Automated discrete electron tomography – Towards routine high-fidelity reconstruction of nanomaterials

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.

IDART: An Improved Discrete Tomography Algorithm for Reconstructing Images With Multiple Gray Levels

The discrete algebraic reconstruction technique has many advantages in computed tomography and electron tomography. However, the number of gray levels and the absolute gray values that should be known in advance are typically not available in experiments especially when there are many gray levels in the image. In this paper, we report an automatic discrete tomography reconstruction algorithm to improve its feasibility in practice, without needing to know these two parameters. In our algorithm, the number of gray levels is estimated by labeling the connected components in the tomogram and the absolute values of them are determined by the modal value of each domain. The proposed algorithm was extensively validated on both simulated and experimental datasets. The results show that our algorithm can accurately recover not only the morphology but also the gray levels of the interested objects, even in the images with multiple gray levels. It is demonstrated that the presented algorithm is robust for eliminating missing wedge artifacts and tolerable for noisy data.

Novel nonlinear reconstruction method with grey-level quantisation units for electron tomography

We report a new computed tomography reconstruction method, named quantisation units reconstruction technique (QURT), applicable to electron and other fields of tomography. Conventional electron tomography methods such as filtered back projection, weighted back projection, simultaneous iterative reconstructed technique, etc. suffer from the 'missing wedge' problem due to the limited tilt-angle range. QURT demonstrates improvements to solve this problem by recovering a structural image blurred due to the missing wedge and substantially reconstructs the structure even if the number of projection images is small. QURT reconstructs a cross-section image by arranging grey-level quantisation units (QU pieces) in three-dimensional image space via unique discrete processing. Its viability is confirmed by model simulations and experimental results. An important difference from recently developed methods such as discrete algebraic reconstruction technique (DART), total variation regularisation-DART, and compressed sensing is that prior knowledge of the conditions regarding the specimen or the expected cross-section image is not necessary.

Electron tomography imaging methods with diffraction contrast for materials research

Transmission electron microscopy (TEM) and scanning transmission electron microscopy (STEM) enable the visualization of three-dimensional (3D) microstructures ranging from atomic to micrometer scales using 3D reconstruction techniques based on computed tomography algorithms. This 3D microscopy method is called electron tomography (ET) and has been utilized in the fields of materials science and engineering for more than two decades. Although atomic resolution is one of the current topics in ET research, the development and deployment of intermediate-resolution (non-atomic-resolution) ET imaging methods have garnered considerable attention from researchers. This research trend is probably not irrelevant due to the fact that the spatial resolution and functionality of 3D imaging methods of scanning electron microscopy (SEM) and X-ray microscopy have come to overlap with those of ET. In other words, there may be multiple ways to carry out 3D visualization using different microscopy methods for nanometer-scale objects in materials. From the above standpoint, this review paper aims to (i) describe the current status and issues of intermediate-resolution ET with regard to enhancing the effectiveness of TEM/STEM imaging and (ii) discuss promising applications of state-of-the-art intermediate-resolution ET for materials research with a particular focus on diffraction contrast ET for crystalline microstructures (superlattice domains and dislocations) including a demonstration of in situ dislocation tomography.

Imaging Beam-Sensitive Materials by Electron Microscopy

Electron microscopy allows the extraction of multidimensional spatiotemporally correlated structural information of diverse materials down to atomic resolution, which is essential for figuring out their structure-property relationships. Unfortunately, the high-energy electrons that carry this important information can cause damage by modulating the structures of the materials. This has become a significant problem concerning the recent boost in materials science applications of a wide range of beam-sensitive materials, including metal-organic frameworks, covalent-organic frameworks, organic-inorganic hybrid materials, 2D materials, and zeolites. To this end, developing electron microscopy techniques that minimize the electron beam damage for the extraction of intrinsic structural information turns out to be a compelling but challenging need. This article provides a comprehensive review on the revolutionary strategies toward the electron microscopic imaging of beam-sensitive materials and associated materials science discoveries, based on the principles of electron-matter interaction and mechanisms of electron beam damage. Finally, perspectives and future trends in this field are put forward.

Computational requirements for real-time ptychographic image reconstruction

Ptychographic imaging techniques can be coupled with tomographic image reconstruction techniques to obtain cross-sectional 3D images with resolution on the nanometer scale. However, such ptychographic x-ray computed tomography (PXCT) techniques require the collection of a large number of diffraction patterns. This work derives a set of equations that can be used to calculate the rate at which data can be collected given an experimental setup. It also determines the computational system requirements needed to process ptychographic data in real time as soon as it has been collected. This will expedite the ptychography step of PXCT. These theoretical results are then applied to performance data collected from reconstructing simulated diffraction patterns in order to determine the computational resources needed for real-time ptychographic processing for representative experimental setups. All of our results are independent of any specific ptychographic reconstruction algorithm.

A modified discrete tomography for improving the reconstruction of unknown multi-gray-level material in the `missing wedge' situation

Full angular rotational projections cannot always be acquired in tomographic reconstructions because of the limited space in the experimental setup, leading to the `missing wedge' situation. In this paper, a recovering `missing wedge' discrete algebraic reconstruction technique algorithm (rmwDART) has been proposed to solve the `missing wedge' problem and improve the quality of the three-dimensional reconstruction without prior knowledge of the material component's number or the material's values. By using oversegmentation, boundary extraction and mathematical morphological operations, `missing wedge' artifact areas can be located. Then, in the iteration process, by updating the located areas and regions, high-quality reconstructions can be obtained from the simulations, and the reconstructed images based on the rmwDART algorithm can be obtained from soft X-ray nano-computed tomography experiments. The results showed that there is the potential for discrete tomography.

Hierarchical spidroin micellar nanoparticles as the fundamental precursors of spider silks

Many natural silks produced by spiders and insects are unique materials in their exceptional toughness and tensile strength, while being lightweight and biodegradable-properties that are currently unparalleled in synthetic materials. Myriad approaches have been attempted to prepare artificial silks from recombinant spider silk spidroins but have each failed to achieve the advantageous properties of the natural material. This is because of an incomplete understanding of the in vivo spidroin-to-fiber spinning process and, particularly, because of a lack of knowledge of the true morphological nature of spidroin nanostructures in the precursor dope solution and the mechanisms by which these nanostructures transform into micrometer-scale silk fibers. Herein we determine the physical form of the natural spidroin precursor nanostructures stored within spider glands that seed the formation of their silks and reveal the fundamental structural transformations that occur during the initial stages of extrusion en route to fiber formation. Using a combination of solution phase diffusion NMR and cryogenic transmission electron microscopy (cryo-TEM), we reveal direct evidence that the concentrated spidroin proteins are stored in the silk glands of black widow spiders as complex, hierarchical nanoassemblies (∼300 nm diameter) that are composed of micellar subdomains, substructures that themselves are engaged in the initial nanoscale transformations that occur in response to shear. We find that the established micelle theory of silk fiber precursor storage is incomplete and that the first steps toward liquid crystalline organization during silk spinning involve the fibrillization of nanoscale hierarchical micelle subdomains.

Three-Dimensional Visualization and Characterization of Polymeric Self-Assemblies by Transmission Electron Microtomography

Self-assembling structures and their dynamical processes in polymeric systems have been investigated using three-dimensional transmission electron microscopy (3D-TEM). Block copolymers (BCPs) self-assemble into nanoscale periodic structures called microphase-separated structures, a deep understanding of which is important for creating nanomaterials with superior physical properties, such as high-performance membranes with well-defined pore size and high-density data storage media. Because microphase-separated structures have become increasingly complicated with advances in precision polymerization, characterizing these complex morphologies is becoming increasingly difficult. Thus, microscopes capable of obtaining 3D images are required. In this article, we demonstrate that 3D-TEM is an essential tool for studying BCP nanostructures, especially those self-assembled during dynamical processes and under confined conditions. The first example is a dynamical process called order-order transitions (OOTs). Upon changing temperature or pressure or applying an external field, such as a shear flow or electric field, BCP nanostructures transform from one type of structure to another. The OOTs are examined by freezing the specimens in the middle of the OOT and then observing the boundary structures between the preexisting and newly formed nanostructures in three-dimensions. In an OOT between the bicontinuous double gyroid and hexagonally packed cylindrical structures, two different types of epitaxial phase transition paths are found. Interestingly, the paths depend on the direction of the OOT. The second example is BCP self-assemblies under confinement that have been examined by 3D-TEM. A variety of intriguing and very complicated 3D morphologies can be formed even from the BCPs that self-assemble into simple nanostructures, such as lamellar and cylindrical structures in the bulk (in free space). Although 3D-TEM is becoming more frequently used for detailed morphological investigations, it is generally used to study static nanostructures. Although OOTs are dynamical processes, the actual experiment is done in the static state, through a detailed morphological study of a snapshot taken during the OOT. Developing time-dependent nanoscale 3D imaging has become a hot topic. Here, the two main problems preventing the development of in situ electron tomography for polymer materials are addressed. First, the staining protocol often used to enhance contrast for electrons is replaced by a new contrast enhancement based on chemical differences between polymers. In this case, no staining is necessary. Second, a new 3D reconstruction algorithm allows us to obtain a high-contrast, quantitative 3D image from fewer projections than is required for the conventional algorithm to achieve similar contrast, reducing the number of projections and thus the electron beam dose. Combining these two new developments is expected to open new doors to 3D in situ real-time structural observation of polymer materials.