some of the most recent examples of high-resolution cryo-EM structures. We put particular emphasis on proteins with pharmacological relevance that have traditionally been inaccessible to crystallography. Furthermore, we discuss examples where interactions with small molecules have been fully characterized at atomic resolution. Finally, we stress the current limits of cryo-EM, and methodological issues related to its usage as a tool for drug development.

Single particle electron cryomicroscopy: trends, issues and future perspective

There has been enormous progress during the last few years in the determination of three-dimensional biological structures by single particle electron cryomicroscopy (cryoEM), allowing maps to be obtained with higher resolution and from fewer images than required previously. This is due principally to the introduction of a new type of direct electron detector that has 2- to 3-fold higher detective quantum efficiency than available previously, and to the improvement of the computational algorithms for image processing. In spite of the great strides that have been made, quantitative analysis shows that there are still significant gains to be made provided that the problems associated with image degradation can be solved, possibly by minimising beam-induced specimen movement and charge build up during imaging. If this can be achieved, it should be possible to obtain near atomic resolution structures of smaller single particles, using fewer images and resolving more conformational states than at present, thus realising the full potential of the method. The recent popularity of cryoEM for molecular structure determination also highlights the need for lower cost microscopes, so we encourage development of an inexpensive, 100 keV electron cryomicroscope with a high-brightness field emission gun to make the method accessible to individual groups or institutions that cannot afford the investment and running costs of a state-of-the-art 300 keV installation. A key requisite for successful high-resolution structure determination by cryoEM includes interpretation of images and optimising the biochemistry and grid preparation to obtain nicely distributed macromolecules of interest. We thus include in this review a gallery of cryoEM micrographs that shows illustrative examples of single particle images of large and small macromolecular complexes.

Direct Electron Detectors

Direct electron detectors have played a key role in the recent increase in the power of single-particle electron cryomicroscopy (cryoEM). In this chapter, we summarize the background to these recent developments, give a practical guide to their optimal use, and discuss future directions.

High Dynamic Range Pixel Array Detector for Scanning Transmission Electron Microscopy

We describe a hybrid pixel array detector (electron microscope pixel array detector, or EMPAD) adapted for use in electron microscope applications, especially as a universal detector for scanning transmission electron microscopy. The 128×128 pixel detector consists of a 500 µm thick silicon diode array bump-bonded pixel-by-pixel to an application-specific integrated circuit. The in-pixel circuitry provides a 1,000,000:1 dynamic range within a single frame, allowing the direct electron beam to be imaged while still maintaining single electron sensitivity. A 1.1 kHz framing rate enables rapid data collection and minimizes sample drift distortions while scanning. By capturing the entire unsaturated diffraction pattern in scanning mode, one can simultaneously capture bright field, dark field, and phase contrast information, as well as being able to analyze the full scattering distribution, allowing true center of mass imaging. The scattering is recorded on an absolute scale, so that information such as local sample thickness can be directly determined. This paper describes the detector architecture, data acquisition system, and preliminary results from experiments with 80-200 keV electron beams.

Electron Microscopy and Image Processing: Essential Tools for Structural Analysis of Macromolecules

Macromolecular electron microscopy typically depicts the structures of macromolecular complexes ranging from ∼200 kDa to hundreds of MDa. The amount of specimen required, a few micrograms, is typically 100 to 1000 times less than needed for X-ray crystallography or nuclear magnetic resonance spectroscopy. Micrographs of frozen-hydrated (cryogenic) specimens portray native structures, but the original images are noisy. Computational averaging reduces noise, and three-dimensional reconstructions are calculated by combining different views of free-standing particles ("single-particle analysis"). Electron crystallography is used to characterize two-dimensional arrays of membrane proteins and very small three-dimensional crystals. Under favorable circumstances, near-atomic resolutions are achieved. For structures at somewhat lower resolution, pseudo-atomic models are obtained by fitting high-resolution components into the density. Time-resolved experiments describe dynamic processes. Electron tomography allows reconstruction of pleiomorphic complexes and subcellular structures and modeling of macromolecules in their cellular context. Significant information is also obtained from metal-coated and dehydrated specimens.

Automatic estimation and correction of anisotropic magnification distortion in electron microscopes

We demonstrate a significant anisotropic magnification distortion, found on an FEI Titan Krios microscope and affecting magnifications commonly used for data acquisition on a Gatan K2 Summit detector. We describe a program (mag_distortion_estimate) to automatically estimate anisotropic magnification distortion from a set of images of a standard gold shadowed diffraction grating. We also describe a program (mag_distortion_correct) to correct for the estimated distortion in collected images. We demonstrate that the distortion present on the Titan Krios microscope limits the resolution of a set of rotavirus VP6 images to ∼7 Å, which increases to ∼3 Å following estimation and correction of the distortion. We also use a 70S ribosome sample to demonstrate that in addition to affecting resolution, magnification distortion can also interfere with the classification of heterogeneous data.

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6

Biological specimens suffer radiation damage when imaged in an electron microscope, ultimately limiting the attainable resolution. At a given resolution, an optimal exposure can be defined that maximizes the signal-to-noise ratio in the image. Using a 2.6 Å resolution single particle cryo-EM reconstruction of rotavirus VP6, determined from movies recorded with a total exposure of 100 electrons/Ų, we obtained accurate measurements of optimal exposure values over a wide range of resolutions. At low and intermediate resolutions, our measured values are considerably higher than obtained previously for crystalline specimens, indicating that both images and movies should be collected with higher exposures than are generally used. We demonstrate a method of using our optimal exposure values to filter movie frames, yielding images with improved contrast that lead to higher resolution reconstructions. This ‘high-exposure’ technique should benefit cryo-EM work on all types of samples, especially those of relatively low-molecular mass.

DOI:http://dx.doi.org/10.7554/eLife.06980.001

Microscopes allow us to visualize objects that are invisible to the naked eye. One type of microscope—called the electron microscope—produces images using beams of particles known as electrons, which enables them to produce more detailed images than microscopes that use light.

There are several ways to prepare samples for electron microscopy. For example, in ‘electron cryo-microscopy’—or cryo-EM for short—a sample is rapidly frozen to preserve its features before it is examined under the microscope. This technique generates images that can be analyzed by computers to produce three-dimensional models of individual viruses, proteins, and other tiny objects. Unfortunately, the samples need to be exposed to high-energy beams of electrons that will damage the sample while the images are gathered, which results in sample movement and blurry images that lack the finer details.

The contrast between the sample and its background is one of the factors that determine the final quality of an image. The higher the contrast, the greater the level of structural information that can be obtained, but this requires the use of longer exposures to the electron beam. To overcome this issue, researchers found that instead of recording a single image, it is possible to record movies in which the movement of the sample under the electron beam can be tracked. After the movies are gathered, the movie frames are aligned using computer software to reduce the blurring caused by the sample moving and can then be used to make three-dimensional models.

Grant and Grigorieff improved this method further by studying how quickly a large virus-like particle called ‘rotavirus double-layered particle’ is damaged under the electron beam. These experiments identified an optimum range of exposure to electrons that provides the highest image contrast at any given level of detail. These findings were used to design an exposure filter that can be applied to the movie frames, allowing Grant and Grigorieff to visualize features of the virus that had not previously been observed by cryo-EM.

This method was also used to study an assembly of proteins known as the proteasome, which is responsible for destroying old proteins. Grant and Grigorieff's findings should be useful for cryo-EM studies on many kinds of samples.

DOI:http://dx.doi.org/10.7554/eLife.06980.002

Comparison of optimal performance at 300keV of three direct electron detectors for use in low dose electron microscopy

Low dose electron imaging applications such as electron cryo-microscopy are now benefitting from the improved performance and flexibility of recently introduced electron imaging detectors in which electrons are directly incident on backthinned CMOS sensors. There are currently three commercially available detectors of this type: the Direct Electron DE-20, the FEI Falcon II and the Gatan K2 Summit. These have different characteristics and so it is important to compare their imaging properties carefully with a view to optimise how each is used. Results at 300 keV for both the modulation transfer function (MTF) and the detective quantum efficiency (DQE) are presented. Of these, the DQE is the most important in the study of radiation sensitive samples where detector performance is crucial. We find that all three detectors have a better DQE than film. The K2 Summit has the best DQE at low spatial frequencies but with increasing spatial frequency its DQE falls below that of the Falcon II.

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Three direct electron detectors offer better DQE than film at 300 keV.

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Recorded 300 keV electron events on the detectors have very similar Landau distributions.

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The Gatan K2 Summit detector has the highest DQE at low spatial frequency.

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The FEI Falcon II detector has the highest DQE beyond one half the Nyquist frequency.

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The Direct Electron DE-20 detector has the fastest data acquisition rate.

Improving signal to noise in labeled biological specimens using energy-filtered TEM of sections with a drift correction strategy and a direct detection device

Energy filtered transmission electron microscopy techniques are regularly used to build elemental maps of spatially distributed nanoparticles in materials and biological specimens. When working with thick biological sections, electron energy loss spectroscopy techniques involving core-loss electrons often require exposures exceeding several minutes to provide sufficient signal to noise. Image quality with these long exposures is often compromised by specimen drift, which results in blurring and reduced resolution. To mitigate drift artifacts, a series of short exposure images can be acquired, aligned, and merged to form a single image. For samples where the target elements have extremely low signal yields, the use of charge coupled device (CCD)-based detectors for this purpose can be problematic. At short acquisition times, the images produced by CCDs can be noisy and may contain fixed pattern artifacts that impact subsequent correlative alignment. Here we report on the use of direct electron detection devices (DDD's) to increase the signal to noise as compared with CCD's. A 3× improvement in signal is reported with a DDD versus a comparably formatted CCD, with equivalent dose on each detector. With the fast rolling-readout design of the DDD, the duty cycle provides a major benefit, as there is no dead time between successive frames.

Detecting single-electron events in TEM using low-cost electronics and a silicon strip sensor

There is great interest in developing novel position-sensitive direct detectors for transmission electron microscopy (TEM) that do not rely in the conversion of electrons into photons. Direct imaging improves contrast and efficiency and allows the operation of the microscope at lower energies and at lower doses without loss in resolution, which is especially important for studying soft materials and biological samples. We investigate the feasibility of employing a silicon strip detector as an imaging detector for TEM. This device, routinely used in high-energy particle physics, can detect small variations in electric current associated with the impact of a single charged particle. The main advantages of using this type of sensor for direct imaging in TEM are its intrinsic radiation hardness and large detection area. Here, we detail design, simulation, fabrication and tests in a TEM of the front-end electronics developed using low-cost discrete components and discuss the limitations and applications of this technology for TEM.

The joys and perils of flexible fitting

While performing their functions, biological macromolecules often form large, dynamically changing macromolecular assemblies. Only a relatively small number of such assemblies have been accessible to the atomic-resolution techniques X-ray crystallography and NMR. Electron microscopy in conjunction with image reconstruction has become the preferred alternative for revealing the structures of such macromolecular complexes. However, for most assemblies the achievable resolution is too low to allow accurate atomic modeling directly from the data. Yet, useful models often can be obtained by fitting atomic models of individual components into a low-resolution reconstruction of the entire assembly. Several algorithms for achieving optimal fits in this context were developed recently, many allowing considerable degrees of flexibility to account for binding-induced conformational changes of the assembly components. This chapter describes the advantages and potential pitfalls of these methods and puts them into perspective with alternative approaches such as iterative modular fitting of rigid-body domains.

Movies of ice-embedded particles enhance resolution in electron cryo-microscopy

Low-dose images obtained by electron cryo-microscopy (cryo-EM) are often affected by blurring caused by sample motion during electron beam exposure, degrading signal especially at high resolution. We show here that we can align frames of movies, recorded with a direct electron detector during beam exposure of rotavirus double-layered particles, thereby greatly reducing image blurring caused by beam-induced motion and sample stage instabilities. This procedure increases the efficiency of cryo-EM imaging and enhances the resolution obtained in three-dimensional reconstructions of the particle. Using movies in this way is generally applicable to all cryo-EM samples and should also improve the performance of midrange electron microscopes that may have limited mechanical stability and beam coherence.