A significant loss in electron probe current can occur before the electron beam enters the specimen chamber of an environmental scanning electron microscope (ESEM). This loss results from electron scattering in a gaseous jet formed inside and downstream (above) the pressure-limiting aperture (PLA), which separates the high-pressure and high-vacuum regions of the microscope. The electron beam loss above the PLA has been calculated for three different ESEMs, each with a different PLA geometry: an ElectroScan E3, a Philips XL30 ESEM, and a prototype instrument. The mass thickness of gas above the PLA in each case has been determined by Monte Carlo simulation of the gas density variation in the gas jet. It has been found that the PLA configurations used in the commercial instruments produce considerable loss in the electron probe current that dramatically degrades their performance at high chamber pressure and low accelerating voltage. These detrimental effects are minimized in the prototype instrument, which has an optimized thin-foil PLA design.

The advent of the Internet has allowed the development of remote access capabilities to a growing variety and number of microscopy systems. To date, the confocal microscope has not been included among these systems. At the California State University (CSU) Confocal Microscopy Core Facility, we have established a remote access confocal laser scanning microscope facility that allows users with virtually any type of computer platform to connect to our system. Our Leica TCS NT confocal system is accessible to any authorized user via the Internet by using a free software program called VNC (Virtual Network Computing). Once connectivity is established, remote users are able to control virtually all the functions to conduct real-time image analysis and quantitative assessments of their specimen. They can also move the motorized stage to view different regions of their specimen by using a software program associated with the stage. At the end of the session, all files generated during the session can be downloaded to the user’s computer from a link on the CSU confocal website. A number of safeguard features have been developed to ensure security and privacy of data acquired during a remote session.

We have implemented a Web-based simulation program for the contrast transfer function and envelope functions in Java and JavaScript. The simulation provides interactive controls of all the parameters in those functions. In addition to the predefined functions, users can easily define new functions that use any of the parameters in the preset functions. The most useful feature of this new simulation program is the convenient, universal accessibility through Web browsers on any computer platform that supports Java, such as Netscape and Internet Explorer.

This article, dedicated to the memory of the late professor Raimond Castaing, will evoke the birth and the first developments of electron probe microanalysis in France.

Cone-beam X-ray microtomography attracts increasing attention due to its applications in biomedical sciences, material engineering, and industrial nondestructive evaluation. Rapid volumetric image reconstruction is highly desirable in all these areas for prompt visualization and analysis of complex structures of interest. In this article, we reformulate a generalized Feldkamp cone-beam image reconstruction algorithm, utilize curved voxels and mapping tables, improve the reconstruction efficiency by an order of magnitude relative to a direct implementation of the standard algorithm, and demonstrate the feasibility with numerical simulation and experiments using a prototype cone-beam X-ray microtomographic system. Our fast algorithm reconstructs a 256-voxel cube from 100 projections within 2 min on an Intel Pentium II® 233 MHz personal computer, produces satisfactory image quality, and can be further accelerated using special hardware and/or parallel processing techniques.

The early days of the electron microprobe were characterized by the variety of designs emerging from different laboratories in Europe, the United States, and the USSR. Examples from Europe illustrate well the diverging trends in the evolutionary process at that time. Later, commercial pressures and a better understanding of user needs forced a rationalization on both sides of the Atlantic, to the point where only few variants have survived. These were memorable days, with scope for healthy rivalry and vigorous debate.

Many of the techniques that have been developed in X-ray crystallography are being applied in electron crystallographic studies of proteins. Electron crystallography has the advantage of measuring structure factor phases directly from high resolution images with an accuracy substantially higher than is common in X-ray crystallography. However, electron diffraction amplitudes are often not as precise as those obtained in X-ray work. We discuss here some approaches to maximizing the reliability of the diffraction amplitudes through choice of exposure and data processing schemes. With accurate measurement of diffraction data, Fourier difference methods can be used in electron crystallographic studies of small, localized changes of proteins that exist in two-dimensional crystals. The mathematical basis for the power of these methods in detecting small changes is reviewed. We then discuss several issues related to optimizing the quality of the diffraction data and derive an expression for the best exposure for recording diffraction patterns. An application of Fourier difference maps in localizing drug binding sites on the protein tubulin is discussed.

The Bugscope project is an educational outreach program for kindergarten to grade 12 (K–12) classrooms. The project provides a resource to classrooms so that they may remotely operate a scanning electron microscope to image insects at high magnification. The microscope is remotely controlled in real time from a classroom computer over the Internet using a Web browser. Bugscope provides a state-of-the-art microscope resource for teachers that can be readily integrated into classroom activities. The Bugscope project provides a low-cost, sustainable model for research groups to support K–12 education outreach projects.

A sample preparation method has been developed whereby sharp needle-shaped specimens for atom probe analysis are fabricated from multilayer thin films deposited onto silicon substrates. The specimens are fabricated in an orientation such that atom probe composition profiles across the layer interfaces can be determined with atomic-layer spatial resolution, i.e., the layer normals are parallel to the needle axis. The method uses standard silicon etching techniques and focused ion-beam milling. The feasibility and utility of this technique are shown through its application to a NiFe/CoFe/Cu/CoFe-based thin film structure.

Reduction of Cr(VI) by the bacterium, Shewanella oneidensis (previously classified Shewanella putrefaciens strain MR-1), was studied by absorption spectrophotometry and in situ, environmental cell–transmission electron microscopy (EC-TEM) coupled with electron energy loss spectroscopy (EELS). Bacteria from rinsed cultures were placed directly in the environmental cell of the transmission electron microscope and examined under 100 Torr pressure. Bright field EC-TEM images show two distinct populations of S. oneidensis in incubated cultures containing Cr(VI)O42−: those that exhibit low image contrast and heavily precipitateencrusted cells exhibiting high image contrast. Several EELS techniques were applied to determine the oxidation state of Cr associated with encrusted cells. The encrusted cells are shown to contain a reduced form of Cr in oxidation state +3 or lower. These results demonstrate the capability to determine the chemistry and valence state of reduction products associated with unfixed, hydrated bacteria in an environmental cell transmission electron microscope.

Imaging techniques often suffer from distortion effects. Former methods of reducing these distortions have been based either on improving the imaging technique (i.e., to avoid distortions) or on the use of reference samples (i.e., to determine the distortion field by imaging of a known structure. We present a novel method of correcting image distortion by evaluating the imaged position changes due to two small sample position shifts. The algorithm allows us to calculate a vector field, which enables us to determine the “undistorted” position of any point of the image. The presented method has very low presuppositions about the sample, requires no reference samples, and is applicable to any type of image distortion. In addition to the presentation of the method's theoretical basis and a description of the computational method, we present corrected secondary ion mass spectroscopy (SIMS) images of a regular structure (a copper grid) as well as a stochastic distribution (sodium impurities) to show the results of empirical data.

The primary cilium, a solitary non-motile structure projecting from the centriole of mammalian cells, has been a subject of interest of anatomists since 1898. Surprisingly, the function of the primary cilium in mammalian cells is completely unknown. Virtually all of the epithelial cells of the mammalian kidney, with the exception of the intercalated cells of the collecting duct, express a single primary cilium on their apical (lumenal) surface. These structures were ignored by physiologists until recently when the mechanical properties of the primary cilia of cultured cells of renal origin were measured and it was proposed that they could serve as flow sensors. The proposal stemmed from the observation that flow rates comparable to those observed in renal tubules resulted in a deflection of the cilium of a few microns and that the stiffness of the cilium was commensurate with mechanosensing.

The primary cilia of renal tubular cells are generally about 2 - 3 μm long whereas those of cultured renal cells become much longer as the cells age and may extend 50 μm or more into the medium. MDCK cells, a cultured cell line derived from the collecting duct of the canine kidney, exhibit two cell types analogous to the principal and intercalated cells of the collecting duct. MDCK principal cells express a primary cilium that is visible by high-resolution DIC microscopy. About one week after splitting, the primary cilium of MDCK principal cells is about 8 μm long and is well suited for testing the hypothesis that the cilium serves as a mechanosensor of fluid flow.

We review our studies of the initial oxidation stages of Cu(001) thin films as investigated by in situ ultra-high vacuum transmission electron microscopy. We present our observations of surface reconstruction and the nucleation to coalescence of copper oxide during in situ oxidation in O2. We have proposed a semi-quantitative model, where oxygen surface diffusion is the dominant mechanism of the initial oxidation stages of Cu. We have also investigated the effect of water vapor on copper oxidation. We have observed that the presence of water vapor in the oxidizing atmosphere retards the rate of Cu oxidation and Cu2O is reduced when exposed directly to steam.

The accurate calculation of characteristic peak intensity is essential for interpreting X-ray spectra in electron microprobe analysis. Conventionally, the measured intensity from a standard of known composition is used as a reference to simplify the calculation. However, if no such standard is available, then all factors influencing X-ray generation and X-ray detection efficiency must be included. If the intensity and energy distribution of the background radiation can also be calculated, the investigator can simulate an entire spectrum from an assumed composition, gaining powerful benefits in setting up an experiment and in confirming the results. The study presented here demonstrates a fast method of spectrum simulation, suitable for energydispersive spectroscopy (EDS), and assesses the accuracy using 309 spectra from samples of known composition. These include K, L, and M lines from elements of atomic number 6–92, excited by beam energies in the range of 5–30 keV. The RMS error between 360 measured and calculated peak intensities was found to be 7.1%. Central to the method is the use of the ratio of peak intensity/total background intensity, which allows spectra to be compared from instruments of differing collection efficiency, thereby easing the collection of data over a wide range of conditions.

Vascular corrosion casting has been used for about 40 years to produce replicas of normal and abnormal vasculature and microvasculature of various tissues and organs that could be viewed at the ultrastructural level. In combination with scanning electron microscopy (SEM), the primary application of corrosion casting has been to describe the morphology and anatomical distribution of blood vessels in these tissues. However, such replicas should also contain quantitative information about that vasculature. This report summarizes some simple quantitative applications of vascular corrosion casting. Casts were prepared by infusing Mercox resin or diluted Mercox resin into the vasculature. Surrounding tissues were removed with KOH, hot water, and formic acid, and the resulting dried casts were observed with routine SEM. The orientation, size, and frequency of vascular endothelial cells were determined from endothelial nuclear imprints on various cast surfaces. Vascular volumes of heart, lung, and avian salt gland were calculated using tissue and resin densities, and weights. Changes in vascular volume and functional capillary density in an experimentally induced emphysema model were estimated from confocal images of casts. Clearly, corrosion casts lend themselves to quantitative analysis. However, because blood vessels differ in their compliances, in their responses to the toxicity of casting resins, and in their response to varying conditions of corrosion casting procedures, it is prudent to use care in interpreting this quantitative data. Some of the applications and limitations of quantitative methodology with corrosion casts are reviewed here.

We have discovered a new method, Fluorescent Speckle Microscopy (FSM), for analyzing the dynamic movement and turnover of macromolecular protein assemblies, such as the cytoskeleton, in living cells (Waterman-Storer et al., 1998). FSM compliments or replaces the techniques of fluorescence recovery after photobleaching or photoactivation of fluorescence for measuring protein dynamics in vivo. For FSM, cells are microinjected with a very low fraction of fluorescently labeled subunits that co-assemble with unlabeled subunits to give a structure with a fluorescent speckled appearance in diffraction-limited wide-field or confocal digital fluorescence images. At low fractions of fluorescent subunits relative to unlabeled subunits, fluorescent speckles vary randomly in intensity according to the number of fluorescent subunits within a diffraction-limited region. in time-lapse FSM image series, movement of the fluorescent speckle pattern indicates translocation of structures, while changes in speckle intensity indicate subunit turnover. We have used FSM to study microtubule and actin behavior in interphase and mitotic cells. We use kymograph analysis to quantitate the movement of speckled structures (Fig 1) and are currently developing analysis procedures to quantify subunit turnover in structures.

We have applied these methods to the study of microtubule and actin cytoskeletal dynamics in migrating vertebrate cells in culture. Interactions between the microtubule and actin cytoskeletons underlie fundamental cellular processes such as cytokinesis and cell locomotion, but are poorly understood.

The history of electron probe analysis in the USA in its first two decades is reviewed, with reference to the personalities which were involved, the development of instrumentation and theory, and the technical problems and limitations of that era.