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.     

Observation of three-dimensional elemental distributions of a Si device using a 360 degrees -tilt FIB and the cold field-emission STEM system

A technique for preparation of a pillar-shaped specimen and its multidirectional observation using a combination of a scanning transmission electron microscope (STEM) and a focused ion beam (FIB) instrument has been developed. The system employs an FIB/STEM compatible holder with a specially designed tilt mechanism, which allows the specimen to be tilted through 360 degrees [T. Yaguchi, M. Konno, T. Kamino, T. Hashimoto, T. Ohnishi, K. Umemura, K. Asayama, Microsc. Microanal. 9 (Suppl. 2) (2003) 118; T. Yaguchi, M. Konno, T. Kamino, T. Hashimoto, T. Ohnishi, M. Watanabe, Microsc. Microanal. 10 (Suppl. 2) (2004) 1030]. This technique was applied to obtain the three-dimensional (3D) elemental distributions around a contact plug of a Si device used in a 90-nm technology. A specimen containing only one contact plug was prepared in the shape of a pillar with a diameter of 200nm and a length of 5mum. Elemental maps were obtained from the pillar specimen using a 200-kV cold-field emission gun (FEG) STEM model HD-2300C equipped with the EDAX genesis X-ray energy-dispersive spectrometry (XEDS) system through a spectrum imaging technique. In this study, elemental distributions of minor elements with weak signals were enhanced by applying principal component analysis (PCA), which is a superior technique to extract weak signals from a large dataset. The distributions of elements, especially the metallization component Ti and minor dopant As in this particular device, were successfully extracted by PCA. Finally, the 3D elemental distributions around the contact plug could be visualized by reconstruction from the tilt series of maps.     

Tomography experiment of an integrated circuit specimen using 3 MeV electrons in the transmission electron microscope

The possibility of utilizing high-energy electron tomography to characterize the micron-scale three dimensional (3D) structures of integrated circuits has been demonstrated experimentally. First, electron transmission through a tilted SiO(2) film was measured with an ultrahigh-voltage electron microscope (ultra-HVEM) and analyzed from the point of view of elastic scattering of electrons, showing that linear attenuation of the logarithmic electron transmission still holds valid for effective specimen thicknesses up to 5 microm under 2 MV accelerating voltages. Electron tomography of a micron-order thick integrated circuit specimen including the Cu/via interconnect was then tried with 3 MeV electrons in the ultra-HVEM. Serial projection images of the specimen tilted at different angles over the range of +/-90 degrees were acquired, and 3D reconstruction was performed with the images by means of the IMOD software package. Consequently, the 3D structures of the Cu lines, via and void, were revealed by cross sections and surface rendering.     

Mean free paths for inelastic electron scattering in silicon and poly(styrene) nanospheres

The mean free paths for inelastic electron scattering, lambda(in), in silicon [Si] and poly(styrene) [PS] have been measured using off-axis electron holography in a field-emission transmission electron microscope (FEG TEM). The holographic imaging method determines both quantitative wave phase information as well as elastic energy-filtered wave amplitude information. Using the energy-filtered amplitude data, two-dimensional t/lambda(in) images are reconstructed. The present work uses spherical nanoparticles as samples, so the sample thickness at any point in a two-dimensional image can be calculated knowing the center and radius of the projected nanosphere. The thickness contribution to t/lambda(in) is removed to obtain quantitative lambda(in) values. This work finds values of lambda(i)Si = 53.8 +/- 5.5 and 88.6 +/- 6.9 nm, and lambda(PS) = 78.1 +/- 3.4 and 113.0 +/- 5.9 nm for 120 and 200 keV incident electron energies, respectively.     

Stacked bilayer helices: a new structural organization of amphiphilic molecules

Intriguing helical fibres can be created by self-assembly of simple chiral amphiphilic molecules. We study the parameters governing this spontaneous self-organization by three-dimensional (3D) electron microscopy of the helical fibres embedded in a vitreous ice-matrix. Different stable helices are generated reproducibly using specific combinations of the control parameters in our system. All fibres with diameters less than 25 nm consist of a narrow stack of compartmented bilayers twisted into a left-handed helix. Our novel helical 3D reconstruction procedures in combination with specialized cryomicroscopical specimen preparation, can rapidly elucidate the structure of such helical assemblies. This approach may complement or even replace existing diffraction-based methodologies.     

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.     

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.     

High resolution biological scanning electron microscopy: A comparative study of low temperature metal coating techniques

Structural information on the surface of biological specimens can be resolved within molecular dimensions by “in-lens” field emission scanning electron microscopes when cryo-methods are used to adequately preserve the native state of the specimen. The visual definition of molecular surface structures depends largely on the metal coating. The thickness of the coating, as well as the temperature at which it is deposited, are among the most important parameters affecting visual definition. These were evaluated on T4 polyheads and T4D phages using chromium double-axis rotary shadowing (DARS). Micrographs of optimally DARS coated T4 polyheads and T4D phages were compared with chromium planar-magnetron sputtering (PMS) and unidirectional shadowing with platinum/carbon. Metal deposition was carried out at low temperatures during all three procedures. Optimal visual definition of structural details on the surface of DARS coated T4 polyheads and T4D phages (capsomeres of T4 polyheads and their subunits with diameters of 8 and 3 nm; T4D phage tail fibres with a thickness of 3 nm) is achieved at a thickness of the chromium film greater than the minimum required for metal film coalescence. Chromium DARS coating at room temperature resulted in poor structural definition, whereas DARS at specimen temperatures of ?85°C and ?150°C, with the chromium thickness optimized for each temperature, yielded good visual detail of polyhead substructures. The visual definition was slightly reduced when DARS coating was carried out at a specimen temperature of ?250°C. Adequate structural visibility of T4D phage and T4 polyhead surface structures was achieved with the three coating techniques tested. Smaller filamentous structures, however (e.g., phage tail fibres), were more clearly identified after chromium DARS coating or unidirectional platinum/carbon shadowing than after optimized PMS with chromium. Each method has its own merits.     

Production of Carbon Nanotubes by the Magnetron DC Sputtering Method

Carbon films containing multiwall nanotubes were produced by the magnetron dc sputtering method. A graphite disc with Y and Ni catalyst plates was used as a target. The structural and morphological properties of the films were investigated using a JEM 2000EXII transmission electron microscope. The films were deposited on glass, nickel, fluoroplastic, and other materials. The films produced contained up to 40% of multiwall carbon nanotubes with diameters of 4–16 nm and a length of ≥200 nm.__________Translated from Pribory i Tekhnika Eksperimenta, No. 3, 2005, pp. 150–152.Original Russian Text Copyright © 2005 by Antonenko, Mal’tsev.     

Three-dimensional view of the chromatin in freeze-fractured chicken erythrocyte nuclei.

The freeze-fracture thaw-fix (FfTF) technique described in earlier papers is applied in the present work to more detailed study of the chicken erythrocyte, by transmission replicas and high resolution scanning electron microscopy (3 nm scan beam size). The three-dimensional structure of the chromatin, and possibly the non-histone protein matrix, of fractured nuclei is to a large extent retained in this method of preparation and seen in stereomicrographs. In these micrographs the helical sub-structure of the 25 nm chromatin strands can be seen at about the same resolution as that of previously published micrographs in which extracted chromatin is viewed by negative contrast or after metal shadowing. The useful resolution of the secondary electron micrographs, for a suitably mounted specimen, is shown to be as good as that of transmission micrographs of platinum-carbon replicas of the same material.     

"Large" and "small" nuclear pore complexes; the influence of glutaraldehyde.

Aliquots of lymphocyte cell suspensions were pretreated according to the following three schedules before freeze fracturing: (a) prefixed with 2% glutaraldehyde before infiltration with 25% glycerol in medium RPMI-1640; (b) frozen in medium RPMI-1640 without additional pretreatment; and (c) frozen after pretreatment with 25% glycerol in medium RPMI-1640. The diameters of the fractured nuclear pore complexes of cells prefixed with glutaraldehyde were normally distributed within the range 70-120 nm (median 90 nm). The nuclear envelopes of 66-75% of cells processed through schedules b and c, which omitted glutaraldehyde fixation, had 70-120 nm diameter pores, while the remainder had pores with diameters in the range 120-175 nm. The large pores were structurally similar to the smaller pores except for their dimensions. These results indicate that glutaraldehyde gives rise to shrinkage of the larger pores to the minimum, smaller, diameter. Apparent orifices of at least 30 nm diameter were sometimes observed at the centres of these large pore complexes. We propose that the variation in pore diameters may indicate opening and closure of this orifice, and that the widely reported "central granule" of the nuclear pore complex corresponds with the orifice in a closed configuration.     

A novel method for focus assessment in atomic resolution STEM HAADF experiments

Analysis of the Fourier components of through-focal images in scanning transmission electron microscopy with a high angle annular dark field detector is used to assess illumination defocus values. The method is based on a least squares fitting of the peculiar dependence of Fourier components of the high angle annular dark field image on defocus. The validity of the method has been checked against simulations and experiments obtaining a good level of accuracy on the defocus measurement (δf=2 nm) for simulated specimen thickness up to 40 nm. The difference between simulated and experimental Fourier coefficients for large defoci can be used to estimate the specimen thickness at least up to 30 nm but with decreasing precision for larger thickness.     

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.     

Optimization of quantitative electron energy loss spectroscopy in the low loss region: phosphorus L-edge.

The purpose of this study was to optimize quantitative electron energy loss spectroscopy (EELS) of elements that have characteristic edges in the low energy loss region and are components of organic matrices. The optimum parameters for phosphorus L2,3-edge (at 135 eV) detection were determined by numerical analysis of computer-generated, Poisson-noisy spectra and by experimental measurements (at 80 keV) of films of the phosphoprotein, phosvitin. When the first, second and third valence electron/plasmon scatterings are included in the multiple least-squares (MLS) fit, the background subtraction of (first-difference) spectra is significantly more accurate than that obtained with the "inverse power law" method, even for a specimen thickness of only 0.25 lambda. Taking into account the effects of plural scattering, the optimal thickness for P quantitation is approximately 0.3 lambda. Signal-to-noise (S/N) ratio decreases rapidly with thickness, and at 1.0 lambda, it is only about 60% of the optimum S/N. The combined effects of the statistical uncertainty of measurements and of the systematic error due to gain variations of the parallel detector were evaluated, and the relative sensitivities of the no-difference (raw spectrum), first-difference and second-difference methods were compared. For channel-to-channel gain variations greater than 0.1% and up to 0.8%, the first-difference method results in the lowest uncertainty of P measurements. In the absence of gain variations, direct fitting provides the greatest sensitivity (least uncertainty), whereas at larger gain variations it may be necessary to use the second-difference method. The optimum energy shift for collecting a first-difference spectrum, approximately 15 eV, did not show any great variation between 5 and 25 eV, and is, in general, specimen dependent. Quantitation with EELS showed excellent correlation with simultaneous electron probe X-ray microanalysis, but, for the detection of P in a 0.25 lambda thick specimen, EELS was approximately five to six times more sensitive than X-ray. The minimal detectable P concentration, with 0.5 nA beam current for 100 s in a 0.25 lambda thick specimen, was 8.4 mmol/kg (0.01 at%) at the 99% confidence level, equivalent to 34 phosphorus atoms for a 15 nm probe. This value is close to the theoretical prediction of 7.5 mmol/kg, and can be improved only by further reducing the gain variation and directly fitting the non-difference spectrum. Appropriate reduction of the gain variations to less than 0.1% would result in a further, approximately two-fold, improvement in the parallel EELS detection system.(ABSTRACT TRUNCATED AT 400 WORDS)     

The influence of lens chromatic aberration on electron energy-loss spectroscopy quantitative measurements.

An investigation has been made into the effect of chromatic aberrations of a pre-spectrometer lens system on quantitative elemental analysis by electron energy loss spectroscopy (EELS). In transmission electron microscopy (TEM) diffraction mode, the measured effects are typically 150-330 times larger than if only objective-lens chromatic aberration were important. We discuss several methods of avoiding errors arising from chromatic aberration, including selection of a suitable optical mode (dependent on the desired spatial resolution), adjustment of the TEM imaging system so as to focus the system for a chosen energy loss, and analysis of a large area of a uniform specimen.     

A combined top and side entry specimen stage for a Hitachi H500 transmission electron microscope

The Hitachi H500 transmission electron microscope has been modified in order that both the top and side entry specimen stages may be fitted simultaneously. This made possible top entry multi-specimen operation up to a maximum magnification of × 100,000 and a resolution of 1.8 nm, combined with the normal side entry stage facilities of ±60° tilt, 0.45 nm resolution and × 400,000 magnification.     

Quantification and thickness correction of EFTEM phosphorus maps

We describe a method for correcting plural inelastic scattering effects in elemental maps that are acquired in the energy filtering transmission electron microscope (EFTEM) using just two energy windows, one above and one below a core edge in the electron energy loss spectrum (EELS). The technique is demonstrated for mapping low concentrations of phosphorus in biological samples. First, the single-scattering EELS distributions are obtained from specimens of pure carbon and plastic embedding material. Then, spectra are calculated for different specimen thicknesses t, expressed in units of the inelastic mean free path lambda. In this way, standard curves are generated for the ratio k0 of post-edge to pre-edge intensities at the phosphorus L2,3 excitation energy, as a function of relative specimen thickness t/lambda. Thickness effects in a two-window phosphorus map are corrected by successive acquisition of zero-loss and unfiltered images, from which it is possible to determine a t/lambda image and hence a background k0-ratio image. Knowledge of the thickness-dependent k0-ratio at each pixel thus enables a more accurate determination of the phosphorus distribution in the specimen. Systematic and statistical errors are calculated as a function of specimen thickness, and elemental maps are quantified in terms of the number of phosphorus atoms per pixel. Further analysis of the k0-curve shows that the EFTEM can be used to obtain reliable two-window phosphorus maps from specimens that are considerably thicker than previously possible.     

Measurement of local thickness by electron energy-loss spectroscopy

We review various methods which can be used to derive the thickness of an electron-microscope specimen from its transmission energy-loss spectrum. We have applied a sum-rule technique to various kinds of specimen, using a variety of electron-optical conditions, and estimate its accuracy to be typically ±10% (or±2nm if larger) over the thickness range 10–150 nm. This method requires no knowledge of the physical or chemical properties of the specimen other than its refractive index (∞ for metal). It involves only a low radiation dose, allowing good lateral resolution (<10 nm) to be achieved even by selected-area techniques.     

Cornea and its adaptation to environment and accommodation function in veiled chameleon (Chamaeleo calyptratus): ultrastructure and 3D transmission electron tomography

We investigate the ultrastructural features and 3D electron tomography of chameleon (Chamaeleon calyptratus) which is a native of desert environments of Saudi Arabia. The corneas of the chameleon were fixed in 2.5% glutaraldehyde containing cuprolinic blue in sodium acetate buffer for electron microscopy and tomography, and observed under a JEOL 1400 transmission electron microscope. The thin cornea (21.92 μm) contained 28–30 collagen fibril lamellae. The middle stromal lamellae (from 13 to 19) contained keratocytes with a long cell process and filled with granular material. The CF diameter increased from lamella 1 (30.44 ± 1.03) to Lamella 5 (52.83 ± 2.00) then decreased towards the posterior stoma. The percentage of large CF diameters (55–65 nm) was very high in the lamellae L14 (38.8%) and L15 (85.7%). The mean PGs area of the posterior stroma (448.21 ± 24.84 nm²) was significantly larger than the mean PGs area of the anterior, (309.86 ± 8.2 nm²) and middle stroma 245.94 ± 8.28 nm²). 3D electron tomography showed the distribution of PGs around and over the CF. Variable diameters of CFs in the anterior stroma may provide compact lamellae which may restrict the low wavelength of light. Variable diameters of CFs in the anterior stroma may provide compact lamellae which may restrict the low wavelength of light. This accommodation function is achieved by bending of the cornea. During bending the anterior stroma was stretched and the posterior stroma was compressed due to the presence of small CFs. The middle stroma remained stiff due to the presence of large CFs. Large proteoglycans not only maintain hydration for a longer period of time, but also act as a lubricant to neutralise the shear forces in the anterior and posterior stroma during bending.     

Structure determination of the hexagonal quasicrystal approximant micro'-(Al,Si)4Cr by the strong reflections approach

A number of different crystalline phases have been found in Al-rich Al-Cr-Si alloys by transmission electron microscopy (TEM). Among these, the new hexagonal phase micro'-(Al,Si)(4)Cr (a=2.01 and c=1.24 nm) often found coexisting with the hexagonal micro-(Al,Si)(4)Cr (a=1.998 and c=2.4673 nm, isostructural with micro-Al(4)Mn) and also with the hexagonal lambda-(Al,Si)(4)Cr (a=2.839 and c=1.239 nm, isostructural with lambda-Al(4)Mn). It is evident from their electron diffraction patterns that the structures of these three phases are related. The strong reflections in all three are distributed in a similar way. They all exhibit a pseudo-icosahedral symmetry. The structure factor amplitudes and phases for the strong reflections of the micro' phase could therefore be adopted from those of the lambda phase, according to the strong reflections approach. A structure model of the micro' phase is thus deduced from the known lambda-Al(4)Mn. micro' consists of chains of 3+3 or 4+2 interpenetrated icosahedra along the 100 directions. Similar to the lambda phase, there are two flat layers (F) and four puckered layers (P) in each unit cell of micro', stacked along the c-axis in a sequence of PFP(PFP)' where the (PFP)' block is related to the PFP block by a 6(3) screw.