Microscopic tomography with ultra-HVEM and applications

The ultra-HVEM with an accelerating voltage of 3 MV at Osaka University is capable of achieving excellent penetration and resolution for thick specimens. We obtained images of 5-microm-thick slices tilted at angles of up to 70 degrees for biological samples and observed stick-shaped samples of Si devices free from missing zone. These features make the ultra-HVEM an invaluable extension of 3D observation by electron tomography. In this paper, we introduce aspects of ultra-HVEM tomography; specifically, the magnification, the amount of image blurring for thick samples and the electron staining method. Finally, we give some typical applications in the fields of cell biology, pathology and electrical engineering.     

Multiple scattering effects of MeV electrons in very thick amorphous specimens

Multiple scattering has an important influence on the analysis of microns-thick specimens with MeV electrons. In this paper, we report on effects of multiple scattering of MeV electrons on electron transmission and imaging of tilted and thick amorphous film specimens by experiment and theoretical analysis. Electron transmission for microns-thick epoxy-resin and SiO₂ specimens calculated by the multiple elastic-scattering theory is in good agreement with measurements in the ultrahigh voltage electron microscope (ultra-HVEM) at Osaka University. Electron transmission and electron energy are then presented in an approximate power law. The bright-field ultra-HVEM images of gold particles on the top or bottom surfaces of 5 and 15 μm thick specimens further illustrate the effect of multiple scattering on image quality. The observed top‐bottom effect for the very thick specimens appears to be mainly caused by multiple elastic scattering. With increase in the accelerating voltage from 1 to 2 MV, image blurring, contrast, the signal-to-noise ratio, and the top‐bottom effect are improved because of reduction in the influence of multiple scattering. However, the effect of specimen thickness on image blurring is shown to be stronger than that of accelerating voltage. At the 2 MV accelerating voltage, the 100 nm gold particle can be imaged with less blurring of ∼4 nm when located at the bottom surface of a 15 μm thick epoxy-resin specimen.     

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.     

Automated high-throughput electron tomography by pre-calibration of image shifts

Electron tomography is a versatile method for obtaining three‐dimensional (3D) images with transmission electron microscopy. The technique is suitable to investigate cell organelles and tissue sections (100–500 nm thick) with 4–20 nm resolution. 3D reconstructions are obtained by processing a series of images acquired with the samples tilted over different angles. While tilting the sample, image shifts and defocus changes of several µm can occur. The current generation of automated acquisition software detects and corrects for these changes with a procedure that incorporates switching the electron optical magnification. We developed a novel method for data collection based on the measurement of shifts prior to data acquisition, which results in a five‐fold increase in speed, enabling the acquisition of 151 images in less than 20 min. The method will enhance the quality of a tilt series by minimizing the amount of required focus‐change compensation by aligning the optical axis to the tilt axis of the specimen stage. The alignment is achieved by invoking an amount of image shift as deduced from the mathematical model describing the effect of specimen tilt. As examples for application in biological and materials sciences 3D reconstructions of a mitochondrion and a zeolite crystal are presented.     

STEM tomography for thick biological specimens

Scanning transmission electron microscopy (STEM) tomography was applied to biological specimens such as yeast cells, HEK293 cells and primary culture neurons. These cells, which were embedded in a resin, were cut into 1-microm-thick sections. STEM tomography offers several important advantages including: (1) it is effective even for thick specimens, (2) 'dynamic focusing', (3) ease of using an annular dark field (ADF) mode and (4) linear contrasts. It has become evident that STEM tomography offers significant advantages for the observation of thick specimens. By employing STEM tomography, even a 1-microm-thick specimen (which is difficult to observe by conventional transmission electron microscopy (TEM)) was successfully analyzed in three dimensions. The specimen was tilted up to 73 degrees during data acquisition. At a large tilt angle, the specimen thicknesses increase dramatically. In order to observe such thick specimens, we introduced a special small condenser aperture that reduces the collection angle of the STEM probe. The specimen damage caused by the convergent electron beam was expected to be the most serious problem; however, the damage in STEM was actually smaller than that in TEM. In this study, the irradiation damage caused by TEM- and STEM-tomography in biological specimens was quantitatively compared.     

Note: direct measurement of the point-to-point resolution for microns-thick specimens in the ultrahigh-voltage electron microscope

We report on a direct measurement method and results of the point-to-point resolution for microns-thick amorphous specimens in the ultrahigh-voltage electron microscope (ultra-HVEM). We first obtain the ultra-HVEM images of nanometer gold particles with different sizes on the top surfaces of the thick epoxy-resin specimens. Based on the Rayleigh criterion, the point-to-point resolution is then determined as the minimum distance between centers of two resolvable tangent gold particles. Some values of resolution are accordingly acquired for the specimens with different thicknesses at the accelerating voltage of 2 MV, for example, 18.5 nm and 28.4 nm for the 5 μm and 8 μm thick epoxy-resin specimens, respectively. The presented method and results provide a reliable and useful approach to quantifying and comparing the achievable spatial resolution for the thick specimens imaged in the mode of transmission electron including the scanning transmission electron microscope.     

Electron tomography of III‐V quantum dots using dark field 002 imaging conditions

We present an evaluation of electron tomography of buried InAs quantum dots using dark field 002 imaging conditions. The compositional sensitivity of this imaging condition gives strong contrast among III‐V materials of differing compositions and, in principle, should allow an accurate 3D model of the buried structures to be produced. The large extinction distance allows specimens several hundred nanometres in thickness to be examined and reduces the effect of strain contrast in the images, with the advantage that it can be performed using conventional transmission electron microscopy techniques. A two‐beam condition must be maintained for all images, and the presence of other strong diffraction effects at certain specimen orientation results reduces the number of orientations available for tomography by approximately 10%. The data presented here are limited due to a lack of angular range in the data set but we find that an acceptable 3D model of a buried quantum dot may be produced by imposing cylindrical symmetry on the data set.     

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-μm-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.     

Multiscale iterative voting for differential analysis of stress response for 2D and 3D cell culture models

Focused ion beam-scanning electron microscope (FIB-SEM) tomography is a powerful application in obtaining three-dimensional (3D) information. The FIB creates a cross section and subsequently removes thin slices. The SEM takes images using secondary or backscattered electrons, or maps every slice using X-rays and/or electron backscatter diffraction patterns. The objective of this study is to assess the possibilities of combining FIB-SEM tomography with cathodoluminescence (CL) imaging. The intensity of CL emission is related to variations in defect or impurity concentrations. A potential problem with FIB-SEM CL tomography is that ion milling may change the defect state of the material and the CL emission. In addition the conventional tilted sample geometry used in FIB-SEM tomography is not compatible with conventional CL detectors. Here we examine the influence of the FIB on CL emission in natural diamond and the feasibility of FIB-SEM CL tomography. A systematic investigation establishes that the ion beam influences CL emission of diamond, with a dependency on both the ion beam and electron beam acceleration voltage. CL emission in natural diamond is enhanced particularly at low ion beam and electron beam voltages. This enhancement of the CL emission can be partly explained by an increase in surface defects induced by ion milling. CL emission enhancement could be used to improve the CL image quality. To conduct FIB-SEM CL tomography, a recently developed novel specimen geometry is adopted to enable sequential ion milling and CL imaging on an untilted sample. We show that CL imaging can be manually combined with FIB-SEM tomography with a modified protocol for 3D microstructure reconstruction. In principle, automated FIB-SEM CL tomography should be feasible, provided that dedicated CL detectors are developed that allow subsequent milling and CL imaging without manual intervention, as the current CL detector needs to be manually retracted before a slice can be milled. Due to the required high electron beam acceleration voltage for CL emission, the resolution for FIB-SEM CL tomography is currently limited to several hundreds of nm in XY and up to 650 nm in Z for diamonds. Opaque materials are likely to have an improved Z resolution, as CL emission generated deeper in the material is not able to escape from it.     

Energy filtering transmission electron microscopy using the new JEM-2010FEF

The new JEM-2010FEF electron microscope provides useful techniques based on energy filtering as an omega-type energy filter is integrated into a thermal field-emission 200 kV transmission electron microscope. For example, the zero-loss imaging improves the contrast of high resolution lattice images as well as images of precipitates or lattice defects in alloys. The acquisition time for elemental mapping with core-loss electrons is one order in magnitude shorter than with energy-dispersive X-ray spectroscopy. The removal of inelastically scattered electrons enables us to observe weak lines in convergent-beam electron diffraction patterns from a thicker specimen with a probe size 1–2 nm in diameter. A combination of the field emission gun and sensitive recording media such as an imaging plate and a slow-scan CCD camera makes the energy filtering more powerful.     

The effect of inelastic scattering on crystal structure refinement from electron diffraction patterns recorded under almost parallel illumination

Recently a number of crystal structures were determined using electron diffraction data with an almost parallel electron beam. In many cases no energy filtering was applied. On the other hand, the contrast in convergent beam electron diffraction patterns is greatly improved by energy filtering of the electrons. To investigate whether energy filtering will improve the accuracy of the structure analysis from diffraction data recorded under an almost parallel beam condition, we recorded diffraction patterns of the [100] zone of YBa(2)Cu(3)O(7) using unfiltered electrons, zero-loss electrons and plasmon-loss electrons, respectively. Subsequently, the structure is refined based on these different electron diffraction datasets, using the program MSLS (Acta Crystallogr. A 54 (1998) 91). The results show that the obtained atomic positions are not significantly different for the chosen filter conditions. Even with amorphous carbon deposited on the specimen, which will cause a significant increase (>40 times) of energy-loss electrons, the structure refinement led to the same atomic positions.     

Effects of tilt on high-resolution ADF-STEM imaging

A study of the effects of small-angle specimen tilt on high-resolution annular dark field images was carried out for scanning transmission electron microscopes with uncorrected and aberration-corrected probes using multislice simulations. The results indicate that even in the cases of specimen tilts of the order of 1 degree a factor of 2 reduction in the contrast of the high-resolution image should be expected. The effect holds for different orientations of the crystal. Calculations also indicate that as the tilted specimen gets thicker the contrast reduction increases. Images simulated with a low-angle annular dark field detector show that tilt effects are more pronounced in this case and suggest that these low-angle detectors can be used to correct specimen tilt during scanning transmission electron microscopes operation.     

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.     

Calibration method of tilt and azimuth angles for alignment of TEM tomographic tilt series

This paper describes the calibration method of the tilt and azimuth angles of specimen using a digital protractor and a laser autocollimator for alignment of electron tomography. It also suggests an easy method to check whether the specimen is tilted by 180.0°, and whether the azimuth angle is 0.0°; the method involves the use of two images of a rod-shaped specimen collected before and after a 180.0° tilt. The method is based on the assumption that these images are symmetric about the tilt axis when the azimuth angle is 0.0°. In addition, we used an experiment to demonstrate the effect of the incorrect angles on reconstructed images and simulated the image quality against distance away from tilt axis.     

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.     

Structure of enamel surface as demonstrated by absorbed electrons.

The current induced by absorbed electrons in electron microprobe analysis was utilized to illustrate the surface structure of dental enamel. The electron images depicted a typical arcade or key-hole pattern on the surface of human incisors, while the surface of rat incisors was characterized by polygonal structures. Differences in electron density of the two specimen materials were observed, probably due to differences in their chemical composition. Absorbed electron images appear to be a valuable supplement to light microscopy, especially in the study of curved surfaces.     

Imaging using inelastically scattered electrons in CTEM and STEM geometry

It is shown that energy filtered transmission electron microscopy images are closely related to energy spectroscopic scanning transmission electron microscopy images. For the case of a single atom, we explore this similarity using both the coupled channels and density matrix approaches. We extend the result to the crystal case and find that the similarity persists, the limiting effects due to energy differences in the scattered electrons being small for typical specimen thicknesses in high-resolution transmission electron microscopy.     

Determination of the mean inner potential in III-V semiconductors by electron holography

The mean inner potential of GaAs(14.18V), InAs(14.50V), GaP(14.35V) and InP(14.50V) has been measured by transmission electron holography using the phase shift of the (000)-beam of the first hologram sideband. To provide a defined specimen geometry we used 90 degrees wedges obtained by the cleavage technique. The exact excitation condition as well as the acceleration voltage of the electrons were determined from convergent beam electron diffraction images. The magnification is extracted from two-beam lattice fringe images and dynamical effects are taken into account by Bloch-wave calculations.