Combined scanning transmission electron microscopy tilt- and focal series

3D reconstruction of a million atoms by multiple-section local-orbital tomography

Three-dimensional (3D) structural analysis is an important field in physical and biological sciences. There exist two groups of electron microscopy methods that are capable of providing 3D structural information of an object, i.e., electron tomography and depth sectioning. Electron tomography is capable of resolving atoms in all three dimensions, but the accuracy in atomic positions is low and the object size that can be reconstructed is limited. Depth sectioning methods give high positional accuracy in the imaging plane, but the spatial resolution in the third dimension is low. In this work, electron tomography and depth sectioning are combined to form a method called multiple-section local-orbital tomography, or nLOT in short. The nLOT method provides high spatial resolution and high positional accuracy in all three dimensions. The object size that can be reconstructed is extended to a million atoms. The present method establishes a foundation for the widespread application of atomic electron tomography.

Optical microscope with a large tilt angle and a long focal length for a nano-size angle-resolved photoemission spectroscopy

Angle-resolved photoemission spectroscopy with nanoscale spatial resolution (Nano-ARPES) is a powerful tool for the investigation of electronic structures of materials and their spatial configurations. In order to capture the area of interest in Nano-ARPES measurements effectively, an optical microscope can be used to provide real space optical images as a reference. In this work, a new type of optical microscope for Nano-APRES spectrometer with a large tilt angle of ∼30 degrees and a long focal length of ∼12 mm has been designed. Large magnifications by 7 × to 20 × and a spatial resolution of 3 um have been achieved, which can effectively assist optical alignment for Nano-ARPES. In addition, the strong boundary sensitivity observed in such a tilt design demonstrates its special capability in detecting the fine features of surface coarseness.

Three-dimensional ultrastructure reconstruction of tendinous components at the bifurcation of the bovine superficial digital flexor tendon using array and STEM tomographies

Tendons transmit force from muscle to bone for joint movement. Tenocytes are a specialized type of fibroblast that produces collagen fibrils in tendons. Their cytoplasmic processes form a network surrounding collagen fibrils to define a collagen fibre. Glycosaminoglycan (GAG) chains link collagen fibrils and adhere at the D-band of the collagen fibril. In this study, we used array and scanning transmission electron microscope (STEM) tomographies to reconstruct the three-dimensional ultrastructure of tenocytes, collagen fibres, collagen fibrils and GAG chains at the bifurcation of the bovine hindlimb superficial digital flexor tendon (SDFT). Collagen fibrils comprising a collagen fibre were not aligned uniformly and had at least two running directions. Spindle-shaped tenocytes were arranged along the long axis of a plurality of collagen fibres, where two groups of collagen fibrils with oblique directions to each other exhibited an oblique overlap of the two collagen fibril layers. Collagen fibrils with different running directions were observed in separating layers of about 300 nm in thickness and had diameters of 0-200 nm. About 40% of all collagen fibrils had a peak in the range of 20-40 nm. STEM analysis of the same site where the crossing of collagen fibres was observed by transmission electron microscopy demonstrated the outline of collagen fibrils with a clear D-banding pattern at a regular interval. Collagen fibrils were reconstructed three-dimensionally using continuous images acquired by STEM tomography, which confirmed that the collagen fibrils at the crossing sites did not orientate in layers, but were woven one by one. Higher magnification observation of GAG chains attached between the crossing collagen fibrils revealed numerous GAG chains arranged either vertically or obliquely on collagen fibrils. Furthermore, GAG chains at the cross of collagen fibrils connected the closest D-bands. GAG chains are thought to be universally present between collagen fibrils of the tendon. These observations by array and STEM tomographies increase our knowledge of the anatomy in the bifurcation of the bovine hindlimb SDFT and demonstrate the utility of these new imaging technologies.

Analysis of depth-sectioning STEM for thick samples and 3D imaging

We derive a model that describes 3D volume imaging in depth-sectioning STEM that is valid for all STEM techniques under three well-defined conditions: linearity, undisturbed probe and elastic scattering. The resulting undisturbed probe model generalizes the widely used idea that the undisturbed probe intensity in three dimensions can be used as the point spread function for depth-sectioning ADF-STEM to all STEM techniques including (A)BF- and iDPC-STEM. The model provides closed expressions for depth-sectioning STEM, which follow directly from the 2D expressions for thin samples, and thereby enables analysis of the 3D resolution. Using the model we explore the consequences of the resulting 3D contrast transfer function (CTF) for the z-resolution at different length scales and illustrate this with experiments. We investigate the validity and limitations of the model using multi-slice simulations showing that it is valid and quantitatively accurate for relatively thick amorphous samples but not for crystalline samples in zone-axis due to channeling. We compare depth-sectioning in iDPC- and ADF-STEM and show that iDPC-STEM can extract information from deeper into the sample, all the way till the bottom of the sample, thereby effectively allowing a thickness measurement. Also the difference in optimal focus conditions between iDPC- and ADF-STEM is explained. Finally, we propose practical criteria for deciding whether a sample is thin or thick.

Exemplar-based inpainting as a solution to the missing wedge problem in electron tomography

A new method for dealing with incomplete projection sets in electron tomography is proposed. The approach is inspired by exemplar-based inpainting techniques in image processing and heuristically generates data for missing projection directions. The method has been extended to work on three dimensional data. In general, electron tomography reconstructions suffer from elongation artifacts along the beam direction. These artifacts can be seen in the corresponding Fourier domain as a missing wedge. The new method synthetically generates projections for these missing directions with the help of a dictionary based approach that is able to convey both structure and texture at the same time. It constitutes a preprocessing step that can be combined with any tomographic reconstruction algorithm. The new algorithm was applied to phantom data, to a real electron tomography data set taken from a catalyst, as well as to a real dataset containing solely colloidal gold particles. Visually, the synthetic projections, reconstructions, and corresponding Fourier power spectra showed a decrease of the typical missing wedge artifacts. Quantitatively, the inpainting method is capable to reduce missing wedge artifacts and improves tomogram quality with respect to full width half maximum measurements.

The Influence of Beam Broadening on the Spatial Resolution of Annular Dark Field Scanning Transmission Electron Microscopy

The spatial resolution of aberration-corrected annular dark field scanning transmission electron microscopy was studied as function of the vertical position z within a sample. The samples consisted of gold nanoparticles (AuNPs) positioned in different horizontal layers within aluminum matrices of 0.6 and 1.0 µm thickness. The highest resolution was achieved in the top layer, whereas the resolution was reduced by beam broadening for AuNPs deeper in the sample. To examine the influence of the beam broadening, the intensity profiles of line scans over nanoparticles at a certain vertical location were analyzed. The experimental data were compared with Monte Carlo simulations that accurately matched the data. The spatial resolution was also calculated using three different theoretical models of the beam blurring as function of the vertical position within the sample. One model considered beam blurring to occur as a single scattering event but was found to be inaccurate for larger depths of the AuNPs in the sample. Two models were adapted and evaluated that include estimates for multiple scattering, and these described the data with sufficient accuracy to be able to predict the resolution. The beam broadening depended on z 1.5 in all three models.

Spherically symmetric volume elements as basis functions for image reconstructions in computed laminography

BACKGROUND

Laminography is a tomographic technique that allows three-dimensional imaging of flat and elongated objects that stretch beyond the extent of a reconstruction volume. Laminography images can be reconstructed using iterative algorithms based on the Kaczmarz method.

OBJECTIVE

This study aims to develop and demonstrate a new reconstruction algorithm that may provide superior image reconstruction quality for this challenged imaging application.

METHODS

The images are initially represented using the coefficients over basis functions, which are typically piecewise constant functions (voxels). By replacing voxels with spherically symmetric volume elements (blobs) based on the generalized Kaiser-Bessel window functions, the images are reconstructed using this new adapted version of the algebraic image reconstruction technique.

RESULTS

Band-limiting properties of blob functions are beneficial particular in the case of noisy projections and with only a limited number of available projections. Study showed that using blob basis functions improved full-width-at-half-maximum resolution from 10.2±1.0 to 9.9±0.9 (p < 0.001). Signal-to-noise ratio also improved from 16.1 to 31.0. The increased computational demand per iteration was compensated by using a faster convergence rate, such that the overall performance is approximately identical for blobs and voxels.

CONCLUSIONS

Despite the higher complexity, tomographic reconstruction from computed laminography data should be implemented using blob basis functions, especially if noisy data is expected.

Preparation and Observation of Thick Biological Samples by Scanning Transmission Electron Tomography

This report describes a protocol for preparing thick biological specimens for further observation using a scanning transmission electron microscope. It also describes an imaging method for studying the 3D structure of thick biological specimens by scanning transmission electron tomography. The sample preparation protocol is based on conventional methods in which the sample is fixed using chemical agents, treated with a heavy atom salt contrasting agent, dehydrated in a series of ethanol baths, and embedded in resin. The specific imaging conditions for observing thick samples by scanning transmission electron microscopy are then described. Sections of the sample are observed using a through-focus method involving the collection of several images at various focal planes. This enables the recovery of in-focus information at various heights throughout the sample. This particular collection pattern is performed at each tilt angle during tomography data collection. A single image is then generated, merging the in-focus information from all the different focal planes. A classic tilt-series dataset is then generated. The advantage of the method is that the tilt-series alignment and reconstruction can be performed using standard tools. The collection of through-focal images allows the reconstruction of a 3D volume that contains all of the structural details of the sample in focus.

Nanomaterial datasets to advance tomography in scanning transmission electron microscopy

Electron tomography in materials science has flourished with the demand to characterize nanoscale materials in three dimensions (3D). Access to experimental data is vital for developing and validating reconstruction methods that improve resolution and reduce radiation dose requirements. This work presents five high-quality scanning transmission electron microscope (STEM) tomography datasets in order to address the critical need for open access data in this field. The datasets represent the current limits of experimental technique, are of high quality, and contain materials with structural complexity. Included are tomographic series of a hyperbranched Co2P nanocrystal, platinum nanoparticles on a carbon nanofibre imaged over the complete 180° tilt range, a platinum nanoparticle and a tungsten needle both imaged at atomic resolution by equal slope tomography, and a through-focal tilt series of PtCu nanoparticles. A volumetric reconstruction from every dataset is provided for comparison and development of post-processing and visualization techniques. Researchers interested in creating novel data processing and reconstruction algorithms will now have access to state of the art experimental test data.

Big Data Analytics for Scanning Transmission Electron Microscopy Ptychography

Electron microscopy is undergoing a transition; from the model of producing only a few micrographs, through the current state where many images and spectra can be digitally recorded, to a new mode where very large volumes of data (movies, ptychographic and multi-dimensional series) can be rapidly obtained. Here, we discuss the application of so-called “big-data” methods to high dimensional microscopy data, using unsupervised multivariate statistical techniques, in order to explore salient image features in a specific example of BiFeO₃ domains. Remarkably, k-means clustering reveals domain differentiation despite the fact that the algorithm is purely statistical in nature and does not require any prior information regarding the material, any coexisting phases, or any differentiating structures. While this is a somewhat trivial case, this example signifies the extraction of useful physical and structural information without any prior bias regarding the sample or the instrumental modality. Further interpretation of these types of results may still require human intervention. However, the open nature of this algorithm and its wide availability, enable broad collaborations and exploratory work necessary to enable efficient data analysis in electron microscopy.

Electron Tomography: A Three-Dimensional Analytic Tool for Hard and Soft Materials Research

Three-dimensional (3D) structural analysis is essential to understand the relationship between the structure and function of an object. Many analytical techniques, such as X-ray diffraction, neutron spectroscopy, and electron microscopy imaging, are used to provide structural information. Transmission electron microscopy (TEM), one of the most popular analytic tools, has been widely used for structural analysis in both physical and biological sciences for many decades, in which 3D objects are projected into two-dimensional (2D) images. In many cases, 2D-projection images are insufficient to understand the relationship between the 3D structure and the function of nanoscale objects. Electron tomography (ET) is a technique that retrieves 3D structural information from a tilt series of 2D projections, and is gradually becoming a mature technology with sub-nanometer resolution. Distinct methods to overcome sample-based limitations have been separately developed in both physical and biological science, although they share some basic concepts of ET. This review discusses the common basis for 3D characterization, and specifies difficulties and solutions regarding both hard and soft materials research. It is hoped that novel solutions based on current state-of-the-art techniques for advanced applications in hybrid matter systems can be motivated.

Matched Backprojection Operator for Combined Scanning Transmission Electron Microscopy Tilt- and Focal Series

Combined tilt- and focal series scanning transmission electron microscopy is a recently developed method to obtain nanoscale three-dimensional (3D) information of thin specimens. In this study, we formulate the forward projection in this acquisition scheme as a linear operator and prove that it is a generalization of the Ray transform for parallel illumination. We analytically derive the corresponding backprojection operator as the adjoint of the forward projection. We further demonstrate that the matched backprojection operator drastically improves the convergence rate of iterative 3D reconstruction compared to the case where a backprojection based on heuristic weighting is used. In addition, we show that the 3D reconstruction is of better quality.

Scanning transmission electron microscopy through-focal tilt-series on biological specimens

Since scanning transmission electron microscopy can produce high signal-to-noise ratio bright-field images of thick (≥500 nm) specimens, this tool is emerging as the method of choice to study thick biological samples via tomographic approaches. However, in a convergent-beam configuration, the depth of field is limited because only a thin portion of the specimen (from a few nanometres to tens of nanometres depending on the convergence angle) can be imaged in focus. A method known as through-focal imaging enables recovery of the full depth of information by combining images acquired at different levels of focus. In this work, we compare tomographic reconstruction with the through-focal tilt-series approach (a multifocal series of images per tilt angle) with reconstruction with the classic tilt-series acquisition scheme (one single-focus image per tilt angle). We visualised the base of the flagellum in the protist Trypanosoma brucei via an acquisition and image-processing method tailored to obtain quantitative and qualitative descriptors of reconstruction volumes. Reconstructions using through-focal imaging contained more contrast and more details for thick (≥500 nm) biological samples.

Dark field transmission electron microscopy as a tool for identifying inorganic nanoparticles in biological matrices

Dark field transmission electron microscopy has been applied herein to visualize the interactions of inorganic nanomaterials with biological systems. This new application of a known technique addresses a deficiency in status quo visualization techniques. High resolution and low noise images can be acquired to locate and identify crystalline nanoparticles in complex biological matrices. Moreover, through the composition of multiple images taken at different angular beam tilts, it is possible to image a majority of nanoparticles present at a site in dark field mode. This facilitates clarity regarding the internalization of nanomaterials in cellular systems. In addition, comparing dark field images recorded at different angular tilts yields insight into the character of nanoparticle faceting.