Minimization of dose as a criterion for the selection of imaging modes in electron microscopy of amorphous specimens.

A fundamental limitation in electron microscopy of organic specimens is radiation damage by the electron beam. To minimize damage it is necessary to have maximum information collection for a given dose. Various modes of operation of conventional and scanning transmission microscopes are compared with respect to their ability to detect small changes in specimen thickness or density with a given signal to noise ratio. Incoherent imaging is assumed, and this is expected to apply to amorphous specimens under a variety of microscope conditions. For either very thin or very thick specimens, the scanning transmission microscope is found to require nearly 10 times less dose than a conventional microscope for the same signal to noise ratio in the image. For specimens of intermediate thickness, scanning and conventional transmission electron microscopes are roughly equivalent.     

Mechanisms of decoherence in electron microscopy

The understanding and where possible the minimisation of decoherence mechanisms in electron microscopy were first studied in plasmon loss, diffraction contrast images but are of even more acute relevance in high resolution TEM phase contrast imaging and electron holography. With the development of phase retrieval techniques they merit further attention particularly when their effect cannot be eliminated by currently available energy filters. The roles of electronic excitation, thermal diffuse scattering, transition radiation and bremsstrahlung are examined here not only in the specimen but also in the electron optical column. Terahertz-range aloof beam electronic excitation appears to account satisfactorily for recent observations of decoherence in electron holography. An apparent low frequency divergence can emerge for the calculated classical bremsstrahlung event probability but can be ignored for photon wavelengths exceeding the required coherence distance or path lengths in the equipment. Most bremsstrahlung event probabilities are negligibly important except possibly in large-angle bending magnets or mandolin systems. A more reliable procedure for subtracting thermal diffuse scattering from diffraction pattern intensities is proposed.     

Fading and broadening of electron diffraction spot from beam-damaged multiple monolayer films

In contrast to the increase in the extinction dose for thick specimens, observed broadening rates of diffraction spots from behenic acid multiple monolayers were independent of specimen thickness. This result leads to the conclusion that specimens are always decaying at the same rate although the periodicity of crystals still remains in thick specimens. The conclusion is interpreted as being the result of the radiation damage mechanism based on longitudinal motions of long chain molecules. For the evaluation of beam damage effect the broadening rate and the extinction dose should be used as indicator for the radiation sensitivity of crystals and for the possibility of observing diffraction patterns, respectively.     

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.     

Morphology visualization of irregular shape bacteria by electron holography and tomography

In the current work, irregular morphology of Staphylococcus aureus bacteria has been visualized by phase retrieval employing off‐axis electron holography (EH) and 3D reconstruction electron tomography using high‐angle annular dark field scanning transmission electron microscopy (HAADF‐STEM). Bacteria interacting with gold nanoparticles (AuNP) acquired a shrunken or irregular shape due to air dehydration processing. STEM imaging shows the attachment of AuNP on the surface of cells and suggests an irregular 3D morphology of the specimen. The phase reconstruction demonstrates that off‐axis electron holography can reveal with a single hologram the morphology of the specimen and the distribution of the functionalized AuNPs. In addition, EH reduces significantly the acquisition time and the cumulative radiation damage (in three orders of magnitude) over biological samples in comparison with multiple tilted electron expositions intrinsic to electron tomography, as well as the processing time and the reconstruction artifacts that may arise during tomogram reconstruction.     

Digital in-line X-ray holography with zone plates

Single pulse imaging with radiation provided by free-electron laser sources is a promising approach towards X-ray microscopy, which is expected to provide high resolution images of biological samples unaffected by radiation damage. One fully coherent imaging technique for this purpose is digital in-line holography. Key to its successful application is the creation of X-ray point sources with high photon flux. In this study we applied zone plates to create such point sources with synchrotron radiation provided by the storage ring BESSY II. The obtained, divergent light cone is applied to holographic microscopy of biological objects such as critical point dried Navicula perminuta diatoms and human cells using photons with an energy of 250 eV. Compared to conventional experiments employing pinholes, exposure times are reduced by two orders of magnitude.     

临床X射线相衬成像研究进展

X射线相衬成像在提高人体软组织成像的衬度分辨率及空间分辨率研究中具有潜在优势,是一项有着广阔发展前景的技术。它利用空间相干X射线投过物体后携带的相位信息进行成像,在临床上适用于软组织物体,可以减少吸收剂量,进而减轻病人的辐射损伤。本文详述了当今几种典型的X射线相衬成像方法,包括X射线干涉相衬,衍射增强相衬以及类同轴相衬的成像原理以及发展历程。通过对比表明了几种成像方法的优缺点。最后对临床X射线相衬成像有待解决的问题作了分析。     

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.     

Dopant profiling of focused ion beam milled semiconductors using off-axis electron holography; reducing artifacts,extending detection limits and reducing the effects of gallium implantation

Focused ion beam (FIB) milling is one of the few specimen preparation techniques that can be used to prepare parallel-sided specimens with nm-scale site specificity for examination using off-axis electron holography in the transmission electron microscope (TEM). However, FIB milling results in the implantation of Ga, the formation of amorphous surface layers and the introduction of defects deep into the specimens. Here we show that these effects can be reduced by lowering the operating voltage of the FIB and by annealing the specimens at low temperature. We also show that the electrically inactive thickness is dependent on both the operating voltage and type of ion used during FIB milling.     

Optimized reflection imaging in laser confocal microscopy and its application to neurobiology: Modificationsa to the biorad MRC-500

Reflection images of biological specimens recorded using laser-scanned confocal microscopes are frequently degraded by low image contrast, poor signal to noise, and the inability to image deeper in the specimen than 10–20 μm. Artifactual internal reflections often are a source of these limitations, but they can be reduced or eliminated by the use of polarization components. Designs for the incorporation and optimum use of these components in the BioRad MRC-500 are presented. The effect of the internal reflections was reduced by optimum rotational alignment of both a quarterwave plate and an analyzer. Absorption of incident and reflected light by both the stained cells and the background tissue of the specimen also seriously degrades image signal to noise, and is a function of specimen preparation and the wavelength of light used. The red line of a helium-neon laser was not as readily absorbed as the blue and green lines of an argon-ion laser when imaging neurobiological specimens contrasted with either peroxidase/diaminobenzidine or Golgi staining. Specimens many times thicker were imaged with red laser light and with superior image quality compared with blue or green laser light.     

Visualizing soft tissue in the mammalian cochlea with coherent hard X-rays

This paper concerns an important aspect of current developments in medical and biological imaging: the possibility for imaging soft tissue at relatively high resolution in the micrometer range or better, without tedious and/or entirely destructive sample preparation. Structures with low absorption contrast have been visualized using in-line phase contrast imaging. The experiments have been performed at the Advanced Photon Source, a third generation source of synchrotron radiation. The source provides highly coherent X-ray radiation with high photon flux (>10(14) photons/s) at high photon energies (5-70 keV). Thick gerbil cochlear slices have been imaged and were compared with those obtained by light microscopy. Furthermore, intact gerbil cochleae have been imaged to identify the soft tissue structures involved in the hearing process. The present experimental approach was essential for visualizing the inner ear structures involved in the hearing process in an intact cochlea.     

Improving image quality by zero-loss energy filtering: quantitative assessment by means of image cross-correlation

Fourier ring correlation and root-mean-square contrast of pairs of images, taken under identical conditions, were used as criteria of image quality for comparing unfiltered with zero-loss energy-filtered imaging using a TEM equipped with a post-column energy filter. For three different specimens (amorphous carbon film, macromolecules in light negative stain, virus particles in deep negative stain) the dependence of these quantities on electron dose, specimen thickness and defocus was investigated. A model, based on simple assumptions, was used to describe quantitatively their dependence on electron dose and specimen thickness. It was found that energy filtering is most advantageous for low-dose imaging and small defocus values. The gain due to energy filtering strongly increases with specimen thickness, whereby the dependence is linear for light scattering elements. For thick specimens, the gain by energy filtering is more pronounced in the resolution range between 4 and 2 nm than for lower spatial frequencies.     

Computed tomography of cryogenic biological specimens based on X-ray microscopic images

Soft X-ray microscopy employs the photoelectric absorption contrast between water and protein in the 2.34-4.38 nm wavelength region to visualize protein structures down to 30 nm size without any staining methods. Due to the large depth of focus of the Fresnel zone plates used as X-ray objectives, computed tomography based on the X-ray microscopic images can be used to reconstruct the local linear absorption coefficient inside the three-dimensional specimen volume. High-resolution X-ray images require a high specimen radiation dose, and a series of images taken at different viewing angles is needed for computed tomography. Therefore, cryo microscopy is necessary to preserve the structural integrity of hydrated biological specimens during image acquisition. The cryo transmission X-ray microscope at the electron storage ring BESSY I (Berlin) was used to obtain a tilt series of images of the frozen-hydrated green alga Chlamydomonas reinhardtii. The living specimens were inserted into borosilicate glass capillaries and, in this first experiment, rapidly cooled by plunging into liquid nitrogen. The capillary specimen holders allow image acquisition over the full angular range of 180 degrees. The reconstruction shows for the first time details down to 60 nm size inside a frozen-hydrated biological specimen and conveys a clear impression of the internal structures. This technique is expected to be applicable to a wide range of biological specimens, such as the cell nucleus. It offers the possibility of imaging the three-dimensional structure of hydrated biological specimens close to their natural living state.     

Quantitative amplitude and phase contrast imaging in a scanning transmission X-ray microscope

Phase contrast in X-ray imaging provides lower radiation dose, and dramatically higher contrast at multi-keV photon energies when compared with absorption contrast. We describe here the use of a segmented detector in a scanning transmission X-ray microscope to collect partially coherent bright field images. We have adapted a Fourier filter reconstruction technique developed by McCallum, Landauer and Rodenburg to retrieve separate, quantitative maps of specimen phase shift and absorption. This is demonstrated in the imaging of a germanium test pattern using 525eV soft X-rays.     

Electron diffraction and diffraction contrast imaging of thin organic films

The applications of electron diffraction and diffraction contrast electron microscopy with which to study the structure and dynamics of organic thin films are discussed. The techniques of making thin film deposits on substrates and of forming free-standing thin films over holes on the substrate are described. Selected area electron diffraction and diffraction contrast imaging techniques for thin film studies are elaborated, and examples are given. Methods to reduce radiation damage and environmental protection of the thin film specimen are outlined. The interpretation of electron diffraction and imaging data is given for three cases: (1) The effects of film tilting and molecular tilting (with respect to the film plane) are examined. (2) The detection of phase transition is illustrated. (3) The use of labels to mark film domains is shown together with the measurement of dynamic movement.     

Off-axis electron holography of electrostatic potentials in unbiased and reverse biased focused ion beam milled semiconductor devices

Off‐axis electron holography in the transmission electron microscope (TEM) is used to measure two‐dimensional electrostatic potentials in both unbiased and reverse biased silicon specimens that each contain a single p–n junction. All the specimens are prepared for examination in the TEM using focused ion beam (FIB) milling. The in situ electrical biasing experiments make use of a novel specimen geometry, which is based on a combination of cleaving and FIB milling. The design and construction of an electrical biasing holder are described, and the effects of TEM specimen preparation on the electrostatic potential in the specimen, as well as on fringing fields beyond the specimen surface, are assessed.     

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.     

Specimen movement in electron-irradiated paraffin crystals — A model for initial beam damage

The importance of possible causes for blurring due to local specimen movement during high-resolution electron microscope imaging experiments on monolamellar paraffin crystals is evaluated in terms of existing data for the beam damage of such materials. For specimens held at liquid helium temperatures, neither unit cell expansion, nor molecular structural change, nor production of large defects are likely causes for this motion. Rather, electron diffraction results indicate that observed changes in local image contrast are due to specimen flattening during the initial damage process, probably involving a longitudinal molecular slippage similar to the motions responsible for production of screw dislocations.     

Image contrast of dielectric specimens in transmission mode near-field scanning optical microscopy: imaging properties and tip artefacts

Near-field scanning optical microscopy (NSOM) is a scanned probe technique utilizing a subwavelength-sized light source for high-resolution imaging of surfaces. Although NSOM has the potential to exploit and extend the experimental utility of the modern light microscope, the interpretation of image contrast is not straightforward. In near-field microscopy the illumination intensity of the source (probe) is not a constant value, rather it is a function of the probe–sample electronic environment. A number of dielectric specimens have been studied by NSOM to elucidate the contrast role of specimen type, topography and crystallinity; a summary of metallic specimen observations is presented for comparative purposes. Near-field image contrast is found to be a result of lateral changes in optical density and edge scattering for specimens with little sample topography. For surfaces with considerable topography the contributions of topographic (Z) axis contrast to lateral (X,Y) changes in optical density have been characterized. Selected near-field probes have also been shown to exhibit a variety of unusual contrast artefacts. Thorough study of polarization contrast, optical edge (scattering) contrast, as well as molecular orientation in crystalline specimens, can be used to distinguish lateral contrast from topographic components. In a few cases Fourier filtering can be successfully applied to separate the topographic and lateral contrast components.