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

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-microm-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.

Electron holography of biological samples

In this paper, we summarise the development of off-axis electron holography on biological samples starting in 1986 with the first results on ferritin from the group of Tonomura. In the middle of the 1990s strong interest was evoked, but then stagnation took place because the results obtained at that stage did not reach the contrast and the resolution achieved by conventional electron microscopy. To date, there exist only a few ( approximately 12) publications on electron holography of biological objects, thus this topic is quite small and concise. The reason for this could be that holography is mostly established in materials science by physicists. Therefore, applications for off-axis holography were powerfully pushed forward in the area of imaging, e.g. electric or magnetic micro- and nanofields. Unstained biological systems investigated by means of off-axis electron holography up to now are ferritin, tobacco mosaic virus, a bacterial flagellum, T5 bacteriophage virus, hexagonal packed intermediate layer of bacteria and the Semliki Forest virus. New results of the authors on collagen fibres and surface layer of bacteria, the so-called S-layer 2D crystal lattice are presented in this review. For the sake of completeness, we will shortly discuss in-line holography of biological samples and off-axis holography of materials related to biological systems, such as biomaterial composites or magnetotactic bacteria.

Electron cryotomography

Electron cryotomography is an emerging technique that allows the structures of unique biological objects such as individual macromolecules, viruses, and even small whole cells to be reconstructed in their near-native states in three dimensions (3-D) to an approximate 5-nm resolution. The required instrumentation, sample preparation and limitations, data collection, typical results, and future prospects are summarized briefly.

Use of energy filtering transmission electron microscopy for image generation and element analysis in plant organisms

Energy filtering TEM (EFTEM) with modern spectrometers and software offers new possibilities for element analysis and image generation in plant cells. In the present review, applications of EFTEM in plant physiology, such as identification of light elements and ion transport, analyses of natural cell incrustations, determination of element exchange between fungi and rootlets during mycorrhiza development, heavy metal storage and detoxification, and employment in plant physiological experiments are summarized. In addition, it is demonstrated that EFTEM can be successfully used in more practical approaches, for example, in phytoremediation, food and wood industry, and agriculture. Preparation methods for plant material as prerequisites for EFTEM analysis are compared with respect to their suitability and technical problems are discussed.

Analysis of element accumulation in cell wall attached and intracellular particles of snow algae by EELS and ESI

Snow algae frequently occur in alpine and polar permanent snow ecosystems and have developed adaptations to their harsh environment, where extreme temperature regimes high irradiation and low nutrient levels prevail. They live in a unique microhabitat, namely the liquid water between snow crystals. The predominant form appears as 'red snow' and in polar environment also 'green snow' frequently occurs. Light microscopy showed that most cells are densely covered by non-biotic particles of so far unknown composition. As snow normally contains very low amounts of nutrients, introduced mainly airborne like dust and precipitation, the inorganic particles at the surface of the snow algae may be important for their survival. By using electron energy loss spectroscopy (EELS) and electron spectroscopic imaging (ESI), we investigated element distribution in ultrathin sections of snow algae from different polar (Svalbard, 5 m a.s.l., 79 degrees N and maritime Antarctic, King George Island, 10 m a.s.l., 62 degrees S) and alpine habitats (2400-3100 m a.s.l. Tyrol) for the present study. It turned out that the main elements of the cell wall attached particles are Si, Al, Fe and O independently from the origin of the snow algae. Interestingly, the same elements were also found in vacuolar compartments inside the cells. These vacuoles contain electron dense granules or crystals and are frequently found to be connected to the cortical cytoplasm. This finding suggests an uptake mechanism of the respective elements by pinocytosis. Co-transport of toxic aluminium together with silicon may be unavoidable as the inorganic nutrient uptake of the snow algae is limited to the thin water layer between the ice crystals. However, formation of insoluble aluminium silicates may serve as detoxification mechanism.

Lessons from tomographic studies of the mammalian Golgi

Basic structure studies of the biosynthetic machinery of the cell by electron microscopy (EM) have underpinned much of our fundamental knowledge in the areas of molecular cell biology and membrane traffic. Driven by our collective desire to understand how changes in the complex and dynamic structure of this enigmatic organelle relate to its pivotal roles in the cell, the comparatively high-resolution glimpses of the Golgi and other compartments of the secretory pathway offered to us through EM have helped to inspire the development and application of some of our most informative, complimentary (molecular, biochemical and genetic) approaches. Even so, no one has yet even come close to relating the basic molecular mechanisms of transport, through and from the Golgi, to its ultrastructure, to everybody's satisfaction. Over the past decade, EM tomography has afforded new insights into structure-function relationships of the Golgi and provoked a re-evaluation of older paradigms. By providing a set of tools for structurally dissecting cells at high-resolution in three-dimensions (3D), EM tomography has emerged as a method for studying molecular cell biology in situ. As we move rapidly toward the establishment of molecular atlases of organelles through advances in proteomics and genomics, tomographic studies of the Golgi offer the tantalizing possibility that one day, we will be able to map the spatio-temporal coordinates of Golgi-related proteins and lipids accurately in the context of 4D cellular space.

Effective phase correction function for high-resolution exit wave reconstruction by a three-dimensional Fourier filtering method

The phase correction function used in the three-dimensional Fourier filtering method (3D-FFM) for compensating lens aberrations was investigated to reconstruct a high-resolution exit wave of a sample. An appropriate function, which hardly suffered from imperfect illumination conditions, was determined by comparing two types of phase correction functions with numerical calculations and experiments using through-focus images of an amorphous thin film and a [110]-oriented Si single crystal taken under tilted illumination or partially coherent illumination. Theoretical calculations indicated that a function in terms of w (an axial Fourier component), available uniquely in the 3D Fourier space, compensated for the phase shift due to the spherical aberration more precisely than did a conventional function in terms of g (the two-dimensional (2D) planar Fourier components). Experimentally, exit waves reconstructed using the w-function showed sample structures at approximately 20% higher resolution than those reconstructed using the g-function. Image contrast simulations proved that the w-function had a significant advantage over the g-function: the former canceled out the effect of illumination divergence, resulting in a high-resolution exit wave. These results demonstrated that exit waves, which are uniquely realized in the 3D-FFM, should be reconstructed using the w-type phase correction function.

Wave field restoration using three-dimensional Fourier filtering method

A wave field restoration method in transmission electron microscopy (TEM) was mathematically derived based on a three-dimensional (3D) image formation theory. Wave field restoration using this method together with spherical aberration correction was experimentally confirmed in through-focus images of amorphous tungsten thin film, and the resolution of the reconstructed phase image was successfully improved from the Scherzer resolution limit to the information limit. In an application of this method to a crystalline sample, the surface structure of Au(110) was observed in a profile-imaging mode. The processed phase image showed quantitatively the atomic relaxation of the topmost layer.

Practical image restoration of thick biological specimens using multiple focus levels in transmission electron microscopy

Three-dimensional electron tomographic studies of thick specimens such as cellular organelles or supramolecular structures require accurate interpretations of transmission electron micrograph intensities. In addition to microscope lens aberrations, thick specimen imaging is complicated by additional distortions resulting from multiple elastic and inelastic scattering. Extensive analysis of the mechanism of image formation using electron energy-loss spectroscopy and imaging as well as exit wavefront reconstruction demonstrated that multiple scattering does not contribute to the coherent component of the exit wave (Han et al., 1996, 1995). Although exit wavefront restored images showed enhanced contrast and resolution, that technique, which requires the collection of more than 30 images at different focus levels, is not practical for routine data collection in 3D electron tomography, where usually over 100 projection views are required for each reconstruction. Using a 0.7-micron-thick specimen imaged at 200 keV, the accuracy of reconstructions using small numbers of defocused images and a simple linear filter (Schiske, 1968) was assessed by comparison to the complete exit wave restoration. We demonstrate that only four optimal focus levels are required to effectively restore the coherent component (deviation 5.1%). By contrast, the optimal single image (zero defocus) shows a 25.5% deviation to the exit wave restoration. Two pairs of under- and over-defocus images should be taken: one pair at quite high defocus (> 10 microns) to differentiate the coherent (single elastic scattering) from the incoherent (multiple elastic and inelastic scattering) components, and the second pair to optimize information content at the highest desired resolution (e.g., 5 microns for (2.5 nm)-1 resolution). We also propose a new interpretation of the restored amplitude and phase components where the specimen mass-density is proportional to the logarithm of the amplitude component and linearly related to the phase component. This approach should greatly facilitate the collection of high resolution tomographic data from thick samples.