Mechanism of image formation for thick biological specimens: exit wavefront reconstruction and electron energy-loss spectroscopic imaging

With increasing frequency, cellular organelles and nuclear structures are being investigated at high resolution using electron microscopic tomography of thick sections (0·3–1·0 μm). In order to reconstruct the structures in three dimensions accurately from the observed image intensities, it is essential to understand the relationship between the image intensity and the specimen mass density. The imaging of thick specimens is complicated by the large fraction of multiple scattering which gives rise to incoherent and partially coherent image components. Here we investigate the mechanism of image formation for thick biological specimens at 200 and 300 keV in order to resolve the coherent scattering component from the incoherent (multiple scattering) components. Two techniques were used: electron energy-loss spectroscopic imaging (ESI) and exit wavefront reconstruction using a through-focus series. Although it is commonly assumed that image formation of thick specimens is dominated by amplitude (absorption) contrast, we have found that for conventionally stained biological specimens phase contrast contributes significantly, and that at resolutions better than ～10 nm, superposed phase contrast dominates. It is shown that the decrease in coherent scattering with specimen thickness is directly related to the increase in multiple scattering. It is further shown that exit wavefront reconstruction can exclude the microscope aberrations as well as the multiple scattering component from the image formation. Since most of the inelastic scattering with these thick specimens is actually multiple inelastic scattering, it is demonstrated that exit wavefront reconstruction can act as a partial energy filter. By virtue of excluding the multiple scattering, the ‘restored’ images display enhanced contrast and resolution. These findings have direct implications for the three-dimensional reconstruction of thick biological specimens, where a simple direct relationship between image intensity and mass density was assumed, and the aberrations were left uncorrected.     

The effect of mechanical vibration and drift on the reconstruction of exit waves from a through focus series of HREM images

Experimental HREM images can show a limited resolution as a result of mechanical vibration and drift. In this paper the effect of such mechanical vibrations on the accuracy of the through focus exit wave reconstruction method is investigated for different thicknesses of a test structure of La₃Ni₂B₂N₃. A through-focus series of HREM images for this structure is simulated for different kinds of mechanical vibration corresponding to an information limit g of about 7 nm⁻¹: (1) no mechanical vibration, (2) isotropic mechanical vibration, and (3) several anisotropic mechanical vibrations. From these through-focus series the reconstructed exit wave is calculated (Ultramicroscopy 64 (1996) 109). The above isotropic and anisotropic mechanical vibrations have a large effect on the reconstructed exit waves when compared with the reconstructed exit wave without mechanical vibration, i.e. the range of amplitudes and phases in a reconstructed exit wave decreases and the background intensity increases. The initial thickness and orientation can be obtained using a least-squares refinement procedure (Acta Crystallogr. A 54 (1998) 91) when there is no mechanical vibration present. In the case of isotropic or anisotropic vibration, the refined thickness and orientation are likely to give wrong results depending on the size of the vibrations and on the number of significant reflections (which is related to the size of the unit cell, the thickness and the misorientation).     

Application of recording and processing of energy-filtered image sequences for the elemental mapping of biological specimens: Imaging-Spectrum

Computerized energy-filtered transmission electron microscope (EFTEM) permits the recording and the processing of energy-filtered images, allowing a part of an electron energy-loss spectrum for each picture element to be obtained. This method, called ‘Imaging-Spectrum’, uses a Zeiss CEM902 coupled to several image analysis systems. The actual configuration records sequences of 48 images, 256 × 256 pixels, in steps of the energy loss, ΔE. Processing these sequences results in part of a core-loss EELS-spectrum for each pixel. This approach produces elemental maps with a short processing time. We have implemented three kinds of background calculation for the image subtraction. The influence of the irradiation dose and of the energy selecting slit width on the quality of the spectra is investigated. The method is applied to the analysis of some biological specimens (pericellular coat behaviour during adhesion between macrophages and red blood cells and location of calcite microcrystals in dental pulp cells). The Imaging-Spectrum method appears to be suitable for the analysis of large areas.     

Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: Implications for tomography of thick biological sections

A Monte Carlo electron-trajectory calculation has been implemented to assess the optimal detector configuration for scanning transmission electron microscopy (STEM) tomography of thick biological sections. By modeling specimens containing 2 and 3 at% osmium in a carbon matrix, it was found that for 1-μm-thick samples the bright-field (BF) and annular dark-field (ADF) signals give similar contrast and signal-to-noise ratio provided the ADF inner angle and BF outer angle are chosen optimally. Spatial resolution in STEM imaging of thick sections is compromised by multiple elastic scattering which results in a spread of scattering angles and thus a spread in lateral distances of the electrons leaving the bottom surface. However, the simulations reveal that a large fraction of these multiply scattered electrons are excluded from the BF detector, which results in higher spatial resolution in BF than in high-angle ADF images for objects situated towards the bottom of the sample. The calculations imply that STEM electron tomography of thick sections should be performed using a BF rather than an ADF detector. This advantage was verified by recording simultaneous BF and high-angle ADF STEM tomographic tilt series from a stained 600-nm-thick section of C. elegans. It was found that loss of spatial resolution occurred markedly at the bottom surface of the specimen in the ADF STEM but significantly less in the BF STEM tomographic reconstruction. Our results indicate that it might be feasible to use BF STEM tomography to determine the 3D structure of whole eukaryotic microorganisms prepared by freeze-substitution, embedding, and sectioning.     

The glycosomes of trypanosomes: number and distribution as revealed by electron spectroscopic imaging and 3-D reconstruction

Computer-aided 3-D reconstruction of typanosomes from 0·35-μm-thick sections imaged on the Zeiss 902 electron microscope are being used to study the dynamics of cell organization. Segregation of glycolytic enzymes into glycosomes raises questions concerning the distribution and biogenesis of these organelles. Direct counts of glycosomes from Trypanosoma evansi indicate 30–40 per cell and for the closely related T. brucei, 65 per cell. These figures contrast with the estimates of others who have used model-based morphometric methods to obtain a value of 230 per cell.     

Imaging thin and thick sections of biological tissue with the secondary electron detector in a field-emission scanning electron microscope

A field-emission scanning electron microscope (FESEM) equipped with the standard secondary electron (SE) detector was used to image thin (70–90 nm) and thick (1–3 μm) sections of biological materials that were chemically fixed, dehydrated, and embedded in resin. The preparation procedures, as well as subsequent staining of the sections, were identical to those commonly used to prepare thin sections of biological material for observation with the transmission electron microscope (TEM). The results suggested that the heavy metals, namely, osmium, uranium, and lead, that were used for postfixation and staining of the tissue provided an adequate SE signal that enabled imaging of the cells and organelles present in the sections. The FESEM was also used to image sections of tissues that were selectively stained using cytochemical and immunocytochemical techniques. Furthermore, thick sections could also be imaged in the SE mode. Stereo pairs of thick sections were easily recorded and provided images that approached those normally associated with high-voltage TEM.     

Low-energy electron microscopy (LEEM) and mirror electron microscopy (MEM) of biological specimens: Preliminary results with a novel beam separating system

Low-energy electron microscopy (LEEM) and mirror electron microscopy (MEM) utilize a parallel beam of slow-moving electrons backscattered from the specimen surface to form an image. If the electrons strike the surface an LEEM image is produced and if they are turned back just before reaching the surface an MEM image results. The applications thus far have been in surface physics. In the present study, applications of LEEM and MEM in the biological sciences are discussed. The preliminary results demonstrate the feasibility of forming images of uncoated cultured cells and cellular components using electrons in the threshold region (i.e. 0–10 V). The results also constitute a successful test of a novel beam-separating system for LEEM and MEM.     

Zero-loss energy-filtered imaging of frozen-hydrated proteins: model calculations and implications for future developments

Energy-filtered transmission electron microscopes operating in zero-loss mode are used increasingly to study biological material in frozen-hydrated conditions. The contrast enhancement and improved structural resolution obtainable by this method have been studied using Monte-Carlo model calculations for the scattering processes occurring in such samples. Three models representing typical situations have been analysed, each normalized to minimal beam damage. It is shown that for proteins in thin layers of ice an optimal signal-to-noise ratio is achieved in the 80–120-keV electron energy range. For proteins which have to be embedded in thicker ice layers, a considerably higher acceleration voltage is required. In particular, electron energies above 200 keV would be desirable for electron diffraction work on microcrystals.     

Towards sub-A atomic resolution electron diffraction imaging of metallic nanoclusters: a simulation study of experimental parameters and reconstruction algorithms

A simulation study is carried out to elucidate the effects of dynamical scattering, electron beam convergence angle and detection noise on atomic resolution diffraction imaging of small particles and to develop effective reconstruction procedures. Au nanoclusters are used as model because of their strong scattering. The results show that the dynamical effects of electron diffraction place a limit on the size of Au nanoclusters that can be reconstructed from the diffraction intensities with sufficient accuracy. For smaller Au nanoclusters, the simulations show that diffraction patterns recorded under the experimental conditions can be reconstructed using a combination of phase retrieval algorithms. The use of a low-resolution image is shown to be effective for reconstructing diffraction patterns without the central beam. A new algorithm for estimating the object support is proposed.     

A new heavy-metal-containing resin for low-temperature embedding and imaging of unstained sections of biological material

A styrene-based, low viscosity, negative-staining resin has been formulated for low-temperature embedding of unstained biological material. The resin, containing 3 atom% tin, permits sample preparations at 243°K, and provides sufficient contrast with bright field conventional transmission electron microscopy (CTEM) and excellent contrast in scanning transmission electron microscopy (STEM) ratio mode.     

Comparison of single‐particle analysis and electron tomography approaches: an overview

Three‐dimensional structure of a wide range of biological specimens can be computed from images collected by transmission electron microscopy. This information integrated with structural data obtained with other techniques (e.g., X‐ray crystallography) helps structural biologists to understand the function of macromolecular complexes and organelles within cells. In this paper, we compare two three‐dimensional transmission electron microscopy techniques that are becoming more and more related (at the image acquisition level as well as the image processing one): electron tomography and single‐particle analysis. The first one is currently used to elucidate the three‐dimensional structure of cellular components or smaller entire cells, whereas the second one has been traditionally applied to structural studies of macromolecules and macromolecular complexes. Also, we discuss possibilities for their integration with other structural biology techniques for an integrative study of living matter from proteins to whole cells.     

High-angle triple-axis specimen holder for three-dimensional diffraction contrast imaging in transmission electron microscopy

Electron tomography requires a wide angular range of specimen-tilt for a reliable three-dimensional (3D) reconstruction. Although specimen holders are commercially available for tomography, they have several limitations, including tilting capability in only one or two axes at most, e.g. tilt-rotate. For amorphous specimens, the image contrast depends on mass and thickness only and the single-tilt holder is adequate for most tomographic image acquisitions. On the other hand, for crystalline materials where image contrast is strongly dependent on diffraction conditions, current commercially available tomography holders are inadequate, because they lack tilt capability in all three orthogonal axes needed to maintain a constant diffraction condition over the whole tilt range. We have developed a high-angle triple-axis (HATA) tomography specimen holder capable of high-angle tilting for the primary horizontal axis with tilting capability in the other (orthogonal) horizontal and vertical axes. This allows the user to trim the specimen tilt to obtain the desired diffraction condition over the whole tilt range of the tomography series. To demonstrate its capabilities, we have used this triple-axis tomography holder with a dual-axis tilt series (the specimen was rotated by 90° ex-situ between series) to obtain tomographic reconstructions of dislocation arrangements in plastically deformed austenitic steel foils.     

Surface imaging microscopy using an ultramiller for large volume 3D reconstruction of wax- and resin-embedded tissues

Three-dimensional reconstruction of large tissue volumes using histological thin sections poses difficulties because of registration of sections, section distortion, and the possibility of incomplete data set collection due to section loss. We have constructed an integrated surface imaging system that successfully addresses these problems. Embedded tissue is mounted on a high precision XYZ stage and the upper surface is iteratively: (i) stained to provide an effective optical section, (ii) imaged using a digital camera, and (iii) removed with an ultramiller. This approach provides for the reconstruction of high-quality 3D images by inherently preserving image registration, eliminates section distortion, thus removing the need for complex realignment and correction, and also ensures full capture of all image planes. The system has the capacity to acquire images of tissue structure with voxel sizes from 0.5 to 50 mum over dimensions ranging from micrometers to tens of millimeters. The ultramiller enables large samples to be imaged by reliably removing tissue over their full extent. The ability to visualize key features of 3D tissue structure across such a range of scale and resolution will facilitate the development of a greater understanding of the relationship between structure and function. This understanding is essential for better analyses of the structural changes associated with different disease states, and the development of structure-based computer models of biological function.     

Immuno-EM using colloidal metal nanoparticles and electron spectroscopic imaging for co-localization at high spatial resolution

Multiple‐labelling immuno‐EM is a powerful tool for localizing and co‐localizing different antigens simultaneously in cells and tissues at high spatial resolution. Commonly used labels for this purpose are differently sized gold spheres. A comparison of results obtained with differently sized markers is often difficult, because the diameters of markers influence labelling efficiency. In the current study, we investigate a method for high‐resolution multiple‐labelling immuno‐EM, using equally sized colloidal markers made of different metals. Energy filtering transmission electron microscopy is used to differentiate particles based on elemental composition. The labels consist of colloidal gold, palladium and platinum‐core gold‐shell particles of approximately 6 nm in diameter, which are conjugated to different primary antibodies. Applicability of the electron spectroscopic imaging, methodology is demonstrated by labelling of actin, α‐actinin and myosin on ultra‐thin cryosections of skeletal muscle tissue.     

A method for the characterization of surface-modified asbestos fibres by electron energy-loss spectroscopy and electron spectroscopic imaging

A method for the characterization of surface-treated asbestos fibres with electron microscopy is presented. Electron spectroscopic imaging (ESI) of organosilane-treated chrysotile asbestos fibres has been carried out. Initially, the region below the carbon edge was inspected in ESI mode for its effectiveness as a background correction. Elemental mapping was performed on standard untreated fibres to take into account non-characteristic signals from extrapolation errors and camera artefacts. The highest resulting pixel value that results from non-characteristic signals was used as a threshold for further background correction in the net images. Samples for electron energy-loss spectroscopy were prepared in two different ways, either by gluing on grids, or by using perforated carbon foils. The results show that the use of a conducting carbon film is necessary for the analysis of such electrically insulating asbestos fibres. Focusing of the electron beam on the individual fibres results in a thermal effect promoting the evaporation of the organosilane reaction products.     

KSpaceNavigator as a tool for computer-assisted sample tilting in high-resolution imaging, tomography and defect analysis

This article describes a novel software tool, the KSpaceNavigator, which combines sample stage and crystallographic coordinates in a control sphere. It also provides simulated kinematic diffraction spot patterns, Kikuchi line patterns and a unit cell view in real time, thus allowing intuitive and transparent navigation in reciprocal space. By the overlay of experimental data with the simulations and some interactive alignment algorithms, zone axis orientations of the sample can be accessed quickly and with great ease. The software can be configured to work with any double-tilt or tilt–rotation stage and overcomes nonlinearities in existing goniometers by lookup tables. A subroutine for matching the polyhedral shape of a nanoparticle assists with 3D analysis and modeling. The new possibilities are demonstrated with the case of a faceted BaTiO₃ nanoparticle, which is tilted into three low-index zone axes using the piezo-controlled TEAM stage, and with a multiply twinned tetrahedral Ge precipitate in Al, which is tilted into four equivalent zone axes using a conventional double-tilt stage. Applications to other experimental scenarios are also outlined.     

A new sample preparation method for biological soft X-ray microscopy: nitrogen-based contrast and radiation tolerance properties of glycol methacrylate-embedded and sectioned tissue

We describe the preparation of a biological tissue for imaging in a transmission soft X-ray microscope. Sections of exocrine pancreas embedded in glycol methacrylate polymer, an embedding medium widely used in visible light and electron microscopy, were examined. Contrast was based primarily on the nitrogen content of the tissue, and dual-wavelength imaging at the nitrogen K-shell absorption edge was used to map the distribution and provide quantitative densitometry of both the protein and embedding matrix components of the sample. The measurements were calibrated by obtaining the absorption spectrum of protein near the nitrogen edge. The contrast was consistent and reproducible, making possible the first large-scale X-ray microscopic study on sections of plastic-embedded soft tissue. At radiation doses of up to 10⁸ Gray, much more than required for routine imaging, no distortion and little mass loss were observed. This sample preparation method should permit routine imaging of tissues in X-ray microscopes, previously a difficult task, as well as multimodal imaging (using visible light, X-ray, electron, and scanned probe microscopies) on the same sample.