Sampling limits for electron tomography with sparsity-exploiting reconstructions

Knowledge of three-dimensional (3D) structures of each individual particles of asymmetric and flexible proteins is essential in understanding those proteins’ functions; but their structures are difficult to determine. Electron tomography (ET) provides a tool for imaging a single and unique biological object from a series of tilted angles, but it is challenging to image a single protein for three-dimensional (3D) reconstruction due to the imperfect mechanical control capability of the specimen goniometer under both a medium to high magnification (approximately 50,000–160,000×) and an optimized beam coherence condition. Here, we report a fully mechanical control method for automating ET data acquisition without using beam tilt/shift processes. This method could reduce the accumulation of beam tilt/shift that used to compensate the error from the mechanical control, but downgraded the beam coherence. Our method was developed by minimizing the error of the target object center during the tilting process through a closed-loop proportional-integral (PI) control algorithm. The validations by both negative staining (NS) and cryo-electron microscopy (cryo-EM) suggest that this method has a comparable capability to other ET methods in tracking target proteins while maintaining optimized beam coherence conditions for imaging.

3D quantitative characterization of metal catalysts supported on heavy oxides by High Angle Annular Dark Field (HAADF) STEM electron tomography (ET) is a very challenging task. Noble metal nanoparticles (Au, Ru) supported on ceria or ceria mixed oxides illustrates the case. The difference, very small in some cases, between the atomic number (Z) of metal and support (Z Ru =44, Z Au =79, Z Ce =58) complicates the discrimination of the small particles. This makes that each step, acquisition, alignment, reconstruction and segmentation, has to be carefully optimized not only to improve the visualization of the nanoparticles but also to extract relevant quantitative results, e.g . metal loading, specific surface area, or particle size distribution. In this work, we have combined advanced image processing algorithms, based on undecimated wavelets transform (UWT) [1], to improve the contrast and denoising the tilt series projections, with new reconstruction algorithms, based on compressed sensing (CS) [2], to study a series of catalysts with a high potential in different processes related to the production of hydrogen, as CeO 2 Nanorods, Au/CeO 2 Nanocubes or Ru/Ce 2 Z 2 O 8 . The results obtained by ET have been compared to those determined by macroscopic characterization techniques as Inductively Coupled Plasma (ICP) or Brunauer, Emmett and Teller (BET) isotherm method. HAADF‐STEM ET has been carried out using a FEI TITAN 3 THEMIS 60‐300 operated at 200kV recently installed at Cadiz University. Data collections were obtained by tilting the specimen about a single axis perpendicular to the electron beam. Series of projections were acquired between ‐70º and +70° either every 2° or 5º. The images series were aligned using Inspect3D and TomoJ and reconstructed using the ASTRA Toolbox implemented in Matlab [3]. In the particular case of CS, Total Variation Minimization (TVM) was carried by using the TVAL3 solver [2]. Figure 1 shows the 3D‐rendered voxel of a catalyst consisting of Au nanoparticles supported on CeO 2 Nanocubes after reconstructing the raw tilt series by SIRT (Figure 1a) and TVM (Figure 1b) and after denoising the tilt series projections by UWT and reconstructed by SIRT (Figure 1c) and TVM (Figure1d). Note how in the case of UWT‐TVM reconstruction an important improvement in terms of morphology of the support and visualization of nanoparticles is obtained. The 3D rendered surface of a similar sample and the 3D quantifications of relevant properties as metal loading, specific surface area and average particle size are shown in Figure 2. It is important to point out how the values are quite similar to those determined by macroscopic characterization techniques. These results indicate that this combination of techniques allows determining nanostructural features representative of the catalysts at macroscopic level.

EPiK-a Workflow for Electron Tomography in Kepler

This paper reports the preliminary results of a new in-situ three-dimensional (3D) imaging system for observing plastic deformation behavior in a transmission electron microscope (TEM) as a directly relevant development of the recently reported straining-and-tomography holder [Sato K et al. (2015) Development of a novel straining holder for transmission electron microscopy compatible with single tilt-axis electron tomography. Microsc. 64: 369-375]. We designed an integrated system using the holder and newly developed straining and image-acquisition software and then developed an experimental procedure for in-situ straining and time-resolved electron tomography (ET) data acquisition. The software for image acquisition and 3D visualization was developed based on the commercially available ET software TEMographyTM. We achieved time-resolved 3D visualization of nanometer-scale plastic deformation behavior in a Pb-Sn alloy sample, thus demonstrating the capability of this system for potential applications in materials science.

Chirality in gold nanostructures offers an exciting opportunity to tune their differential optical response to left- and right-handed circularly polarized light, as well as their interactions with biomolecules and living matter. However, tuning and understanding such interactions demands quantification of the structural features that are responsible for the chiral behavior. Electron tomography (ET) enables structural characterization at the single-particle level and has been used to quantify the helicity of complex chiral nanorods. However, the technique is time-consuming and consequently lacks statistical value. To address this issue, we introduce herein a high-throughput methodology that combines images acquired by secondary electron-based electron beam-induced current (SEEBIC) with quantitative image analysis. As a result, the geometric chirality of hundreds of nanoparticles can be quantified in less than 1 h. When combining the drastic gain in data collection efficiency of SEEBIC with a limited number of ET data sets, a better understanding of how the chiral structure of individual chiral nanoparticles translates into the ensemble chiroptical response can be reached.

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.

Isotropic and anisotropic filtering norm-minimization: A generalization of the TV and TGV minimizations using NESTA

Using a first-order k ⋅ p model for electron intersubband scattering in quantum wells (QW), our group re-analyzed pump-probe experiments performed in the mid-nineties that investigated the intersubband and intrasubband electron dynamics in two InGaAs/AlInAs QWs grown in the same molecular beam epitaxy (MBE) laboratory. This work confirms that the measured electron lifetime can only be interpreted through a rigorous k ⋅ p approach that not only considers the hyperbolic subband dispersion but also band-mixing’s k-dependence, which slows down all scattering mechanisms. The latter includes the enhanced wavefunction confinement with k. Concomitantly, this analysis investigated the range of interface roughness parameters (IFR) and the potential for alloy disorder (AD), whose values are very important for designing many existing/new quantum devices. Just by using the one-band model, the overall 2–1 scattering rate is ∼66% overestimated in a QW tuned at λ 21 ∼ 5 µm, while using the eight-band model, good agreement with the experimental data is obtained by properly choosing these material parameters. However, due to the inherent time resolution of the pump-probe experiments and the fact that AD and IFR scatterings are processes of the same nature, these material parameters are fitted with a large uncertainty. The suggested IFR parameters are in line with what is typically used in quantum cascade laser simulations, but the AD potential is smaller. Pump-probe experiments are not sufficient to capture the material parameters with sufficient accuracy and, therefore, should be associated with other material characterization techniques, such as ultra-high vacuum scanning tunneling microscope or electron tomography. The quantum devices’ simulation tools could benefit from the IFR and AD material parameters derived in this work, but above all, this analysis reaffirms that for modeling and optimizing intersubband devices, it is crucial to consider not only the correct dispersion but, most of all, the band-mixing, which is strongly k-dependent.

CT reconstruction from few-views with anisotropic edge-guided total variance

The compressed sensing(CS) theory has provided a new solution for the low-rate sampling design of Impulse Radio Ultra-WideBand (IR-UWB) signal. This paper gives full consideration of the influence of quantization noise in IR-UWB system, and designs an effective quantization and reconstruction mechanism with high performance of resisting noise. Based on the analysis of noise distribution characteristics in compressed sampling value, the signal reconstruction model is revised, and then the performances of Dantzig-Selector (DS) method, Subspace Pursuit(SP) method, and traditional reconstruction algorithms are compared. On this basis, a signal reconstruction method (hybrid DS-SP method) with self-adaptability in DS and SP is proposed. Based on hybrid DS-SP method and consideration of overload uniform quantization, overload hybrid DS-SP mechanism is proposed which considered both the digital rear-end and analog front-end of IR-UWB receiver under compressed sensing framework. Simulation results show that the overload hybrid DS-SP mechanism achieves the exceptional reconstruction performance compared to the traditional reconstruction algorithms under different noise conditions with a compromised complexity between DS and SP.

Dual-head small-animal positron emission tomography (DHAPET) has characteristics of high detection sensitivity and flexible system configurations. However, the system geometry may result in severe parallax errors and undetected events along the trans-axial directions, thus reducing the image quality. With the advancement of detector hardware, time-of-flight (TOF) of photons can be detected, which has demonstrated significant improvement in image quality, and can greatly benefit its use in research studies and clinics. Algorithms like total variation (TV) minimization methods that aim to compensate the effects of data truncation can be employed to reconstruct images with better resolution and quality. In this work, we will numerically compute the DHAPET system response matrix that includes TOF information and propose a TOF-PET reconstruction algorithm based on TV-minimization. By applying both TOF information and TV minimization in the iterative algorithm, the reconstructed images can be anticipated to have improved quality with better spatial resolution.

Optical computed tomography (optical-CT) is a high-resolution, fast, and easily accessible readout modality for gel dosimeters. This paper evaluates a hybrid iterative image reconstruction algorithm for optical-CT gel dosimeter imaging, namely, the simultaneous algebraic reconstruction technique (SART) integrated with ordered subsets (OS) iteration and total variation (TV) minimization regularization. The mathematical theory and implementation workflow of the algorithm are detailed. Experiments on two different optical-CT scanners were performed for cross-platform validation. For algorithm evaluation, the iterative convergence is first shown, and peak-to-noise-ratio (PNR) and contrast-to-noise ratio (CNR) results are given with the cone-beam filtered backprojection (FDK) algorithm and the FDK results followed by median filtering (mFDK) as reference. The effect on spatial gradients and reconstruction artefacts is also investigated. The PNR curve illustrates that the results of SART + OS + TV finally converges to that of FDK but with less noise, which implies that the dose-OD calibration method for FDK is also applicable to the proposed algorithm. The CNR in selected regions-of-interest (ROIs) of SART + OS + TV results is almost double that of FDK and 50% higher than that of mFDK. The artefacts in SART + OS + TV results are still visible, but have been much suppressed with little spatial gradient loss. Based on the assessment, we can conclude that this hybrid SART + OS + TV algorithm outperforms both FDK and mFDK in denoising, preserving spatial dose gradients and reducing artefacts, and its effectiveness and efficiency are platform independent.

The porous structure and the periodic array of cavities in ordered mesoporous materials with large, three-dimensionally arranged and interconnected pores is thoroughly described by combining electron tomography, small-angle X-ray diffraction, and nitrogen sorption techniques. We used the ability of the electron tomography to provide local three-dimensional information of a nano-object and compared the results to those of the other characterization techniques which furnish global information. We showed thus that the face-centered cubic (fcc) structure usually assigned to the FDU-12 materials is in fact an intergrowth of cubic and hexagonal close-packing structures. This agrees with small-angle X-ray scattering (SAXS) modeling, but for the first time a direct visualization of these stacking faults was achieved. Three-dimensional transmission electron microscopy (3D-TEM) provides also a direct and unique evidence of peculiar stacking defects ("z-shifted [111] areas"), as well as an estimate of their density, which have never been reported elsewhere. In addition, interstitial cavities were also observed, revealing the complex defective structure of this material. A direct observation of the nature of the connecting pores was also achieved for the first time, with a resolution limit of 2 nm. Finally, the characteristics of the porous network evidenced by 3D-TEM are used to explain and validate the results obtained by nitrogen sorption experiments.

Electron tomography based on a total variation minimization reconstruction technique

The total variation (TV) minimization image reconstruction algorithm for inverting the divergent-beam x-ray transform is applied to image reconstruction in circular cone-beam computed tomography (CT). Reconstructions for the disk phantom are shown and compared with that of projection onto convex sets (POCS). The preliminary results appear to show that TV-minimization yields accurate image reconstructions that are robust against data inconsistencies due to noise or mismatch in the system matrix.