Reliability of phases retrieved from 400-kV spot-scan images of purple membranes acquired on a slow-scan CCD camera

Glucose-embedded purple membranes were used as a test specimen to evaluate the reliability of phases retrieved from 400-kV spot-scan images acquired on a 1024 × 1024 slow-scan CCD camera. This specimen was chosen because it represents a broad class of low-contrast radiation-sensitive biological objects and its structure is well established. The amplitudes of computed reflections from these images were strongly damped by the modulation transfer function of the camera. Nevertheless, their phases on average were < 12° different from the reference data of Henderson et al . (1986), Ultramicroscopy , 19 , 147–178, up to 8.8 Å resolution, which corresponds to 0.8 of the Nyquist frequency of the camera.     

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.     

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.     

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.     

Use of spot-scan procedure for recording low-dose micrographs of beam-sensitive specimens

Electron micrographs of monolayer crystals of paraffin have been recorded with a spot-scan mode of imaging which uses a small 50 nm diameter moving beam. In comparison with normal stationary beam images using 5 μm illuminating beams, the spot-scan micrographs show a higher and more consistent contrast from the 3.8–4.2 Å hydrocarbon chain spacings. On average the improvement in contrast is twofold, but this still leaves scope for further improvement: the best spot-scan images still do not quite reach the level of contrast calculated theoretically from electron diffraction. We believe that the cause of the low contrast in paraffin images must be specimen motion caused by radiation damage rather than a charging effect, for two reasons. First, it does not occur in control images of vermiculite, a non-beam-sensitive mineral, when treated identically. Secondly, although charging might still be a problem with paraffin, when images are taken with the objective aperture in the column, a procedure which is normally expected to reduce charging, no improvement in contrast is found. Thus we think that the use of the small beam minimizes the effect of specimen motion on image contrast by minimizing the specimen area exposed at each instant and therefore the resultant image blurring. Further improvements with even smaller illumination beam diameters might be expected.     

HREM image simulations for small particle catalysts on crystalline supports

The imaging conditions for electron microscope studies of supported ultrafine particle catalysts have been investigated by multislice simulations. Images of Pt and ReO₄ particles ranging from 0·4 to 2·3 nm in size were simulated in both plan view and profile view with a rutile (TiO₂) support. It was shown that particle visibility varied greatly with the objective lens defocus. Optimum defocus was not favourable for supported particles in plan view since the ultrafine supported particles were least visible at this defocus. Underfocusing, especially at defoci corresponding to half-spacing fringes in the TiO₂ support, led to improved visibility and resolution of the supported particles. Although the structure and shape of supported ultrafine particles should be resolved better with a 400-kV high-resolution electron microscope, their detectability is poorer than with a 200-kV instrument. An ReO₄ cluster should be detectable at 200 kV on TiO₂ supports up to 5 nm in thickness, whereas it is only likely to be detectable at 400 kV on supports up to 3 nm in thickness. The simulations confirmed that optimum defocus is most favourable for imaging supported particles in profile view. Atomic information for particles as small as a 13-atom Pt cuboctahedral cluster should be resolvable with a 400-kV instrument. The crystalline Ti monolayer observed on surfaces of Pt particles, which could explain the mechanism known as SMSI, was simulated as an example of profile imaging.     

A high-performance source of high-power nanosecond ultrawideband radiation pulses

A source of high-power nanosecond ultrawideband electromagnetic pulses is described. The 3-ns-long bipolar voltage pulse with a 90-kV amplitude is applied to the input of four-element antenna array. The effective radiation potential values E _p R = 560 kV were obtained at a 100-Hz pulse repetition rate.     

High resolution electron microscope observations of microstructures in A15 type Nb3X superconductors

Microstructures of superconducting Nb₃X(A15) compounds are studied by means of high resolution electron microscopy. Structure images are obtained with the 400kV high resolution electron microscope for both the annealed and ion-irradiated crystals. The images obtained from the annealed crystals show bright contrast patterns similar to the projections of Nb and X atoms comprising the A15 structure. Defects observed in the annealed crystal irradiated with 40 kV Nb⁺ ions show characteristic features in contrast. The dependence of image contrast on the element X and the atomic structures of the defects are discussed by comparison with the calculated images.     

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.     

Direct imaging of paracrystalline phospholipid structure in the electron microscope

A long chain amphiphilic molecule—the phospholipid 1,2-dihexadecyl sn glycerophosphoethanolamine—has been crystallized epitaxially so that the interlamellar molecular periodicity is parallel to the substrate and hence normal to the electron beam in the electron microscope. This has permitted the direct resolution of the 55·6 Å lamellae in unstained crystals at room temperature. The lattice images have shown the presence of line dislocations and lenticular cracks in the crystals. Of significance to their biological properties is that the lattice is undulating with a periodicity of 0·1–0·5 μm. This would also account for the difficulties encountered by X-ray and electron diffraction techniques when examining these crystals.     

An electron diffraction study of paramylon storage granules from Euglena gracilis

Paramylon storage granules from Euglena gracilis were characterized by electron diffraction techniques using electrons of various accelerating voltages: 2 MV for the thick granules and 100 kV for the thinner ones. Intact granules gave well resolved, characteristic (1→3)-β-d glucan fibre diffraction diagrams with the glucan molecular orientation parallel to the longer axis of the granule. Hydrated electron diffraction patterns with better resolution were obtained from thinner granules by examination at low temperatures of quench-frozen specimens. In this case, the pattern indexed on an hexagonal system with a = b= 1·55 + 0·01 nm and c (fibre axis) = 1·86 ± 0·01 nm. Sections of embedded granules provided single crystal-like electron diffraction patterns corresponding to various sections of the reciprocal lattice of (1→3)-β-d glucan (including the hko section). Finally, by scanning electron microscopy, it was shown that the granules swell on contact with water and take up a characteristic ribbed, pumpkin-like shape.     

Applications of medium-voltage STEM for the 3-D study of organelles within very thick sections

Scanning transmission electron microscopy at 300 kV enables the visualization of nucleolar silver-stained structures within thick sections (3–8 μm) of Epon-embedded cells at high tilt angles (–50°; + 50°). Thick sections coated with gold particles were used to determine the best conditions for obtaining images with high contrast and good resolution. For a 6-μm-thick section the values of thinning and shrinkage under the beam are 35 to 10%, respectively. At the electron density used in these experiments (100e^—/Å₂/s) it is estimated that these modifications of the section stabilized in less than 10 min. The broadening of the beam through the section was measured and calculations indicated that the subsequent resolution reached 100 nm for objects localized near the lower side of 4-μm-thick sections with a spot-size of 5·6 nm. Comparing the same biological samples, viewed alternately in CTEM and STEM, demonstrated that images obtained in STEM have a better resolution and contrast for sections thicker than 3 μm. Therefore, the visualization of densely stained structures, observed through very thick sections in the STEM mode, will be very useful in the near future for microtomographic reconstruction of cellular organelles.     

About the role of the various types of secondary electrons (SE1; SE2; SE3) on the performance of LVSEM

The relative weight, δ_Β, of the yield of secondary electrons, SE₂, induced by the backscattered electrons, BSE, with respect to that, δ_P, of secondary electrons, SE₁, induced by the primary electrons, PE, is deduced from simple theoretical considerations. At primary energies E₀ larger than E_M (where the total SE yield δ = δ_P + δ_B is maximum), the dominant role of the backscattering events is established. It is illustrated in SEM by a direct comparison of the contrast between SE images and BSE images obtained at E₀ ～ 5 keV and E₀ ～ 15 keV on a stratified specimen. At energies E₀ less than E_M, the dominant role of SE₁ electrons with respect to SE₂ (and SE₃) is established. It is illustrated by the better practical resolution of diamond images obtained with an in‐lens detection in low voltage SEM E₀ ～ 0.2–1 keV range compared with that obtained with a lateral detector. The present contribution illustrates the improved performance of LVSEM in terms of contrast and of practical resolution as well as the importance of variable voltage methods for subsurface imaging. The common opinion that the practical lateral resolution is given by the incident spot diameter is also reconsidered in LVSEM.     

Oxygen ordering and twinning in YBa2Cu3O7−x

Direct structure images of the YBa₂Cu₃O_7−x high T_c superconducting ceramic (also called the 1–2–3 compound) at 1.7 Å resolution have been obtained for the [100] and [001] orientations. It was found that for the purposes of studying oxygen ordering in this compound it is better to use lattice images of lower resolution. The oxygen ordering was studied via the measurement of the bending of (100) and (11 0) lattice planes on crossing the (110) twin boundaries in crystals oriented in the [001] zone. Significant variations were found in the b/a ratios, owning to a variation in oxygen ordering, between different crystal grains, and between different regions in the same grain. For the three different 1–2–2 samples studied, the average b/a ration was 1.016, the same value as was found in neutron diffraction studies. The twin boundaries in the orthorhombic 1–2–3 phase are sharp and planar. It seems likely that the transformation from the high-temperature tetragonal phase to the lower-temperature orthorhombic phase is martensitic in nature. A new phase has been discovered on some of the twin boundaries. The new phase can be indexed as tetragonal with a = 7.5 ± 0.2 Å, and c = 6.8 ± 0.2 Å. It is possible that the new phase is stabilized by the stress which occurs at the twin boundaries.     

An electron microscopy study of the phase Al3Fe

The phase Al₃Fe (monoclinic C2/m, a = 1·549 nm, b = 0·808 nm, c = 1·248 nm, β = 107·8°) has been studied by transmission electron microscopy (TEM) and high resolution electron microscopy (HREM). Crystals were obtained from a direct chill-cast ingot of an Al-0·25 wt% Fe-0·13 wt% Si alloy. Extracted crystals were prepared by dissolving the aluminium phase in butanol and filtering off the particles. The extracted Al₃Fe crystals were mainly (100) platelets. The monclinic lattice was confirmed by tilt experiments and the mirror plane was confirmed by convergent beam electron diffraction. Experimental HREM images from the [100] and [110] projection agreed with images calculated by the multislice method. The interpretation of images in terms of a projected crystal structure is discussed. Common defects in Al₃Fe crystals were: twins on (100) and faults on (001). The (001) faults could be described by a displacement 1/2·[100] on a fault plane at z = 0·5 in the unit cell. A model for (001) faults, based on multiple twinning, is proposed.     

Micro‐CT versus synchrotron radiation phase contrast imaging of human cochlea

High‐resolution images of the cochlea are used to develop atlases to extract anatomical features from low‐resolution clinical computed tomography (CT) images. We compare visualization and contrast of conventional absorption‐based micro‐CT to synchrotron radiation phase contrast imaging (SR‐PCI) images of whole unstained, nondecalcified human cochleae. Three cadaveric cochleae were imaged using SR‐PCI and micro‐CT. Images were visually compared and contrast‐to‐noise ratios (CNRs) were computed from n = 27 regions‐of‐interest (enclosing soft tissue) for quantitative comparisons. Three‐dimensional (3D) models of cochlear internal structures were constructed from SR‐PCI images using a semiautomatic segmentation method. SR‐PCI images provided superior visualization of soft tissue microstructures over conventional micro‐CT images. CNR improved from 7.5 ± 2.5 in micro‐CT images to 18.0 ± 4.3 in SR‐PCI images (p < 0.0001). The semiautomatic segmentations yielded accurate reconstructions of 3D models of the intracochlear anatomy. The improved visualization, contrast and modelling achieved using SR‐PCI images are very promising for developing atlas‐based segmentation methods for postoperative evaluation of cochlear implant surgery.     

STM imaging of the complete bacterial cell sheath of Methanospirillum hungatei

Using a large range scanning tunnelling microscope (STM) we have obtained images of the complete outer cell wall of the archaebacterium Methanospirillum hungatei, deposited on a graphite substrate and over-coated with an Au or Pt evaporated film. The width of the collapsed cylindrical sheath structure was found to be 5000 Å ± ***10%, which agrees closely with the value from previously published electron microscope (EM) studies. The double thickness of the collapsed sheath was found to be 160 Å ± 10%, which is about 20% smaller than that from the EM results. Higher resolution STM images taken on top of the collapsed sheaths show corrugations running perpendicular to the cylinder axis and having widths which are multiples of ～ 30 Å, the minimum period expected from EM studies. The height of the corrugations have a minimum value of about 4 Å. The expected 2-D crystalline structure was not seen in the STM images.     

High-resolution imaging of organic pharmaceutical crystals by transmission electron microscopy and scanning moiré fringes

Formulation processing of organic crystalline compounds can have a significant effect on drug properties, such as dissolution rate or tablet strength/hardness. Transmission electron microscopy (TEM) has the potential to resolve the atomic lattice of these crystalline compounds and, for example, identify the defect density on a particular crystal face, provided that the sensitivity of these crystals to irradiation by high-energy electrons can be overcome. Here, we acquire high-resolution (HR) lattice images of the compound furosemide using two different methods: low-dose HRTEM and bright-field (BF) scanning TEM (STEM) scanning moiré fringes (SMFs). Before acquiring HRTEM images of furosemide, a model system of crocidolite (asbestos) was used to determine the electron flux/fluence limits of low-dose HR imaging for our scintillator-based, complementary metal-oxide semiconductor (CMOS) electron camera by testing a variety of electron flux and total electron fluence regimes. An electron flux of 10 e⁻/(Ų s) and total fluence of 10 e⁻/Ų was shown to provide sufficient contrast and signal-to-noise ratio to resolve 0.30 nm lattice spacings in crocidolite at 300 kV. These parameters were then used to image furosemide which has a critical electron fluence for damage of ≥10 e⁻/Ų at 300 kV. The resulting HRTEM image of a furosemide crystal shows only a small portion of the total crystal exhibiting lattice fringes, likely due to irradiation damage during acquisition close to the compound's critical fluence. BF-STEM SMF images of furosemide were acquired at a lower electron fluence (1.8 e⁻/Ų), while still indirectly resolving HR details of the (001) lattice. Several different SMFs were observed with minor variations in the size and angle, suggesting strain due to defects within the crystal. Overall BF-STEM SMFs appear to be more useful than BF-STEM or HRTEM (with a CMOS camera) for imaging the crystal lattice of very beam-sensitive materials since a lower electron fluence is required to reveal the lattice. BF-STEM SMFs may thus prove useful in improving the understanding of crystallization pathways in organic compounds, degradation in pharmaceutical formulations and the effect of defects on the dissolution rate of different crystal faces. Further work is, however, required to quantitatively determine properties such as the defect density or the amount of relative strain from a BF-STEM SMF image.     

Recent advances and applications of high resolution electron microscopy

This review covers several broad areas: firstly, recent developments in HREM instrumentation, and then novel techniques for imaging are discussed, including some of the problems of image interpretation. Applications of HREM techniques to a wide range of materials problems are described and include solid state chemistry, ceramics, semiconductors, metals and natural diamonds. The next generation of high resolution microscopes will operate in the 300–400 kV range, have low C_s objective lenses, and have sufficiently good vacuum to allow the combined use of CBED and EELS facilities with imaging in the sub-2 Å range. Microprocessor control of instrumental parameters such as astigmatism, alignment and defocus are seen as an important way forward in achieving the optimum performance of these instruments.     

Electron crystallography at atomic resolution: The structure of the odd-chain paraffin n-tritriacontane

The crystal structure of the odd-chain paraffin, n-tritriacontane, nC₃₃H₆₈, is determined directly by using low-dose electron microscope images and electron diffraction intensity data from epitaxially grown microcrystals. Phases of the most intense “polyethylene” reflections are determined from triplet structure-invariant relationships often used in X-ray crystallography. Low-dose electron microscopic images provide phases of the low-angle “lamellar” reflections and these can be used with one-dimensional structure-invariant relationships to determine other phases on the 00? reciprocal row. The phase set is sufficient to calculate an electrostatic potential map which is directly interpretable as a structure image at atomic resolution.