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.     

Three-dimensional distributions of elements in biological samples by energy-filtered electron tomography

By combining electron tomography with energy-filtered electron microscopy, we have shown the feasibility of determining the three-dimensional distributions of phosphorus in biological specimens. Thin sections of the nematode, Caenorhabditis elegans were prepared by high-pressure freezing, freeze-substitution and plastic embedding. Images were recorded at energy losses above and below the phosphorus L2,3 edge using a post-column imaging filter operating at a beam energy of 120 keV. The unstained specimens exhibited minimal contrast in bright-field images. After it was determined that the specimen was sufficiently thin to allow two-window ratio imaging of phosphorus, pairs of pre-edge and post-edge images were acquired in series over a tilt range of +/-55 degrees at 5 degrees increments for two orthogonal tilt axes. The projected phosphorus distributions were aligned using the pre-edge images that contained inelastic contrast from colloidal gold particles deposited on the specimen surface. A reconstruction and surface rendering of the phosphorus distribution clearly revealed features 15-20 nm in diameter, which were identified as ribosomes distributed along the stacked membranes of endoplasmic reticulum and in the cytoplasm. The sensitivity of the technique was estimated at < 35 phosphorus atoms per voxel based on the known total ribosomal phosphorus content of approximately 7000 atoms. Although a high electron dose of approximately 10(7)e/nm2 was required to record two-axis tilt series, specimens were sufficiently stable to allow image alignment and tomographic reconstruction.     

A 360° single-axis tilt stage for the high-voltage electron microscope

A new type of specimen stage that permits more than 180° of tilting about the axis of a side-entry rod has been developed for a high-voltage electron microscope (HVEM). Roughly cylindrical specimens, with radial dimensions of less than a few micrometres, that can be mounted on the tip of a microneedle or micropipette are applicable. For glass micropipettes, the energy of the 1-MeV beam of the HVEM is sufficient to image specimens through both walls. The stage employs a spindle mechanism that holds these needles or micropipettes coaxial with the tilt axis, allowing the specimen to be rotated without restriction. This arrangement, along with the cylindrical form of the specimen, is an important development for single-axis tomography, because it permits a complete 180° set of projections to be recorded. The angular accuracy of the stage was demonstrated to be within ±0.20°, with a cumulative error of less than 1.0° over a 180° span. The new stage was tested using puffball spores mounted on a micropipette. A 180° tilt series was recorded and processed to yield a tomographic three-dimensional reconstruction which was displayed both as a cross-sectional view perpendicular to the tilt axis, and as a shaded surface viewed from different directions. The same computations were repeated using subsets of the tilt series to assess the effect of various amounts of missing information. Visual inspection of a selected cross-section from these reconstructions indicated that limiting the angular range to 160° produced results nearly as good as the full data set. Limiting the range to 140°, however, produced a noticeable geometric distortion, which became increasingly severe with ranges of 120° and 100°.     

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.     

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.     

Nanoparticle shape and configuration analysis by transmission electron tomography

Tomographic reconstruction by transmission electron microscopy is used to reveal three‐dimensional nanoparticle shapes and the stacking configurations of nanoparticle ensembles. Reconstructions are generated from bright‐field image tilt series, with a sample tilt range up to ± 70°, using single or dual tilt axes. We demonstrate the feasibility of this technique for the analysis of nanomaterials, using appropriate acquisition conditions. Tomography reveals both cubic and hexagonal close‐packing configurations in multi‐layered arrays of size‐selected In nanospheres. By tomography and phase‐contrast lattice imaging, we relate the three‐dimensional shape of PbSe octahedral nanoparticles to the underlying crystal structure. We also confirm simple‐cubic packing in multi‐layers of PbSe nanocubes and see evidence that the particle shapes have cubic symmetry. The shapes of TiO₂ nanorod bundles are shown by tomographic reconstruction to resemble flattened ellipsoids.     

Comparison of intensity distributions in tomograms from BF TEM,ADF STEM,HAADF STEM,and calculated tilt series

The three-dimensional (3D) morphology of a nanometer-sized object can be obtained using electron tomography. Variations in composition or density of the object cause variations in the reconstructed intensity. When imaging homogeneous objects, variations in reconstructed intensity are caused by the imaging technique, imaging conditions, and reconstruction. In this paper, we describe data acquisition, image processing, and 3D reconstruction to obtain and compare tomograms of magnetite crystals from bright field (BF) transmission electron microscopy (TEM), annular dark-field (ADF) scanning transmission electron microscopy (STEM), and high-angle annular dark field (HAADF) STEM tilt series. We use histograms, which plot the number of volume elements (voxels) at a given intensity vs. the intensity, to measure and quantitatively compare intensity distributions among different tomograms. In combination with numerical simulations, we determine the influence of maximum tilt angle, tilt increment, contrast changes with tilt (diffraction contrast), and the signal-to-noise ratio (SNR) as well as the choice of the reconstruction approach (weighted backprojection (WB) and sequential iterative reconstruction technique (SIRT)) on the histogram. We conclude that because ADF and HAADF STEM techniques are less affected by diffraction, and because they have a higher SNR than BF TEM, they are better suited for tomography of nanometer-sized crystals.     

Towards automated diffraction tomography: part I--data acquisition

The ultimate aim of electron diffraction data collection for structure analysis is to sample the reciprocal space as accurately as possible to obtain a high-quality data set for crystal structure determination. Besides a more precise lattice parameter determination, fine sampling is expected to deliver superior data on reflection intensities, which is crucial for subsequent structure analysis. Traditionally, three-dimensional (3D) diffraction data are collected by manually tilting a crystal around a selected crystallographic axis and recording a set of diffraction patterns (a tilt series) at various crystallographic zones. In a second step, diffraction data from these zones are combined into a 3D data set and analyzed to yield the desired structure information. Data collection can also be performed automatically, with the recent advances in tomography acquisition providing a suitable basis. An experimental software module has been developed for the Tecnai microscope for such an automated diffraction pattern collection while tilting around the goniometer axis. The module combines STEM imaging with diffraction pattern acquisition in nanodiffraction mode. It allows automated recording of diffraction tilt series from nanoparticles with a size down to 5nm.     

Comparison of intensity distributions in tomograms from BF TEM, ADF STEM, HAADF STEM, and calculated tilt series

The three-dimensional (3D) morphology of a nanometer-sized object can be obtained using electron tomography. Variations in composition or density of the object cause variations in the reconstructed intensity. When imaging homogeneous objects, variations in reconstructed intensity are caused by the imaging technique, imaging conditions, and reconstruction. In this paper, we describe data acquisition, image processing, and 3D reconstruction to obtain and compare tomograms of magnetite crystals from bright field (BF) transmission electron microscopy (TEM), annular dark-field (ADF) scanning transmission electron microscopy (STEM), and high-angle annular dark field (HAADF) STEM tilt series. We use histograms, which plot the number of volume elements (voxels) at a given intensity vs. the intensity, to measure and quantitatively compare intensity distributions among different tomograms. In combination with numerical simulations, we determine the influence of maximum tilt angle, tilt increment, contrast changes with tilt (diffraction contrast), and the signal-to-noise ratio (SNR) as well as the choice of the reconstruction approach (weighted backprojection (WB) and sequential iterative reconstruction technique (SIRT)) on the histogram. We conclude that because ADF and HAADF STEM techniques are less affected by diffraction, and because they have a higher SNR than BF TEM, they are better suited for tomography of nanometer-sized crystals.     

Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography

An image alignment method for electron tomography is presented which is based on cross-correlation techniques and which includes a simultaneous refinement of the tilt geometry. A coarsely aligned tilt series is iteratively refined with a procedure consisting of two steps for each cycle: area matching and subsequent geometry correction. The first step, area matching, brings into register equivalent specimen regions in all images of the tilt series. It determines four parameters of a linear two-dimensional transformation, not just translation and rotation as is done during the preceding coarse alignment with conventional methods. The refinement procedure also differs from earlier methods in that the alignment references are now computed from already aligned images by reprojection of a backprojected volume. The second step, geometry correction, refines the initially inaccurate estimates of the geometrical parameters, including the direction of the tilt axis, a tilt angle offset, and the inclination of the specimen with respect to the support film or specimen holder. The correction values serve as an indicator for the progress of the refinement. For each new iteration, the correction values are used to compute an updated set of geometry parameters by a least squares fit. Model calculations show that it is essential to refine the geometrical parameters as well as the accurate alignment of the images to obtain a faithful map of the original structure.     

Effect of small crystal tilt on atomic-resolution high-angle annular dark field STEM imaging

Using a slightly tilted convergent electron beam, high-angle annular dark field scanning transmission electron microscopy observations have been performed of a [0 11]-oriented Si crystal. A small tilt of the crystal zone axis with respect to the coma-axis of the probe-forming lens causes a difference in intensity between bright spots of a Si dumbbell. The semiangle of the beam probe and the tilting angle with respect to the specimen hormal were determined by means of convergent beam micro-diffraction. The simulation using these parameters accounts for the image contrasts satisfactorily.     

Effects of specimen tilt in ADF-STEM imaging of a-Si/c-Si interfaces

Annular dark field scanning transmission electron microscopy (ADF-STEM) imaging of a crystal depends strongly on specimen orientation, but for an amorphous sample it is insensitive to orientation changes. To fully investigate the effects of specimen tilt, an interface of amorphous Si (a-Si) and crystalline Si (c-Si) was rotated systematically off a zone axis in a STEM equipped with low-angle ADF (LAADF) and high-angle ADF (HAADF) detectors. The change of relative intensity across the interface shows very different trends in the LAADF and the HAADF images upon tilting. More importantly, it is found that the HAADF signal decreases much more rapidly when tilted off a zone axis than does the LAADF signal. The high-resolution lattice fringes also disappear much faster in the HAADF image than in the LAADF image. These trends reflect the fact that the channeling peaks that are responsible for scattering into the HAADF detector decrease more quickly upon tilting than the lower angle scattering to the LAADF detector does.     

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.     

Automated microscopy for electron tomography.

Instrumentation and methodology for the automatic collection of tomographic tilt series data for the three-dimensional reconstruction of single particles is described. The system consists of a Philips EM 430 TEM, with a Gatan 673 cooled slow-scan CCD camera and a Philips C400 microscope computer control unit attached. The procedure for data collection includes direct digital recording of the images on the CCD camera and the automatic measurement and correction of (a) image shifts resulting from tilting the specimen, (b) variation of defocus and (c) the eucentric height position of the specimen. Experiments are described illustrating the possibilities and limitations of automatic data collection. Data collection at a magnification of 30k shows that the exposure time of the specimen to the beam is reduced by a factor of 10-100 compared to manual operation of the TEM.     

An improved double-tilt stage for the AEI EM7 high-voltage electron microscope

Vibration transmitted by the specimen rod of a side-entry stage frequently decreases image resolution, and the length of the rod in the high-voltage electron microscope can make the problem severe. A detachable tip clamped to the translation stage minimizes the effect, but eliminates the rod as a means of tilting. Furthermore, the second tilt mechanism is usually built into the rod. Thus the sample is coupled not clamped to the rod, increasing the effect. The image resolution attainable with our double-tilt stage was 1·5 nm along the rod's axis and 5·0 nm perpendicular to it before modification. An isotropic resolution of 0·5 nm was achieved by attaching the specimen tip to the rod with a flexible coupling and clamping both ends of the tip to the translation ring. The couplings used transmit the torque to rotate the specimen holder but dampen vibration. Ion-pumping the vacuum system with all other pumps off also improved specimen stability.     

Specimen shift correction in tilting experiments

An easy method to correct for specimen shift during tilting experiments is described. The tilt is done while viewing the specimen and correcting for the shift in dark field mode, using a reflection g_hkl parallel to the axis of tilt. The tedious procedure of going back and forth between imaging and diffraction modes can thus be avoided.     

Improved grid holders for an all-purpose electron microscope specimen stage

The general requirements necessary for a specimen grid holder (cup) to meet the rather stringent demands set by an all-purpose specimen stage are discussed. Two models made from platinum or aluminum are described, which provide for the grid to be either on or off the axes of tilt, and allow the cup and grid to be ultrasonically cleaned. The stability, tilt movements, anticontamination, and furnace characteristics of the cups have proved to be excellent.     

A method of using the incident beam tilt as a eucentric goniometer in transmission electron microscopy

The principal difficulties in constructing and operating a eucentric specimen tilting goniometer in a transmission electron microscope are discussed, together with the goniometric function of the incident beam tilt. The latter function is found easy to operate in a eucentric manner. The imaging beam then will have a non-axial path, which will increase particularly the field chromatic aberration. Earlier, however, a technique for the compensation of the chromatic aberration during displaced aperture dark field image formation has been developed. In combination with this technique, it proved possible to use the ordinary incident beam tilt as a eucentric goniometer. Image sequences were obtained, with accurately varied diffraction conditions. The tilt angles and the direction of the tilt axis can be very accurately determined from the displacements of the diffraction pattern.     

Automated electron tomography with scanning transmission electron microscopy

We report the successful implementation of a fully automated tomographic data collection system in scanning transmission electron microscopy (STEM) mode. Autotracking is carried out by combining mechanical and electronic corrections for specimen movement. Autofocusing is based on contrast difference of a focus series of a small sample area. The focus gradient that exists in normal images due to specimen tilt is effectively removed by using dynamic focusing. An advantage of STEM tomography with dynamic focusing over TEM tomography is its ability to reconstruct large objects with a potentially higher resolution.     

High-precision tilt stage for the high-voltage electron microscope

The high-voltage electron microscope is used to study thick samples (0.25 to several micrometers) to obtain three-dimensional information at ultrastructural resolution. Three-dimensional image reconstructions are often employed to extract, process and display this information. The sets of images used to form reconstructions must be recorded for precisely known specimen-beam orientations, especially if tomographic methods are employed. The design and operation of a precision (+/- 0.06 degrees) single-tilt stage to support this type of imaging is reported. All motions including two translations, height adjustment and tilting are accomplished via a single objective lens entry port. The specimen rod is supported on two rubber gaskets for vibration isolation, and motorized precision micrometers with encoder readouts for position monitoring drive the motions. The stage is stable to 0.6 nm for at least 16 s and is capable of tilt angles of +/- 70 degrees.