The electron backscatter coefficient (η) and the related correction factor for X-ray intensity (R) are both strongly dependent on atomic number and although quite good data are available for pure elements, the derivation of values for compounds is problematic. This issue is addressed by Donovan, Pingitore, and Westphal (Microscopy and Microanalysis, Vol. 9, No. 3, June 2003, pp. 202–215), in which an “electron fraction” averaging method is advocated as an improvement on “traditional” mass fraction averaging, which is known to be only an approximation. (The difference, according to Table 3, is only significant, however, for samples containing heavy elements such as Pb and Th.) New thinking on this topic is welcome, but I believe this proposal should be treated with caution pending more rigorous testing.

High-resolution transmission electron microscopy (HR-TEM) has been used as the ultimate method of thickness measurement for thin films. The appearance of phase contrast interference patterns in HR-TEM images has long been confused as the appearance of a crystal lattice by nonspecialists. Relatively easy to interpret crystal lattice images are now directly observed with the introduction of annular dark-field detectors for scanning TEM (STEM). With the recent development of reliable lattice image processing software that creates crystal structure images from phase contrast data, HR-TEM can also provide crystal lattice images. The resolution of both methods has been steadily improved reaching now into the sub-Ångstrom region. Improvements in electron lens and image analysis software are increasing the spatial resolution of both methods. Optimum resolution for STEM requires that the probe beam be highly localized. In STEM, beam localization is enhanced by selection of the correct aperture. When STEM measurement is done using a highly localized probe beam, HR-TEM and STEM measurement of the thickness of silicon oxynitride films agree within experimental error. In this article, the optimum conditions for HR-TEM and STEM measurement are discussed along with a method for repeatable film thickness determination. The impact of sample thickness is also discussed. The key result in this article is the proposal of a reproducible method for film thickness determination.

We have used fluctuation microscopy to reveal the presence of structural order on length scales of 1–2 nm in metallic glasses. We compare results of fluctuation microscopy measurements with high resolution transmission electron microscopy and electron diffraction observations on a series of metallic glass samples with differing degrees of structural order. The agreement between the fluctuation microscopy results and those of the other techniques is good. In particular, we show that the technique used to make thin specimens for electron microscopy affects the structure of the metallic glass, with ion thinning inducing more structural order than electropolishing. We also show that relatively minor changes in the composition of the alloy can have a significant effect on the medium-range order; this increased order is correlated with changes in mechanical behavior.

In this article, we report a technique for growing carbon nanotubes in a more controllable fashion, which enables us to synthesize nanotubes directly in various forms of designed patterns. This nanofabrication process is based on a combination of focused ion beam (FIB) and chemical vapor deposition (CVD) techniques. In this process, arrays of conductive patterns were first deposited on silicon substrates by directing a gaseous compound (C9H16Pt) via the capillary needle-sized nozzles within a FIB system. The substrates were then coated with catalyst and further modified by the FIB to localize the position of the catalyst. Finally, the growth of carbon nanotubes on the designed substrates was carried out by CVD of hydrocarbon gases. This fabrication technique has the advantage of positioning carbon nanotubes in selected locations. This may open up opportunities for the direct synthesis of carbon nanotubes onto almost any substrate material, thus allowing fabrication of carbon nanotube-based devices.

This article reports on the use of high pressure freezing followed by freeze substitution (HPF/FS) to study ultrastructural details of host–pathogen interactions in fungal diseases of plants. The specific host–pathogen systems discussed here include a powdery mildew infection of poinsettia and rust infections of daylily and Indian strawberry. The three pathogens considered here all attack the leaves of their hosts and produce specialized hyphal branches known as haustoria that invade individual host cells without killing them. We found that HPF/FS provided excellent preservation of both haustoria and host cells for all three host–pathogen systems. Preservation of fungal and host cell membranes was particularly good and greatly facilitated the detailed study of host–pathogen interfaces. In some instances, HPF/FS provided information that was not available in samples prepared for study using conventional chemical fixation. On the other hand, we did encounter various problems associated with the use of HPF/FS. Examples included freeze damage of samples, inconsistency of fixation in different samples, separation of plant cell cytoplasm from cell walls, breakage of cell walls and membranes, and splitting of thin sections. However, we believe that the outstanding preservation of ultrastructural details afforded by HPF/FS significantly outweighs these problems and we highly recommend the use of this fixation protocol for future studies of fungal host-plant interactions.

Angiogenesis, a biologic process whereby endothelial cells divide and migrate to form new blood vessels, is a key step in tumor growth, invasion, and metastasis. In the present study, we investigated the differences in angioarchitecture between two different tumors induced by cloned cell lines (MT-8 and MT-9), derived from a transplantable rat malignant fibrous histiocytoma, by scanning electron microscopy of vascular corrosion casts. During a 3-week observation period after implantation, the growth of MT-8 tumors appeared to be faster than that of MT-9 tumors. Histologically, MT-8 tumors were of the uniformly undifferentiated sarcoma type arranged in characteristic organoid structures, and MT-9 tumors showed a storiform growth pattern. In MT-8 tumors, neovascularization occurred by sprouting at postimplantation (PI) week 1, and the newly formed capillaries gradually became more tortuous. In MT-9 tumors, at PI week 1, the corrosion casts of newly formed capillaries mainly showed a wavy course but no fingerlike outgrowths of capillaries were seen. At PI weeks 2 and 3, the sprouting was seen specifically in MT-9 tumors, forming basketlike structures and glomeruloid structures of capillaries. These results indicate that angiogenesis or angioarchitecture of MT-8 tumors is different from that of MT-9 tumors, depending on the differences in their tumor histology and by the features like absence or presence of basketlike structures and glomeruloid structures of capillaries.

The length scales on which materials microstructures are being formed, grown, and even designed are becoming increasingly small and increasingly three-dimensional. For such complex structures two-dimensional transmission electron microscopy (TEM) analysis is often inadequate and occasionally misleading. One approach to this problem is the modification of electron tomography techniques, developed for structural biology, for use in materials science. Energy-Filtered (EF) TEM elemental distribution images approximate to true projections of structure, and, as such, can be used to reconstruct the three-dimensional distribution of chemical species. A sample holder has been modified to allow the high tilt (±60°) required for tomography and a semiautomatic acquisition script designed to manage energy-loss acquisition. Tilt series data sets have been acquired from two widely different experimental systems, Cr carbides in 316 stainless steel and magnetite nanocrystals in magnetotactic bacteria, demonstrating single- and multiple-element tomography. It is shown that both elemental maps and jump-ratio images are suitable for reconstruction, despite the effects of diffraction contrast in the former and thickness changes in the latter. It is concluded that the image contrast, signal, and signal-to-noise ratio (SNR) are key to the achievable reconstruction quality and, as such, the technique may be of limited value for high energy loss/small inelastic cross section edges.

As high-resolution biological transmission electron microscopy (TEM) has increased in popularity over recent years, the volume of data and number of projects underway has risen dramatically. A robust tool for effective data management is essential to efficiently process large data sets and extract maximum information from the available data. We present the Electron Microscopy Electronic Notebook (EMEN), a portable, object-oriented, web-based tool for TEM data archival and project management. EMEN has several unique features. First, the database is logically organized and annotated so multiple collaborators at different geographical locations can easily access and interpret the data without assistance. Second, the database was designed to provide flexibility to the user, so it can be used much as a lab notebook would be, while maintaining a structure suitable for data mining and direct interaction with data-processing software. Finally, as an object-oriented database, the database structure is dynamic and can be easily extended to incorporate information not defined in the original database specification.

Biological macromolecules embedded in vitreous ice are known to suffer from charging while being imaged in an electron transmission cryomicroscope. We developed an electron beam coater that deposits conductive films onto the surface of frozen-hydrated specimens. The conductive films help to dissipate charge during electron irradiation of poorly conductive ice-embedded biological samples. We observed significant reduction in charging of ice-embedded catalase crystals suspended over holes in a holey carbon film after coating them with a 30-Å-thick layer of an amorphous alloy, Ti88Si12. Images of the crystals after coating showed diffraction spots of up to 3 Å resolution.

Recent evidence supports the notion that biological functions of extracellular matrix (ECM) are highly correlated to not only its composition but also its structure. This article integrates confocal microscopy imaging and image-processing techniques to analyze the microstructural properties of ECM. This report describes a two- and three-dimensional fiber middle-line tracing algorithm that may be used to quantify collagen fibril organization. We utilized computer simulation and statistical analysis to validate the developed algorithm. These algorithms were applied to confocal images of collagen gels made with reconstituted bovine collagen type I, to demonstrate the computation of orientations of individual fibers.