Scanning transmission ion micro-tomography (STIM-T) of biological specimens

Computed tomography (CT) was applied to sets of Scanning Transmission Ion Microscopy (STIM) projections recorded at the LIPSION ion beam laboratory (Leipzig) in order to visualize the 3D-mass distribution in several specimens. Examples for a test structure (copper grid) and for biological specimens (cartilage cells, cygospore) are shown. Scanning Transmission Micro-Tomography (STIM-T) at a resolution of 260 nm was demonstrated for the first time. Sub-micron features of the Cu-grid specimen were verified by scanning electron microscopy. The ion energy loss measured during a STIM-T experiment is related to the mass density of the specimen. Typically, biological specimens can be analysed without staining. Only shock freezing and freeze-drying is required to preserve the ultra-structure of the specimen. The radiation damage to the specimen during the experiment can be neglected. This is an advantage compared to other techniques like X-ray micro-tomography. At present, the spatial resolution is limited by beam position fluctuations and specimen vibrations.     

Contrast and resolution from biological objects examined in the electron microscope with particular reference to negatively stained specimens

For the practical biologist applying electron microscopy to the study of biological macromolecules, there are serious problems in obtaining high resolution images showing detail below 2.5–3.0 nm. The limitation in resolution from biological specimens can be attributed to support film thickness and granularity, specimen preparation, irradiation damage, focusing effects and possible contamination in the electron beam. Specimens possessing repeating features can be analysed and averaged by optical diffraction and image reconstruction methods which offer some improvement to the signal to noise ratio. The above problems, with particular reference to irradiation damage, still impose the basic limitation for high resolution applications. When considered together they offer formidable difficulties in practical terms in attempting to make full use of the potential resolving power of modern electron microscopes.     

Instrumental requirements for high resolution imaging

The resolution of modern transmission electron microscopes reaches the physical limits imposed by lens aberrations and energy width. One of the many conditions to be fulfilled, the alignment of illuminating and imaging beam onto the coma-free objective axis, is particularly discussed here since axial coma cannot be detected by the usual resolution-checking methods. Space consumption of specimen stages prevents the full utilization of the magnetic saturation limit only in the 100 keV range. With higher energies, this handicap is obviated, and some additional advantages can be gained which promote material investigations at atomic resolution, and which are presently utilized in instrumental research projects. High resolution with biological specimens has up to now been unsuccessful because of radiation damage. Optimum utilization of all electrons scattered at the specimen must thus be given priority over optical resolution. Important instrumental requirements are minimum exposure beam control, imaging modes with high collection efficiency, and recording devices with high detection quantum efficiency connected on-line to image processors. A remarkable decrease in beam sensitivity of organic crystals, by more than one order, has been found by cooling the specimen down to 4 K which, by the use of superconducting lenses, can be combined with both ultra high vacuum and the stability requirements for high resolution. Yet up to now, such protection has not been achieved with He cryostates in conventional lenses, perhaps because a temperature increase even of only a few degree K is harmful. Purely magnetic imaging energy filters are about to be developed to a high optical quality but have been employed so far in only a few high resolution instruments. Such filters allow removal of the inelastic background and thus improvement of contrast of images of low-Z specimens, particularly in the dark field mode. Finally, some ‘non-conventional’ projects have made progress. Correction of spherical and chromatic aberration by multipole lenses offers a chance to improve remarkably the resolution in the 100 keV range, to extend the bandwidth of phase contrast transfer and to obtain highly resolved information about inelastic images when an energy filter is also applied. Electron holography provides possibly useful large area phase contrast, particularly if the electron energy is decreased, which may be of great benefit in investigations of unstained specimens.     

Parallel recording of electron energy loss spectra

Two silicon photo diode array devices were tested as parallel recording detectors for electron energy loss spectrometry (EELS). The direct bombardment of a Reticon photodiode array detector with high energy electrons (80 keV) causes an irreversible increase in diode dark current. The dark current saturates the detector amplifier after a dose of 10^?6 C/diode making it unsuitable for EELS. A scintillator coupled SIT vidicon is sensitive enough to count two high energy electrons with a spatial resolution of 100 μm, corresponding to 5 eV energy resolution with the electron optical system described. The large pixel-to-pixel gain variation inherent in the scintillator and vidicon can be reduced by averaging the spectrum over a large area of the target perpendicular to the dispersion direction. The L-edge of calcium for a 4 × 10^?3 weight fraction concentration biological specimen is observable in a 40 s parallel recorded spectrum. The minimum detectable concentration of calcium is estimated tobe ten times better for EELS than EDS X-ray analysis.     

Use of permanent marker to deposit a protection layer against FIB damage in TEM specimen preparation

Permanent marker deposition (PMD), which creates permanent writing on an object with a permanent marker, was investigated as a method to deposit a protection layer against focused ion beam damage. PMD is a simple, fast and cheap process. Further, PMD is excellent in filling in narrow and deep trenches, enabling damage‐free observation of high aspect ratio structures with atomic resolution in transmission electron microscopy (TEM). The microstructure, composition, gap filling ability and planarization of the PMD layer were studied using dual beam focused ion beam, transmission electron microscopy, energy dispersive X‐ray spectroscopy and electron energy loss spectroscopy. It was found that a PMD layer is basically an amorphous carbon structure, and that such a layer should be at least 65 nm thick to protect a surface against 30 keV focused ion beam damage. We suggest that such a PMD layer can be an excellent protection layer to maintain a pristine sample structure against focused ion beam damage during transmission electron microscopy specimen preparation.     

STEM tomography for thick biological specimens

Scanning transmission electron microscopy (STEM) tomography was applied to biological specimens such as yeast cells, HEK293 cells and primary culture neurons. These cells, which were embedded in a resin, were cut into 1-microm-thick sections. STEM tomography offers several important advantages including: (1) it is effective even for thick specimens, (2) 'dynamic focusing', (3) ease of using an annular dark field (ADF) mode and (4) linear contrasts. It has become evident that STEM tomography offers significant advantages for the observation of thick specimens. By employing STEM tomography, even a 1-microm-thick specimen (which is difficult to observe by conventional transmission electron microscopy (TEM)) was successfully analyzed in three dimensions. The specimen was tilted up to 73 degrees during data acquisition. At a large tilt angle, the specimen thicknesses increase dramatically. In order to observe such thick specimens, we introduced a special small condenser aperture that reduces the collection angle of the STEM probe. The specimen damage caused by the convergent electron beam was expected to be the most serious problem; however, the damage in STEM was actually smaller than that in TEM. In this study, the irradiation damage caused by TEM- and STEM-tomography in biological specimens was quantitatively compared.     

Very low energy microscopy in commercial SEMs

Minimum necessary adaptations are described that are sufficient for obtaining very low energy electron micrographs (VLEEMs) from commercially available routine scanning electron micrographs (SEMs) with the electrons accelerated to an energy of the order of tens of keV. A cathode lens inserted into the specimen chamber enables one to decelerate electrons in front of the specimen surface to a desired low landing energy, which can be freely varied even down to zero. When a potential slightly more negative than the accelerating voltage is applied, a scanning mirror electron microscopy mode can be effected. The achievable point resolution at very low energies proves to be not too dependent on the objective lens parameters, so that the physical limit of aberrations of the homogeneous field of the cathode lens is nearly attainable. The detection efficiency for the standard Everhart-Thornley secondary electron detector is discussed, and results for the routine Tesla BS 340 SEM are presented.     

Image contrast in high-resolution electron microscopy of biological macromolecules: TMV in ice.

It is shown that the contrast in high-resolution electron micrographs of biological macromolecules, illustrated by a study of TMV in ice, falls considerably below the level which should theoretically be attained. The factors which contribute to the low contrast include radiation damage, inelastic scattering, specimen movement and charging. Future progress depends on improved understanding of their contributions and relative importance. Contrast is defined as the amplitude of a particular Fourier component extracted from an image in comparison to that expected by extrapolation from separate electron or X-ray diffraction measurements. The fall in contrast gets worse with increased resolution and is particularly serious at 10 A and beyond for specimens embedded in vitreous ice, a method of specimen preparation which is otherwise particularly desirable because of the expectation that the embedded molecules should be well preserved in a near-native environment. This low contrast at high resolution is the principal limitation to atomic-resolution structure determination by electron microscopy. In spite of good progress in the direction of better images, it remains a major problem which prevents electron microscopy from becoming a simple and rapid method for biological atomic structure determination.     

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.     

Image Contrast And Localized Signal Selection Techniques

A survey is made of a number of the localized signal selection methods and related techniques which may be used to improve the electron microscope image contrast from small regions of material and thereby bring the specimen resolution actually achieved somewhat closer to the electron-optical resolution of present-day instruments. Geometrical and stereo methods are discussed, as well as weak-beam and other coherent elastic scattering methods. Localization effects in inelastic scattering and the image contrast in energy loss electrons are examined in greater detail.     

Unconventional immuno double labelling by energy filtered transmission electron microscopy

A new method of immuno double labelling of biological specimens with a very high spatial resolution is presented. The advantage over conventional techniques is the possibility of using two very small labels leading to higher labelling efficiency, better penetration into the specimen and reduced steric hindrance between labels at closely spaced sites. The two labels are distinguished by their electron energy loss spectra using principal component analysis and then identified by comparison with an external standard using discriminant function analysis. The method is tested on samples of insect flight muscle labelled with 8 nm colloidal gold and silver and the statistical reliability of the classification is assessed. Extensions of the method are suggested and its potential for biological research is discussed.     

Top-bottom effect in energy-selecting transmission electron microscopy

Energy-selecting TEM can avoid the chromatic error of large specimen thicknesses when selecting an energy window at the most probable energy loss. The resolution is limited by the spatial beam broadening for structures at the top (electron entrance) of the specimen layer. A test experiment with polystyrene spheres of 1.1 μm in diameter shows a blurring of 8 nm when imaging with ΔE = 250 eV and E = 80 keV.     

Observation of dislocations and microplasma sites in semiconductors by direct correlations of STEBIC,STEM and ELS

A high voltage electron microscope, equipped with scanning transmission (STEM) attachment, electron beam induced conductivity (EBIC) facilities, and electron energy loss spectrometer (ELS), has been used to investigate semiconductor devices. The capability of STEM to produce, simultaneously or sequentially, conductive and transmission images of the same specimen region, which can also be ELS analysed, is exploited in order to establish direct and unambiguous correlations between EBIC and STEM images of defective regions (dislocations and microplasma sites) in silicon devices. The results obtained are discussed in terms of correlations, resolution, contrast, and radiation damage; in addition, a comparison is made between this method and the other correlation methods based on EBIC/SEM (scanning electron microscope) and TEM (transmission electron microscope).     

High spatial resolution analysis using parallel detection eels

The application of parallel detection electron energy loss spectroscopy to the characterization of small particles or interfaces is demonstrated. Data are presented that show variations of low energy loss plasmons, Al L23 edge near edge fine structure, and oxygen concentration with spatial resolution better than 10 nm. The use of this technique for chemical and electronic structure measurements from very small specimen volumes is discussed.     

Quantification and thickness correction of EFTEM phosphorus maps

We describe a method for correcting plural inelastic scattering effects in elemental maps that are acquired in the energy filtering transmission electron microscope (EFTEM) using just two energy windows, one above and one below a core edge in the electron energy loss spectrum (EELS). The technique is demonstrated for mapping low concentrations of phosphorus in biological samples. First, the single-scattering EELS distributions are obtained from specimens of pure carbon and plastic embedding material. Then, spectra are calculated for different specimen thicknesses t, expressed in units of the inelastic mean free path lambda. In this way, standard curves are generated for the ratio k0 of post-edge to pre-edge intensities at the phosphorus L2,3 excitation energy, as a function of relative specimen thickness t/lambda. Thickness effects in a two-window phosphorus map are corrected by successive acquisition of zero-loss and unfiltered images, from which it is possible to determine a t/lambda image and hence a background k0-ratio image. Knowledge of the thickness-dependent k0-ratio at each pixel thus enables a more accurate determination of the phosphorus distribution in the specimen. Systematic and statistical errors are calculated as a function of specimen thickness, and elemental maps are quantified in terms of the number of phosphorus atoms per pixel. Further analysis of the k0-curve shows that the EFTEM can be used to obtain reliable two-window phosphorus maps from specimens that are considerably thicker than previously possible.     

Advances in EELS spectroscopy by using new detector and new specimen preparation technologies

First results obtained with a Gatan UHV Enfina system, which was attached to a VG HB 501 UX dedicated STEM, are reported. The Enfina system is based on a CCD detector and offers, compared to the previously used photodiode array, a narrower point‐spread function, higher sensitivity, and faster read‐out capabilities. These improvements are demonstrated with electron energy‐loss measurements on various oxides, such as Al₂O₃, TiO₂ and SrTiO₃. It is shown that a better energy resolution is achieved and that acquisition of high‐energy absorption edges with a reasonable signal‐to‐noise ratio becomes possible. Furthermore, we report on the influence of the TEM specimen quality on the energy‐loss spectra. Thin amorphous layers at the specimen surfaces, which are induced by ion‐milling processes, can modify specific electron energy‐loss near‐edge structure features. We found that for the investigated ceramics the use of low‐energy ion‐milling systems is highly recommended, since the loss of energy‐loss near‐edge structure details by the presence of the amorphous layers is considerably reduced. This is especially true for very thin specimens.     

A simple liquid-He-cooled specimen stage for an ultra-high resolution transmission electron microscope

A simple top-entry specimen holder for an ultra-high resolution transmission electron microscope which has demonstrated 2.5 Å point-to-point resolution at 30 K is described. The stage has proved useful in studying low-temperature solid phases and phase transformations and is expected to be effective in reducing radiation damage for some organic specimens.     

Rationale for the application of thin,continuous metal films in high magnification electron microscopy

Various metal films of different thicknesses were deposited on to a particle test specimen and their effects on topographic contrast generation and specimen preservation were determined. Tobacco mosaic virus adsorbed on to thin carbon supports or silicon chips was imaged in TEM or high resolution SE-I SEM at a magnification of 350,000×. Tantalum films of 1–2 nm (average mass) thickness produced best contrasts and prevented volume loss of the particles from electron beam damage. Excessively thick films of 5–10 nm thickness blanketed fine structures and caused severe volume losses. Discontinuous 2 nm thick films of gold or platinum decorated the surfaces, caused a loss in topographic contrasts and induced very high volume losses. Thin continuous metal films were necessary to generate high topographic contrast and to prevent volume loss from beam damage by providing sufficient mechanical stability for small topographic features and increased thermal conductivity of the specimen surface.     

Optimal strategies for imaging thick biological specimens: exit wavefront reconstruction and energy-filtered imaging

In transmission electron microscopy (TEM) of thick biological specimens, the relationship between the recorded image intensities and the projected specimen mass density is distorted by incoherent electron–specimen interactions and aberrations of the objective lens. It is highly desirable to develop a strategy for maximizing and extracting the coherent image component, thereby allowing the projected specimen mass density to be directly related to image intensities. For this purpose, we previously used exit wavefront reconstruction to understand the nature of image formation for thick biological specimens in conventional TEM. Because electron energy-loss filtered imaging allows the contributions of inelastically scattered electrons to be removed, it is potentially advantageous for imaging thick, biological samples. In this paper, exit wavefront reconstruction is used to quantitatively analyse the imaging properties of an energy-filtered microscope and to assess its utility for thick-section microscopy. We found that for imaging thick biological specimens (> 0.5 μm) at 200 keV, only elastically scattered electrons contribute to the coherent image component. Surprisingly little coherent transfer was seen when using energy-filtering at the most probable energy loss (in this case at the first plasmon energy-loss peak). Furthermore, the use of zero-loss filtering in combination with exit wavefront reconstruction is considerably more effective at removing the effects of multiple elastic and inelastic scattering and microscope objective lens aberrations than either technique by itself. Optimization of the zero-loss signal requires operation at intermediate to high primary voltages (> 200 keV). These results have important implications for the accurate recording of images of thick biological specimens as, for instance, in electron microscope tomography.     

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.