Transmission electron microtomography without the "missing wedge" for quantitative structural analysis

A three-dimensional (3D) visualization and structural analysis of a rod-shaped specimen of a zirconia/polymer nanocomposite material were carried out by transmission electron microtomography (TEMT) with particular emphasis on complete rotation of the specimen (tilt angular range: +/-90 degrees ). In order to achieve such an ideal experimental condition for the TEMT, improvements in the specimen as well as the sample holder were made. A rod-shaped specimen was necessary in order to obtain a high transmission of the specimen upon tilting to large angles. The image resolution of the reconstructed tomogram was isotropic, in sharp contrast to the anisotropic image resolution of the conventional TEMT with a limited angular range (the "missing wedge" problem). A volume fraction of zirconia, phi, evaluated from the 3D reconstruction was in quantitative agreement with the known composition of the nanocomposite. A series of 3D reconstructions was made from the tilt series with complete rotation by limiting the maximum tilt angle, alpha, from which a couple of structural parameters, the volume fraction and surface area per unit volume, Sigma, of the zirconia, were evaluated as a function of alpha. It was confirmed from actual experimental data that both phi and Sigma slightly decreased with the increasing alpha and reached constant values at around alpha=80 degrees , suggesting that the specimen may have to be tilted to +/-80 degrees for truly quantitative measurements.     

Correlation of the orientation of stacked aragonite platelets in nacre and their connection via mineral bridges

In this work, we studied the correlation of the orientation of stacked aragonite platelets of Haliotis laevigata nacre, using selected area diffraction (SAD) in transmission electron microscopy (TEM). From the position of the center of Laue circle (COLC) within the diffraction patterns the tilt angles of the investigated platelets relatively to a reference platelet (oriented in zone axis) are determined. The strong correlation of the platelets supports the existence of mineral bridges, which connect the stacked platelets and enable a transfer of the platelet orientation during growth. Electron tomography and subsequent reconstruction of the obtained data yield information about the shape of the mineral bridges. The crystalline structure of the material within the mineral bridges was investigated by high resolution TEM (HRTEM).     

A novel "ghost"-free tomographic image reconstruction method applicable to rotary-shadowed replica specimens

Electron tomography by conventional filtered back-projection is often seriously impaired by anisotropic resolution due to unavoidable limitation in specimen tilt-angles. We propose a new approach to overcome the problem for thin film-like replica-type specimens in which internal density is supposed as homogenous and contiguously distributed, by imposing a reasonable constraint of density-existing region in the reconstruction procedure. The objects were approximated as a distribution of binary voxels and the intensity of the projected images being proportional to the thickness along the projection ray. The new reconstruction algorithm consists of initial determination of approximate constraint region by a topographic analysis by stereo-photogrammetry, followed by iterative computation to find the unique solution of simultaneous equations, so that all the intensity distribution in tilt-series images are included within pre-determined voxel arrangement. During a trial run with a new methodology, we realized its significantly advantageous feature that much less number of projection images than conventional back-projection is required to perform the reconstruction of almost equivalent quality. Here, we show the performance of this novel algorithm by 3-D reconstruction of quick-freeze deep-etch replica specimens without any trace of spurious ghosting caused by missing-wedge problems.     

Towards better 3-D reconstructions by combining electron tomography and atom-probe tomography

Scanning transmission electron microscope tomography and atom-probe tomography are both three-dimensional techniques on the nanoscale. We demonstrate here the combination of the techniques by analyzing the very same volume of an Al-Ag alloy specimen. This comparison allows us to directly visualize the theoretically known artifacts of each technique experimentally, providing insight into the optimal parameters to use for reconstructions and assessing the quality of each reconstruction. The combination of the techniques for accurate morphology and compositional information in three dimensions at the nanoscale provides a route for a new level of materials characterization and understanding.     

Characterization of JEOL 2100F Lorentz-TEM for low-magnification electron holography and magnetic imaging

We present results that characterize the performance and capabilities of the JEOL 2100F-LM electron microscope to carry out holography and quantitative magnetic imaging. We find the microscope is well-suited for studies of magnetic materials, or for semi-conductor dopant profiling, where a large hologram width ( approximately 1 microm) and fine fringe spacing ( approximately 1.5 nm) are obtained with good contrast ( approximately 20%). We present, as well, measurements of the spherical aberration coefficient Cs=(108.7+/-9.6)mm and minimum achievable focal step delta f=(87.6+/-1.4)nm for the specially designed long-focal-length objective lens of this microscope. Further, we detail experiments to accurately measure the optical parameters of the imaging system typical of conventional holography setup in a transmission electron microscope. The role played by astigmatic illumination in the hologram formation is also assessed with a wave-optical model, which we present and discuss. The measurements obtained for our microscope are used to simulate realistic holograms, which we compare directly to experimental holograms finding good agreement. These results indicate the usefulness of measuring these optical parameters to guide the optimization of the experimental setup for a given microscope, and to provide an additional degree of practical experimental possibility.     

Development of atom probe specimen preparation techniques for specific regions in steel materials

More elaborated specimen preparation techniques for atom probe analysis were developed using a focused ion beam with a sample lift-out system so as to expand the application field in steel materials. The techniques enable atom probe analysis of sample steel at site-specific regions of interest. The preferable form of the needle specimen was provided by electrostatic field calculation using a finite element method. The new techniques were applied to the observation of a bainite-ferrite interface in a low carbon steel, and atomic-scale partitioning and segregation of alloying elements at the phase interface were directly observed in three dimensions.     

A procedure to analyze surface profiles of the protein molecules visualized by quick-freeze deep-etch replica electron microscopy

Quick-freeze deep-etch replica electron microscopy gives high contrast snapshots of individual protein molecules under physiological conditions in vitro or in situ. The images show delicate internal pattern, possibly reflecting the rotary-shadowed surface profile of the molecule. As a step to build the new system for the "Structural analysis of single molecules", we propose a procedure to quantitatively characterize the structural property of individual molecules; e.g. conformational type and precise view-angle of the molecules, if the crystallographic structure of the target molecule is available. This paper presents a framework to determine the observed face of the protein molecule by analyzing the surface profile of individual molecules visualized in freeze-replica specimens. A comprehensive set of rotary-shadowed views of the protein molecule was artificially generated from the available atomic coordinates using light-rendering software. Exploiting new mathematical morphology-based image filter, characteristic features were extracted from each image and stored as template. Similar features were extracted from the true replica image and the most likely projection angle and the conformation of the observed particle were determined by quantitative comparison with a set of archived images. The performance and the robustness of the procedure were examined with myosin head structure in defined configuration for actual application.     

Limits to the spatial, energy and momentum resolution of electron energy-loss spectroscopy

We discuss various factors that determine the performance of electron energy-loss spectroscopy (EELS) and energy-filtered (EFTEM) imaging in a transmission electron microscope. Some of these factors are instrumental and have undergone substantial improvement in recent years, including the development of electron monochromators and aberration correctors. Others, such as radiation damage, delocalization of inelastic scattering and beam broadening in the specimen, derive from basic physics and are likely to remain as limitations. To aid the experimentalist, analytical expressions are given for beam broadening, delocalization length, energy broadening due to core-hole and excited-electron lifetimes, and for the momentum resolution in angle-resolved EELS.     

A formula for the image intensity of phase objects in Zernike mode

I present an analytical expression for the image intensity of a phase object visualized in Zernike phase contrast mode. The formula is valid for periodic and non-periodic weak and strong objects, and accounts for the effects of finite illumination. The expression provided is intended as a generalization of the standard reference formula given in the Born and Wolf [Principles of Optics, sixth ed., Pergamon Press, New York, 1980, p. 427] textbook as well as of the formalism employed to evaluate imaging doses in Zernike mode [M. Malac, M. Beleggia, R. Egerton, Y. Zhu, Ultramicroscopy 108 (2008) 126]. I illustrate the usefulness of the improved expression by means of three examples: a sinusoidal phase grating, a Gaussian object, and a phase step. The optimal Zernike phase angle yielding maximum image contrast is found to be object-dependent and not necessarily equal to pi/2. Phase plate optimization criteria are derived and presented for two of the examples considered.     

In situ measurements and transmission electron microscopy of carbon nanotube field-effect transistors

We present the design and operation of a transmission electron microscopy (TEM)-compatible carbon nanotube (CNT) field-effect transistor (FET). The device is configured with microfabricated slits, which allows direct observation of CNTs in a FET using TEM and measurement of electrical transport while inside the TEM. As demonstrations of the device architecture, two examples are presented. The first example is an in situ electrical transport measurement of a bundle of carbon nanotubes. The second example is a study of electron beam radiation effect on CNT bundles using a 200 keV electron beam. In situ electrical transport measurement during the beam irradiation shows a signature of wall- or tube-breakdown. Stepwise current drops were observed when a high intensity electron beam was used to cut individual CNT bundles in a device with multiple bundles.     

Imaging of radiation-sensitive samples in transmission electron microscopes equipped with Zernike phase plates

We have optimized a bright-field transmission electron microscope for imaging of high-resolution radiation-sensitive materials by calculating the imaging dose n(0) needed to obtain a signal-to-noise ratio (SNR)=5. Installing a Zernike phase plate (ZP) decreases the dose needed to detect single atoms by as much as a factor of two at 300 kV. For imaging larger objects, such as Gaussian objects with full-width at half-maximum larger than 0.15 nm, ZP appears more efficient in reducing the imaging dose than correcting for spherical aberration. The imaging dose n(0) does not decrease with extending of chromatic resolution limit by reducing chromatic aberration, using high accelerating potential (U(0)=300 kV), because the image contrast increases slower than the reciprocal of detection radius. However, reducing chromatic aberration would allow accelerating potential to be reduced leading to imaging doses below 10 e(-)/A(2) for a single iodine atom when a CS-corrector and a ZP are used together. Our simulations indicate that, in addition to microscope hardware, optimization is heavily dependent on the nature of the specimen under investigation.     

Depth sectioning in scanning transmission electron microscopy based on core-loss spectroscopy

Recent and ongoing improvements in aberration correction have opened up the possibility of depth sectioning samples using the scanning transmission electron microscope in a fashion similar to the confocal scanning optical microscope. We explore questions of principle relating to image interpretability in the depth sectioning of samples using electron energy loss spectroscopy. We show that provided electron microscope probes are sufficiently fine and detector collection semi-angles are sufficiently large we can expect to locate dopant atoms inside a crystal. Furthermore, unlike high angle annular dark field imaging, electron energy loss spectroscopy can resolve dopants of smaller atomic mass than the supporting crystalline matrix.     

Preparation of biomolecule gel matrices for electron microscopy

We report a new sample preparation method that allows the direct transmission electron microscopy evaluation of the architectural characteristics of biomolecules entrapped in gel matrices. We demonstrate that this sample preparation technique can be used for the identification and ultrastructural characterization of liposomes, collagen I and collagen III embedded in gel matrices, and has the potential to be useful for transmission electron microscopy (TEM) characterization of other biomolecule-gel matrix systems.     

On the interpretation of the forbidden spots observed in the electron diffraction patterns of flat Au triangular nanoparticles

In many cases nanostructures present forbidden spots in their electron diffraction patterns when they are observed by transmission electron microscopy (TEM). To interpret their TEM and high resolution transmission electron microscopy (HRTEM) images properly, an understanding of the origin of these spots is necessary. In this work we comment on the origin of the forbidden spots observed in the [111] and [112] electron diffraction patterns of flat gold triangular nanoparticles. The forbidden spots were successfully indexed as corresponding to the first laue Zone (FOLZ) and the HRTEM images presented a contrast produced by the interference of the zero-order Laue zone (ZOLZ) and FOLZ spots. We discuss the use of the forbidden spots in the study of the structure of nanoparticles and show that they are related to the shape and incompleteness of layers in the very thin particles.     

An electron microscope for the aberration-corrected era

Improved resolution made possible by aberration correction has greatly increased the demands on the performance of all parts of high-end electron microscopes. In order to meet these demands, we have designed and built an entirely new scanning transmission electron microscope (STEM). The microscope includes a flexible illumination system that allows the properties of its probe to be changed on-the-fly, a third-generation aberration corrector which corrects all geometric aberrations up to fifth order, an ultra-responsive yet stable five-axis sample stage, and a flexible configuration of optimized detectors. The microscope features many innovations, such as a modular column assembled from building blocks that can be stacked in almost any order, in situ storage and cleaning facilities for up to five samples, computer-controlled loading of samples into the column, and self-diagnosing electronics. The microscope construction is described, and examples of its capabilities are shown.     

Quantitative electron holographic tomography for the 3D characterisation of semiconductor device structures

Electron tomography and electron holography experiments have been combined to investigate the 3D electrostatic potential distribution in semiconductor devices. The experimental procedure for the acquisition and data reconstruction of holographic tilt series of silicon p-n junction specimens is described. A quantitative analysis of the experimental results from specimens of two different thicknesses is presented, revealing the 3D electrostatic potential variations arising from the presence of surfaces and damage generated by focused ion beam (FIB) sample preparation. Close to bulk-like properties are measured in the centre of the tomographic reconstruction of the specimen, revealing higher electrically active dopant concentrations compared to the measurements obtained at the specimen surfaces. A comparison of the experimental results from the different thickness specimens has revealed a 'critical' thickness for this specimen preparation method of 350nm that is required for this device structure to retain 'bulk'-like properties in the centre of the membrane.     

Determination of chromium valence over the range Cr(0)–Cr(VI) by electron energy loss spectroscopy

Chromium is a redox active 3d transition metal with a wide range of valences (−2 to +6) that control the geochemistry and toxicity of the element. Therefore, techniques that measure Cr valence are important bio/geochemical tools. Until now, all established methods to determine Cr valence were bulk techniques with many specific to a single, or at best, only a few oxidation state(s). We report an electron energy loss spectroscopy (EELS) technique along with an extensive suite of affined reference spectra that together, unlike other methods, can determine Cr valence (or at least constrain the possible valences) at high-spatial resolution (tens-of-nanometer scale) across a wide valence range, Cr(0)–Cr(VI). Fine structure of Cr-L_2,3 edges was parametrized by measurement of the chemical shift of the L₃ edge and the ratio of integrated intensity under the L₃ and L₂ edges. These two parameterizations were correlated to Cr valence and also the dⁿ orbital configuration which has a large influence on L-edge fine structure. We demonstrate that it is not possible to unambiguously determine Cr valence from only one fine-structure parameterization which is the method employed to determine metal valence by nearly all previous EELS studies. Rather, multiple fine-structure parameterizations must be used together if the full range of possible Cr valences is considered. However even with two parameterizations, there are limitations. For example, distinguishing Cr(IV) from Cr(III) is problematic and it may be difficult to distinguish low-spin Cr(II) from Cr(III). Nevertheless, when Cr is known to be divalent, low- and high-spin dⁿ orbital configurations can be readily distinguished.     

Practical factors affecting the performance of a thin-film phase plate for transmission electron microscopy

A number of practical issues must be addressed when using thin carbon films as quarter-wave plates for Zernike phase-contrast electron microscopy. We describe, for example, how we meet the more stringent requirements that must be satisfied for beam alignment in this imaging mode. In addition we address the concern that one might have regarding the loss of some of the scattered electrons as they pass through such a phase plate. We show that two easily measured parameters, (1) the low-resolution image contrast produced in cryo-EM images of tobacco mosaic virus particles and (2) the fall-off of the envelope function at high resolution, can be used to quantitatively compare the data quality for Zernike phase-contrast images and for defocused bright-field images. We describe how we prepare carbon-film phase plates that are initially free of charging or other effects that degrade image quality. We emphasize, however, that even though the buildup of hydrocarbon contamination can be avoided by heating the phase plates during use, their performance nevertheless deteriorates over the time scale of days to weeks, thus requiring their frequent replacement in order to maintain optimal performance.     

In-line holographic electron microscopy in the presence of external magnetic fields

It is now a well-known fact that the phase of electron waves is altered by external magnetic fields via the Aharonov-Bohm effect. This implies that any electron interference effects will be to some degree affected by the presence of such fields. In this study we examine the distortion effects of external (constant and variable) magnetic fields on electron interference and holography. For digital holography, the reconstruction of the object is done via numerical calculations and this leaves the door open for correcting phase distortions in the hologram reconstruction. We design and quantitatively assess such correction schemes, which decidedly depend on our knowledge of the magnetic field values in the holographic recording process. For constant fields of known value we are able to correct for magnetic distortions to a great extent. We find that variable fields are more destructive to the holographic process than constant fields. We define two criteria, related respectively to global and local contrast of the hologram to establish the maximum allowed external field which does not significantly hinder the accuracy of in-line holographic microscopy with electrons.