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.     

A method for structure analysis of nanomaterials by electron diffraction: Phase identification and unit cell determination

We report a quick and easy method for a random selected area electron diffraction (SAED) pattern without rotating and tilting the specimen to perform phase identification and unit cell determination by combined with the XRD softwares. If your TEM is well aligned and camera length is carefully corrected, two‐dimensional (2D)‐SAED pattern can be directly transformed to 1D‐profile after the center determination of pattern, this profile is then imported to XRD analysis packages. Finally, phase identification and unit cell determination can be performed after peak search or precise peak position determined by profile fitting. Two examples, flaky‐like TiO₂ nanomaterial and TiO₂ nanotubes precipitated by the silver nanoparticles, were tested and verified for the validation of phase identification and unit cell determination using this method; the successful crystallographic analysis of one single gold nanocrystal indicates it is still validate for the nanocrystals with the smaller diffraction volume, but need two or more random tilt SAED patterns. This method could be further used in the quantitative phase analysis, structure determination and Rietveld refinement for the nanomaterials if the reliable integrated intensity can be extracted. Microsc. Res. Tech. 76:641–647, 2013. © 2013 Wiley Periodicals, Inc.     

High-angle triple-axis specimen holder for three-dimensional diffraction contrast imaging in transmission electron microscopy

Electron tomography requires a wide angular range of specimen-tilt for a reliable three-dimensional (3D) reconstruction. Although specimen holders are commercially available for tomography, they have several limitations, including tilting capability in only one or two axes at most, e.g. tilt-rotate. For amorphous specimens, the image contrast depends on mass and thickness only and the single-tilt holder is adequate for most tomographic image acquisitions. On the other hand, for crystalline materials where image contrast is strongly dependent on diffraction conditions, current commercially available tomography holders are inadequate, because they lack tilt capability in all three orthogonal axes needed to maintain a constant diffraction condition over the whole tilt range. We have developed a high-angle triple-axis (HATA) tomography specimen holder capable of high-angle tilting for the primary horizontal axis with tilting capability in the other (orthogonal) horizontal and vertical axes. This allows the user to trim the specimen tilt to obtain the desired diffraction condition over the whole tilt range of the tomography series. To demonstrate its capabilities, we have used this triple-axis tomography holder with a dual-axis tilt series (the specimen was rotated by 90° ex-situ between series) to obtain tomographic reconstructions of dislocation arrangements in plastically deformed austenitic steel foils.     

Precession electron diffraction using a digital sampling method

A software-based method for collecting precession electron diffraction (PED) patterns is described. The PED patterns are obtained on a computer controlled transmission electron microscope. A series of electron diffraction (ED) patterns are collected as still ED frames at equal intervals, while the electron beam is precessed by one period (360°) around the optical axis. A PED pattern is obtained by combining the different ED frames, which resembles the sampling of a conventional PED pattern. Since intermediate ED frames are collected, it is possible to perform different post-processing strategies on the ED data. This can be used for geometric corrections to obtain accurate integrated intensities. The alignments and data collection are fully automated and controlled by software. The data quality is comparable to what can be achieved using specialized hardware for precession. The PED data can be used for structure solution and refinement with reasonably good R-values.     

Precession electron diffraction using a digital sampling method

A software-based method for collecting precession electron diffraction (PED) patterns is described. The PED patterns are obtained on a computer controlled transmission electron microscope. A series of electron diffraction (ED) patterns are collected as still ED frames at equal intervals, while the electron beam is precessed by one period (360°) around the optical axis. A PED pattern is obtained by combining the different ED frames, which resembles the sampling of a conventional PED pattern. Since intermediate ED frames are collected, it is possible to perform different post-processing strategies on the ED data. This can be used for geometric corrections to obtain accurate integrated intensities. The alignments and data collection are fully automated and controlled by software. The data quality is comparable to what can be achieved using specialized hardware for precession. The PED data can be used for structure solution and refinement with reasonably good R-values.     

Crystallographic structural analysis in atom probe microscopy via 3D Hough transformation

Whereas the atom probe is regarded almost exclusively as a technique for 3D chemical microanalysis of solids with the highest chemical and spatial resolution, we demonstrate that the technique can be used for detailed crystallographic determinations. We present a new method for the quantitative determination of crystal structure (plane spacings and angles) using a Hough transformation of the reconstructed atom probe data. The resolving power is shown to be high enough to identify poorly established, discontinuous planes that are typical in semiconducting materials. We demonstrate the determination of crystal geometry around a grain boundary and the use of the technique for the optimisation of tomographic reconstruction. We propose that this method will enable automatic spatial analysis and, ultimately, automated tomographic reconstruction in atom probe microscopy.     

Computer programs for unit-cell determination in electron diffraction experiments

A set of computer programs for unit-cell determination from an electron diffraction tilt series and pattern indexing has been developed on the basis of several well-established algorithms. In this approach, a reduced direct primitive cell is first determined from experimental data, in the means time, the measurement errors of the tilt angles are checked and minimized. The derived primitive cell is then checked for possible higher lattice symmetry and transformed into a proper conventional cell. Finally a least-squares refinement procedure is adopted to generate optimum lattice parameters on the basis of the lengths of basic reflections in each diffraction pattern and the indices of these reflections. Examples are given to show the usage of the programs.     

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.     

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.     

“Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique

Using a combination of our recently developed automated diffraction tomography (ADT) module with precession electron technique (PED), quasi-kinematical 3D diffraction data sets of an inorganic salt (BaSO₄) were collected. The lattice cell parameters and their orientation within the data sets were found automatically. The extracted intensities were used for “ab initio” structure analysis by direct methods. The data set covered almost the complete set of possible symmetrically equivalent reflections for an orthorhombic structure. The structure solution in one step delivered all heavy (Ba, S) as well as light atoms (O). Results of the structure solution using direct methods, charge flipping and maximum entropy algorithms as well as structure refinement for three different 3D electron diffraction data sets were presented.     

Consistent indexing of a (set of) single crystal SAED pattern(s) with the ProcessDiffraction program

A computer program called "ProcessDiffraction" helps indexing a set of single crystal selected area electron diffraction (SAED) patterns by determining which of the presumed structures can fit all the measured patterns simultaneously. Distances and angles are measured in the digitalized patterns with a graphical tool by clicking on the two shortest non-collinear vectors (spots), using user-supplied calibration data. Centers of the spots and center of the pattern are optionally refined by the program. Suggested individual indexing solutions (consistent with an assumed unit cell) are listed by the program for each pattern. Simulated patterns are also consulted to check if the shortest calculated distances coincide with measured ones. Common solutions for the set are selected by checking the angles between the suggested zone axes against the angles between the experimental goniometer settings. The indexing process is manually controlled by selecting the candidate structures (one-by-one) for indexing and by specifying the tolerances for d-values, plane angles and zone angles. Patterns of any crystal system can be indexed successfully. Although error bars are larger in electron diffraction than in X-ray diffraction (XRD), frequently, many unrelated indexings are possible for any one electron diffraction pattern (irrespective of the indexing method), a set of SAED patterns can generally be indexed unambiguously, i.e. the three-dimensional reciprocal space can be identified correctly. Two other tools also help planning tilting experiments: zones along a plane can be listed (with their angles extended from a pre-selected zone in that plane) and zones lying at a given angle (specified with a tolerance) from a zone can also be identified (as they are situated between two cones). Another tool searches the XRD database directly either for advice on possible structures for a composition or to help calibration.     

Towards automated electron holographic tomography for 3D mapping of electrostatic potentials

Electron-holographic tomography (EHT), that is, the combination of off-axis electron holography with electron tomography, was successfully applied for the quantitative 3D mapping of electrostatic potentials at the nanoscale. Here we present the first software package (THOMAS) for semi-automated acquisition of holographic tilt series, a prerequisite for efficient data collection. Using THOMAS, the acquisition time for a holographic tilt series, consisting of object and reference holograms, is reduced by a factor of five on average, compared to the previous, completely manual approaches. Moreover, the existing software packages for retrieving amplitude and phase information from electron holograms have been extended, now including a one-step procedure for holographic tilt series reconstruction. Furthermore, a modified SIRT algorithm (WSIRT) was implemented for the quantitative 3D reconstruction of the electrostatic potential from the aligned phase tilt series. Finally, the application of EHT to a polystyrene latex sphere test-specimen and a pn-doped Ge ‘needle’-shaped specimen are presented, illustrating the quantitative character of EHT. For both specimens the mean inner potential (MIP) values were accurately determined from the reconstructed 3D potential. For the Ge specimen, additionally the ‘built-in’ voltage across the pn junction of 0.5 V was obtained.     

光学元件表面的数字全息在线检测

针对光学元件表面质量在线检测的特点,设计了基于数字全息的三维再现检测系统.该系统采用离轴光路,避开了被测元件的光轴,在数字全息再现过程中应用倾斜相差补偿技术去除了由于离轴检测引入的倾斜相位畸变.在检测过程中,利用围绕光轴旋转被测元件的方法来改变入射照明光方向矢量和相应的观察方向,实现了多照明矢量合成孔径技术的应用,扩展了系统的检测距离,提高了系统分辨率.同时,多照明角度下检测数据的叠加,还有效地抑制了检测过程中出现的散斑噪声对结果准确度的影响.通过对分辨率板、高精度玻璃反射镜的检测实验,验证了该系统在光学元件表面检测中的作用.当记录距离为40 cm时,其分辨率能够达到10 μm,满足光学元件表面检测的需要.     

Comparison of quartz crystallographic preferred orientations identified with optical fabric analysis,electron backscatter and neutron diffraction techniques

Three techniques are used to measure crystallographic preferred orientations (CPO) in a naturally deformed quartz mylonite: transmitted light cross‐polarized microscopy using an automated fabric analyser, electron backscatter diffraction (EBSD) and neutron diffraction. Pole figure densities attributable to crystal‐plastic deformation are variably recognizable across the techniques, particularly between fabric analyser and diffraction instruments. Although fabric analyser techniques offer rapid acquisition with minimal sample preparation, difficulties may exist when gathering orientation data parallel with the incident beam. Overall, we have found that EBSD and fabric analyser techniques are best suited for studying CPO distributions at the grain scale, where individual orientations can be linked to their source grain or nearest neighbours. Neutron diffraction serves as the best qualitative and quantitative means of estimating the bulk CPO, due to its three‐dimensional data acquisition, greater sample area coverage, and larger sample size. However, a number of sampling methods can be applied to FA and EBSD data to make similar approximations.     

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.     

Towards automated diffraction tomography. Part II--Cell parameter determination

Automated diffraction tomography (ADT) allows the collection of three-dimensional (3d) diffraction data sets from crystals down to a size of only few nanometres. Imaging is done in STEM mode, and diffraction data are collected with quasi-parallel beam nanoelectron diffraction (NED). Here, we present a set of developed processing steps necessary for automatic unit-cell parameter determination from the collected 3d diffraction data. Cell parameter determination is done via extraction of peak positions from a recorded data set (called the data reduction path) followed by subsequent cluster analysis of difference vectors. The procedure of lattice parameter determination is presented in detail for a beam-sensitive organic material. Independently, we demonstrate a potential (called the full integration path) based on 3d reconstruction of the reciprocal space visualising special structural features of materials such as partial disorder. Furthermore, we describe new features implemented into the acquisition part.     

Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.     

TRICE - A program for reconstructing 3D reciprocal space and determining unit-cell parameters

A program system-Trice-for reconstructing the 3D reciprocal lattice from an electron diffraction tilt series is described. The unit-cell parameters can be determined from electron diffraction patterns directly by Trice. The unit cell can be checked and the lattice type and crystal system can be determined from the 3D reciprocal lattice. Trice can be applied to all crystal systems and lattice types.     

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°.