Reduction of charging in protein electron cryomicroscopy

Charging causes a loss of resolution in electron cryomicroscopy with biological specimens prepared without a continuous carbon support film. Thin conductive films were deposited onto catalase crystals prepared across holes using ion-beam sputtering and thermal evaporation and evaluated for the effectiveness of charge reduction. Deposits applied by ion-beam sputtering reduced charging but concurrently resulted in structural damage. Coatings applied by thermal evaporation also reduced charging, and preserved the specimen structure beyond 5 Å resolution as judged from electron diffraction patterns and images of glucose-embedded catalase crystals tilted to 45° in the microscope. This study demonstrates for the first time the feasibility of obtaining high-resolution data from unstained, unsupported protein crystals with a conductive surface coating.     

Radiation damage relative to transmission electron microscopy of biological specimens at low temperature: a review.

When biological specimens are irradiated by the electron beam in the electron microscope, the specimen structure is damaged as a result of molecular excitation, ionization, and subsequent chemical reactions. The radiation damage that occurs in the normal process of electron microscopy is known to present severe limitations for imaging high resolution detail in biological specimens. The question of radiation damage at low temperatures has therefore been investigated with the view in mind of reducing somewhat the rate at which damage occurs. The radiation damage protection found for small molecule (anhydrous) organic compounds is generally rather limited or even non-existent. However, large molecular, hydrated materials show as much as a 10-fold reduction at low temperature in the rate at which radiation damage occurs, relative to the damage rate at room temperature. In the case of hydrated specimens, therefore, low temperature electron microscopy offers an important advantage as part of the overall effort required in obtaining high resolution images of complex biological structures.     

High resolution at low beam energy in the SEM: resolution measurement of a monochromated SEM

The resolution of secondary electron low beam energy imaging of a scanning electron microscope equipped with a monochromator is quantitatively measured using the contrast transfer function (CTF) method. High-resolution images, with sub-nm resolutions, were produced using low beam energies. The use of a monochromator is shown to quantitatively improve the resolution of the SEM at low beam energies by limiting the chromatic aberration contribution to the electron probe size as demonstrated with calculations and images of suitable samples. Secondary electron image resolution at low beam energies is ultimately limited by noise in the images as shown by the CTFs.     

Enhanced EDX images by fusion of multimodal SEM images using pansharpening techniques

The goal of this paper is to explore the potential interest of image fusion in the context of multimodal scanning electron microscope (SEM) imaging. In particular, we aim at merging the backscattered electron images that usually have a high spatial resolution but do not provide enough discriminative information to physically classify the nature of the sample, with energy‐dispersive X‐ray spectroscopy (EDX) images that have discriminative information but a lower spatial resolution. The produced images are named enhanced EDX. To achieve this goal, we have compared the results obtained with classical pansharpening techniques for image fusion with an original approach tailored for multimodal SEM fusion of information. Quantitative assessment is obtained by means of two SEM images and a simulated dataset produced by a software based on PENELOPE.     

Low-dose aberration corrected cryo-electron microscopy of organic specimens

Spherical aberration (C(s)) correction in the transmission electron microscope has enabled sub-angstrom resolution imaging of inorganic materials. To achieve similar resolution for radiation-sensitive organic materials requires the microscope to be operated under hybrid conditions: low electron dose illumination of the specimen at liquid nitrogen temperature and low defocus values. Initial images from standard inorganic and organic test specimens have indicated that under these conditions C(s)-correction can provide a significant improvement in resolution (to less than 0.16nm) for direct imaging of organic samples.     

Analytical scanning electron microscopy for solid surface

A scanning electron microscope of ultra-high-vacuum (UHV-SEM) with a field emission gun (FEG) is operated at the primary electron energies of from 100 eV to 3 keV. The instrument can form the images that contain information on surface chemical composition, chemical bonding state (electronic structure), and surface crystal structure in a microscopic resolution of several hundred angstroms (Å) using the techniques of scanning Auger electron microscope, scanning electron energy loss microscope, and scanning low-energy electron diffraction (LEED) microscope. A scanning tunneling microscope (STM) also has been combined with the SEM in order to obtain the atomic resolution for the solid surface. The instrumentation and examples of their applications are presented both for scanning LEED microscopy and STM.     

Computer-controlled spot-scan imaging of crotoxin complex crystals with 400 keV electrons at near-atomic resolution.

400 keV electrons yield a better relative image contrast than 100 keV electrons for a beam-sensitive organic crystal when spot-scan imaging is used [J. Brink and W. Chiu, J. Microscopy 161 (1991) 279]. A FORTRAN 77 program has been written to operate the spot-scan imaging system on a computer workstation under the VMS operating system which is interfaced serially to the JEOL4000 electron microscope. We demonstrate the application of this implementation by imaging crotoxin complex crystals embedded in either vitreous ice or glucose to 2.5 A resolution. The intensity strength of the structure factors of this protein crystal are different at low (> 10 A) resolution but similar at high resolution (< 10 A) for the two embedding media as expected from their scattering contrast difference. Based on our experience as judged from the electron diffraction patterns of highly tilted crystals, flat crystals embedded in glucose can be readily obtained. Furthermore, our spot-scan imaging system also has the option of correcting the focus gradient that is present in images of tilted specimens.     

Polycrystal orientation maps from TEM

Determination of topography of crystallite orientations is an important technique of investigation of polycrystalline materials. A system for creating orientation maps using transmission electron microscope (TEM) Kikuchi patterns and Convergent beam electron diffraction patterns is presented. The orientation maps are obtained using a step-by-step beam scan on a computer-controlled TEM equipped with a CCD camera. At each step, acquired diffraction patterns are indexed and orientations are determined. Although, the approach used is similar to that applied in SEM/electron back scattered diffraction (EBSD) orientation imaging setups, the TEM-based system considerably differs from its SEM counterpart. The main differences appear due to specific features of TEM and SEM diffraction patterns. Also, the resulting maps are not equivalent. On these generated by TEM, the accuracy of orientation determination can be better than 0.1 degrees. The spatial resolution is estimated to be about 10nm. The latter feature makes the TEM orientation mapping system an important tool for studies at fine scale unreachable by SEM/EBSD systems. The automatic orientation mapping is expected to be a useful complement of the conventional TEM contrast images. The new technique will be essential for characterization of fine structure materials. To illustrate that, example maps of an aluminum sample produced by severe plastic deformation are included.     

Correction of image drift and distortion in a scanning electron microscopy

Continuous research on small‐scale mechanical structures and systems has attracted strong demand for ultrafine deformation and strain measurements. Conventional optical microscope cannot meet such requirements owing to its lower spatial resolution. Therefore, high‐resolution scanning electron microscope has become the preferred system for high spatial resolution imaging and measurements. However, scanning electron microscope usually is contaminated by distortion and drift aberrations which cause serious errors to precise imaging and measurements of tiny structures. This paper develops a new method to correct drift and distortion aberrations of scanning electron microscope images, and evaluates the effect of correction by comparing corrected images with scanning electron microscope image of a standard sample. The drift correction is based on the interpolation scheme, where a series of images are captured at one location of the sample and perform image correlation between the first image and the consequent images to interpolate the drift–time relationship of scanning electron microscope images. The distortion correction employs the axial symmetry model of charged particle imaging theory to two images sharing with the same location of one object under different imaging fields of view. The difference apart from rigid displacement between the mentioned two images will give distortion parameters. Three‐order precision is considered in the model and experiment shows that one pixel maximum correction is obtained for the employed high‐resolution electron microscopic system.     

Coherent nano-area electron diffraction

We describe the new coherent nano-area electron diffraction (NED) and its application for structure determination of individual nanostructures. The study is motivated by the challenge and the general lack of analytical techniques for characterizing nanometer-sized, heterogeneous phases. We show that by focusing electrons on the focal plane of the pre-objective lens using a 3rd condenser lens and a small condense aperture, it is possible to achieve a nanometer-sized highly parallel illumination or probe. The high angular resolution of diffraction pattern from the parallel illumination allows over-sampling and consequently the solution of phase problem based on the recently developed ab initio phase retrieval technique. From this, a high-contrast and high-resolution image can be reconstructed at resolution beyond the performance limit of the image-forming objective lens. The significance of NED for nanostructure characterization will be exemplified by single-wall carbon nanotubes and small metallic clusters. Imaging from diffraction patterns, or diffractive imaging, will be demonstrated using double-wall carbon nanotubes.     

Towards 1.0 Å resolution: taking advantage of dynamical scattering, and the benefits for structure retrieval

This paper is an exploration of the behaviour of high-resolution transmission electron microscope (HRTEM) images at up to 1 Å resolution. The ultimate limits to HRTEM (structure) resolution and the manner in which strong scattering may lead to weak diffraction in heavy fcc metals are discussed. A resolution of 1.0 Å is somewhat better than the ultimate resolution presently achievable in a 400-kV electron microscope. In heavy metals, such as platinum, it is found that the lattice fringe contrast is very low in the [011] projection, but that fringe contrast may be improved by imaging in the [111] projection. For atomic resolution imaging of the heavy metals in the [111] projection a resolution of 1.2 Å is required. For the study of oxygen position in high-temperature superconducting (HTS) oxides a resolution of between 1.2 and 1.4 Å is required. At better than 1.2 Å resolution the thick crystal images in HTS oxides remain simple and are easily interpreted. At such resolution all atomic columns are separated for the HTS [010] projection and the dynamical diffraction effects improve the contrast of oxygen atoms relative to the metal atoms.     

Position-sensitive diffractive imaging in STEM by an automated chaining diffraction algorithm

The diffractive imaging process used for retrieval of an aberration-free exit-wave function of a complex-valued object is optimized with a newly developed automated chaining diffraction (ACD) algorithm. Our algorithm enables automatic recovery of the amplitude and phase of the complex-valued objects with diffraction-limited resolution, starting from selected-area electron diffraction (SAED) patterns recorded from partially overlapping regions in STEM/CTEM. Based on a ‘differential map’ (DM) approach, the ACD algorithm meets very general requirements and, similar to ‘hybrid input–output’ (HIO) algorithm, can be applied to non-periodic, real or complex structures. In contrast to many other algorithms, it is not limited by the object's finite size or tight object support. Wide-field-of-view reconstructions for the complex-object-wave amplitude and phase made with ACD algorithm from SAED patterns down to sub-Angström resolution show the potential of diffractive imaging for quantitative analysis of functional materials at different length scales in terms of absorption and scattering mechanisms. The method can be applied also for imaging magnetic properties of samples by the electron or neutron microscopy and/or imaging of non-periodic objects with X-ray microscopy.     

The principles and practice of the weak-beam method of electron microscopy

The weak-beam method of electron microscopy enables the high resolution capabilities of the electron microscope to be used in the study of lattice defects. In this paper, the principles of the method are outlined and the experimental procedures for obtaining weak-beam images are discussed. The experimental diffraction conditions necessary for obtaining quantitative results and the limitations of the method are summarized, and applications of the method to various problems in defect studies are reviewed.     

Zero-loss electron microscopy with the Zeiss EM902

The recently introduced Zeiss EM902 is the first commercially available electron microscope to incorporate a magnetic spectrometer capable of forming directly energy-filtered images and diffraction patterns. We have briefly assessed the potential usefulness of this microscope for structural studies of thin biological specimens, through removal of inelastically scattered electrons. The improvements we find in image contrast, without significant loss of resolution, suggest energy-filtering may prove particularly worthwhile with unstained specimens.     

Electron backscatter diffraction of grain and subgrain structures — resolution considerations

Characterization of microstructures containing small grains or low-angle grain boundaries by electron backscattered diffraction (EBSD) is limited by the spatial and angular resolution limits of the technique. It was found that the best effective spatial resolution (60 nm) for aluminium alloys in a tungsten-filament scanning electron microscope (SEM) was obtained for an intermediate probe current which provided a compromise between pattern quality and specimen interaction volume. The same specimens and EBSD equipment when used with a field-emission gun SEM showed an improvement in spatial resolution by a factor of 2–3. For characterizing low-angle boundary microstructures, the precision of determining relative orientations is a limiting factor. It was found that the orientation noise was directly related to the probe current and this was interpreted in terms of the effect of probe current on the quality of the diffraction patterns.     

Computation of contrasts in atomic resolution electron spectroscopic images of planar defects in crystalline specimens

The image obtained in a conventional transmission electron microscope contains contributions from elastically and from inelastically scattered electrons. The electron spectroscopic imaging mode of an energy-filtering transmission electron microscope allows us to separate these two different contributions by inserting an energy-selecting slit in the energy-dispersive plane of an imaging energy filter. Selecting a specific energy loss corresponding to the ionization of the inner shell of a particular element one can obtain information on the distribution of the element within the specimen. The contrast is then caused by inelastically scattered electrons. For crystalline specimens, however, the contrast will be influenced additionally by the elastic contrast. This elastic contrast arises from electron diffraction and increases with increasing crystal thickness. Therefore the intensity distribution in the image cannot directly be interpreted as an elemental map. For a reliable interpretation of contrast formation in elemental maps it is therefore necessary to compute theoretical energy-loss images for various crystal thicknesses and compare these images with the experimental images. As an example we discuss the influence of electron diffraction effects on energy-loss images of two crystals with planar defects. Linescans are computed for various thicknesses of these crystals. Our calculations are performed using first-order perturbation theory to describe the transitions between the Bloch-wave states of the incident electron. The computed linescans for various crystal thicknesses show clearly that the influence of the elastic contrast on an image increases when we investigate thicker specimens. Furthermore, the comparison between elastic and energy-loss images demonstrates the partial preservation of the elastic contrast as a function of thickness. We find that for specimens thicker than about one third of the extinction length (here approximately 80-100 A) it is impossible to interpret an energy-loss image directly as elemental map.     

Quantitative analysis of image contrast in electron micrographs of beam-sensitive crystals

The contrast in high resolution electron micrographs of three different thin crystals has been compared quantitatively with that predicted theoretically from separate measurements of thier electron diffraction patterns. The crystals were vermiculite, a mineral which is not greatly affected by the electron beam, and two organic specimens, n-paraffin and purple membrane, which are both destroyed by doses of about 1 electron/Ų. The results, all at 4.0 to 4.5 Å resolution, show that the absolute contrast in images of vermiculite is roughly 1/5th of that expected for a theoretically perfect microscope, whereas images of paraffin and purple membrane seldom reach more than 1/25th of theoretical contrast. Much of this loss of contrast can be explained on the basis of known microscope parameters in the case of the non-beam-sensitive specimens. However, for the images of paraffin and purple membrane, it is necessary to postulate that beam-induced specimen movement results in further substantial blurring of the image. The tendency for such movement to occur may be unavoidable since the molecular structure is being destroyed during the exposure. The magnitude of this movement must be reduced before the image contrast will be able to approach the theoretical limit.     

Spot-scan imaging of microcrystals of an influenza neuraminidase-antibody fragment complex

Electron micrographs of two-dimensional microcrystals of a complex of an avian influenza virus neuraminidase and an antibody Fab fragment, termed 32/3, have been recorded using the spot-scan method of imaging. The crystals have a large unit cell (159.5 A x 159.5 A x 130.5 A) and a high solvent content (approximately 71% by volume) and are a challenging specimen for testing the spot-scan methodology. Crystalline order was preserved to beyond 4 A resolution as demonstrated by electron diffraction, using an embedding medium of a mixture of glucose and neutral potassium phosphotungstate. Using a Philips C400 computer control system interfaced to an EM420 electron microscope, and with the inclusion of additional software in the system, we have been able to record micrographs at low temperature with a relatively narrow (1500 A diameter) moving beam. There is evidence that the use of such a spot-scan beam reduces the effects of beam-induced specimen motion on the quality of micrographs. Conventional low-dose "flood-beam" images showed good isotropic optical diffraction in only 15% of cases whereas 30% of spot-scan images showed good diffraction. The best flood-beam images gave phases to only 15 A resolution after computer processing, whereas the best spot-scan images gave phases to 7 A resolution. Electron diffraction patterns were also recorded at low temperature, and the resulting diffraction amplitudes combined with phases from spot-scan images to yield a projection map of the structure. A 7 A resolution projection map of the complex is presented, and is compared with the projection map of the same avian influenza neuraminidase complexed with a different monoclonal Fab fragment, NC41, which has been solved to high resolution by X-ray diffraction.     

Platinum/iridium/carbon: a high-resolution shadowing material for TEM,STM and SEM of biological macromolecular structures

Thin Pt/Ir/C coating films (1.5 nm) show a fine granularity and provide a high structural resolution in the transmission electron microscope (TEM) when applied to freeze-dried biological macromolecules. They keep their structure when exposed to atmospheric conditions, without the need of an additional stabilizing carbon layer, in contrast to conventional high-resolution shadowing materials such as Ta/W and Pt/C. However, the correct ratio of the components has turned out to be crucial. When evaporating Pt/Ir/C from the source electrode in an electron-beam-heated evaporator, the ratio of the three elements changes progressively, and, consequently, the properties of such films depend strongly on the mass that has been pre-evaporated. In this paper we present a quantitative analysis of the composition of Pt/Ir/C films by wavelength-dispersive X-ray analysis (WDX) undertaken in association with TEM experiments. We applied Pt/Ir/C shadowing to two regular biological test specimens, the phage T4 type III polyhead and the HPI-layer of Deinococcus radiodurans. It turns out that Pt/Ir/C films containing at least 25% C are three-dimensionally stable on the freeze-dried macromolecular samples. By the dramatically improved resolution power of the latest scanning electron microscopes (SEM) and the invention of the scanning tunnelling microscope (STM), two new surface-sensitive tools for the investigation of biological macromolecular structures became available. The Pt/Ir/C coating has proved to be well suited for STM and SEM imaging of freeze-dried biological structures because of its good electrical conductivity and its direct three-dimensional stability. We compare STM, SEM and TEM images of freeze-dried and Pt/Ir/C-coated polyheads.     

Transmission EBSD from 10 nm domains in a scanning electron microscope

The spatial resolution of electron diffraction within the scanning electron microscope (SEM) has progressed from channelling methods capable of measuring crystallographic characteristics from 10 μm regions to electron backscatter diffraction (EBSD) methods capable of measuring 120 nm particles. Here, we report a new form of low‐energy transmission Kikuchi diffraction, performed in the SEM. Transmission‐EBSD (t‐EBSD) makes use of an EBSD detector and software to capture and analyse the angular intensity variation in large‐angle forward scattering of electrons in transmission, without postspecimen coils. We collected t‐EBSD patterns from Fe–Co nanoparticles of diameter 10 nm and from 40 nm‐thick Ni films with in‐plane grain size 15 nm. The patterns exhibited contrast similar to that seen in EBSD, but are formed in transmission. Monte Carlo scattering simulations showed that in addition to the order of magnitude improvement in spatial resolution from isolated particles, the energy width of the scattered electrons in t‐EBSD is nearly two orders of magnitude narrower than that of conventional EBSD. This new low‐energy transmission diffraction approach builds upon recent progress in achieving unprecedented levels of imaging resolution for materials characterization in the SEM by adding high‐spatial‐resolution analytical capabilities.