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

Janus nanoparticles are nanoparticles (NPs) displaying two sides of different chemical nature which makes them of high interest. The formation of the Janus shell provides the NPs an amphiphilic character, which can therefore self‐assemble in a tunable fashion by varying different experimental parameters such as size, polymer ratio and temperature. Here, Au NPs coated by polyethylene glycol (PEG) and both polystyrene (PS) and poly(N‐isopropylacrylamide) (PNIPAM) were investigated. [1] The true Janus character of the NPs was determined by electron tomography. Characterization of polymer coated particles by electron microscopy is challenging due to the low contrast of the organic materials. The goal was to distinguish the two different polymers in two types of particles (PEG+PNIPAM and PEG+PS coated Au NPs). Different approaches were used to improve the contrast between the two polymers. The PEG+PNIPAM particles were characterized by specific staining of the hemispheres while the character of the PEG+PS particles was investigated by the growth of silica. First, the PEG+PNIPAM coated NPs were stained with 3 mM CuSO 4 .5H 2 O solution to generate sufficient contrast in the Transmission Electron Microscope (TEM). PNIPAM‐coated NPs showed damage of the polymer upon electron beam irradiation. For PEG‐coated NPs a stable shell was observed. In an attempt to distinguish PNIPAM and PEG, PEG+PNIPAM coated particles were stained and investigated with TEM (Fig. 1). Since conventional TEM images are 2D projections from a 3D object, electron tomography was performed. It must be noted that the conventional technique for tomography in materials science, high angle annular dark field scanning TEM (HAADF‐STEM), could not be applied due to the large difference in atomic number Z for Au and the elements in the polymer shell. Instead, Bright‐Field TEM tomography was applied. Images were acquired over the largest possible range (‐76° to +76°) every 2°, aligned and reconstructed by the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm in the Astra Toolbox. [2] The obtained 3D reconstruction displayed rather low contrast between the shell and the background. Manual segmentation based on the orthoslices (xy‐, yx‐ and zx‐direction) could be carried out. This method provided a 3D reconstruction that clearly confirms the formation of stained half‐shells (Fig. 3). In the second case of PEG+PS coated Au NPs, an attempt of staining with calcium phosphate was carried out. In TEM images hemispheres could be observed, but selective staining could not be confirmed. Due to the high affinity of PEG by silica, PEG is able to act as a primer to promote silica condensation. Since PS is hydrophobic and does not allow silica nucleation, the silica shell was expected to occur only at the parts of the NPs that are coated by PEG (Fig. 2). Either staining or silica shell growth over PEG‐coated areas resulted in the observation of semi‐shells (Janus character) in Au NPs by TEM and electron tomography.

Ultra-sparse-view computed tomography (CT) algorithms can reduce radiation exposure for patients, but these algorithms lack an explicit cycle consistency loss minimization and an explicit log-likelihood maximization in testing. Here, we propose X2CT-FLOW for the maximum a posteriori (MAP) reconstruction of a three-dimensional (3D) chest CT image from a single or a few two-dimensional (2D) projection images using a progressive flow-based deep generative model, especially for ultra-low-dose protocols. The MAP reconstruction can simultaneously optimize the cycle consistency loss and the log-likelihood. We applied X2CT-FLOW for the reconstruction of 3D chest CT images from biplanar projection images without noise contamination (assuming a standard-dose protocol) and with strong noise contamination (assuming an ultra-low-dose protocol). We simulated an ultra-low-dose protocol. With the standard-dose protocol, our images reconstructed from 2D projected images and 3D ground-truth CT images showed good agreement in terms of structural similarity (SSIM, 0.7675 on average), peak signal-to-noise ratio (PSNR, 25.89 dB on average), mean absolute error (MAE, 0.02364 on average), and normalized root mean square error (NRMSE, 0.05731 on average). Moreover, with the ultra-low-dose protocol, our images reconstructed from 2D projected images and the 3D ground-truth CT images also showed good agreement in terms of SSIM (0.7008 on average), PSNR (23.58 dB on average), MAE (0.02991 on average), and NRMSE (0.07349 on average).

Access to structural information at the nanoscale enables fundamental insights into many complex biological systems. The development of the transmission electron microscope (TEM) has vastly increased our understanding of multiple biological systems. However, when attempting to visualize and understand the organizational and functional complexities that are typical of cells and tissues, the standard 2-D analyses that TEM affords often fall short. In recent years, high-resolution electron tomography methods, coupled with advances in specimen preparation and instrumentation and computational speed, have resulted in a revolution in the biological sciences. Electron tomography is analogous to medical computerized axial tomography (CAT-scan imaging) except at a far finer scale. It utilizes the TEM to assemble multiple projections of an object which are then combined for 3-D analyses. For biological specimens, tomography enables the highest 3-D resolution (5 nm spatial resolution) of internal structures in relatively thick slices of material (0.2-0.4 microm) without requiring the collection and alignment of large numbers of thin serial sections. Thus accurate and revealing 3-D reconstructions of complex cytoplasmic entities and architecture can be obtained. Electron tomography is now being applied to a variety of biological questions with great success. This review gives a brief introduction into cryopreservation and electron tomography relative to aspects of cytoplasmic organization in the hyphal tip of Aspergillus nidulans.

Electron tomography (ET) is an outstanding technique to access information about nanoparticles whose properties are critically dependent on their 3D shape and structure. A particularly relevant application of ET concerns plasmonic chiral nanoparticles, which exhibit strong correlation between optical activity and asymmetric morphology. Thus, it is crucial to go beyond qualitative visual inspection of ET reconstructions and extract quantitative shape or chirality descriptors. However, the time‐consuming nature of conventional ET, where a series of 2D projection images is used for one 3D reconstruction, makes it challenging to collect statistically representative data. A recently proposed semi‐automated approach for the acquisition of the required tilt series can reduce the data collection time from typically ≈ 45 minutes–1 hour to less than 10 minutes. What remains unclear is how this method influences the quality of the reconstruction and the accuracy of the samples’ quantitative descriptors. Here, two sets of chiral gold nanoparticles with wrinkled or twisted morphological chirality are used. It is demonstrated that the fast tilt series acquisitions yield results that are consistent with conventional ET, provided a standardized data processing protocol is used. Finally, a practical example of how fast ET can be used to obtain more statistically relevant measurements is presented.

High-Throughput Immunofluorescence and Electron Tomography to Characterize Centrosomal Aberrations in Plasma Cell Neoplasia

Size distributions of cellulose nanocrystals (CNCs), extracted from softwood pulp via strong sulfuric acid hydrolysis, exhibit large variability when analyzed from transmission electron microscopy (TEM) images. In this article, the causes of this variability are studied and discussed. In order to obtain results comparable with those reported, a reference material of CNCs (CNCD-1) was used to evaluate size distribution. CNC TEM specimens were prepared as-stained and dried with a rapid-flushing staining method or hydrated and embedded in vitreous ice with the plunge-freezing method. Several sets of bright-field TEM (BF-TEM), annular dark-field scanning TEM (ADF-STEM) and cryogenic-TEM (cryo-TEM) images were acquired for size distribution analysis to study the contributing factors. The rapid-flushing staining method was found to be the most effective for contrast enhancement of CNCs, not only revealing the helical structure of single CNCs but also resolving the laterally jointed CNCs. During TEM specimen preparation, CNCs were fractionated on TEM grids driven by the coffee-ring effect, as observed from contrast variation of CNCs with a stain-depth gradient. From the edge to the center of the TEM grids, the width of CNCs increases, while the aspect ratio (length to width) decreases. This fractionated dispersion of CNCs suggests that images taken near the center of a droplet would give a larger mean width. In addition to particle fractionation driven by the coffee-ring effect, the arrangement and orientation of CNC particles on the substrate significantly affect the size measurement when CNC aggregation cannot be resolved in images. The coexistence of asymmetric cross-section CNC particles introduces a large variation in size measurement, as TEM images of CNCs are mixed projections of the width and height of particles. As a demonstration of how this contributes to inflated size measurement, twisted CNC particles, rectangular cross-section particles and end-to-end jointed CNCs were revealed in reconstructed three-dimensional (3D) micrographs by electron tomography (ET).

In electron tomography (ET) based on a transmission electron microscope, the effective thickness of a specimen increases with the tilt angle and, therefore, the projection quality may deteriorate because of electron scattering. The information-missing region, however, can be reduced by broadening the specimen tilt range. To clarify the general influence of these effects on ET, the projection quality varying with the tilt angle was quantitatively evaluated for a 5-microm thick specimen observed with a 3 MV ultrahigh-voltage electron microscope. Simulations of three-dimensional reconstruction were then performed for different specimen thicknesses and tilt ranges. As a result, the ET accuracy was shown to decrease as the specimen thickness increased. However, an optimum specimen-tilt range, at which ET could reach its highest accuracy, was found to exist and become small with the increase of the specimen thickness. The presented results are helpful for determining the specimen thickness limitation on the ET resolution and improving the ET fidelity of thick specimens.

In previous optimization-based methods of 3D planar-faced object reconstruction from single 2D line drawings, the missing depths of the vertices of a line drawing (and other parameters in some methods) are used as the variables of the objective functions. A 3D object with planar faces is derived by finding values for these variables that minimize the objective functions. These methods work well for simple objects with a small number N of variables. As N grows, however, it is very difficult for them to find expected objects. This is because with the nonlinear objective functions in a space of large dimension N, the search for optimal solutions can easily get trapped into local minima. In this paper, we use the parameters of the planes that pass through the planar faces of an object as the variables of the objective function. This leads to a set of linear constraints on the planes of the object, resulting in a much lower dimensional nullspace where optimization is easier to achieve. We prove that the dimension of this nullspace is exactly equal to the minimum number of vertex depths which define the 3D object. Since a practical line drawing is usually not an exact projection of a 3D object, we expand the nullspace to a larger space based on the singular value decomposition of the projection matrix of the line drawing. In this space, robust 3D reconstruction can be achieved. Compared with two most related methods, our method not only can reconstruct more complex 3D objects from 2D line drawings, but also is computationally more efficient.

Purpose: Myosin binding protein C is an accessory protein of vertebrate striated muscle thick filaments. Many studies have aimed to elucidate both its structure and function since mutations in the cardiac isoform (cMyBP-C) gene (MYBPC3) are known to be a leading cause of familial hypertrophic cardiomyopathy (HCM) affecting millions of people worldwide. There is strong evidence that phosphorylation of N-terminus M-domain of cMyBP-C is essential for normal cardiac function and that their dephosphorylation is associated with contractile dysfunction and HCM. However, the details of the underlying molecular-level ultrastructure are still poorly understood. The aim of this work is to provide details of the ultrastructure of thick filaments in different states of cMyBP-C phosphorylation. Methods: Two transgenic mouse strains expressing a constitutive phosphorylation or a non-phosphorylatable cMyBP-C have been compared to a homozygous knockout mouse for cMyBP-C and a wild-type (WT) control. We have carried out detailed transmission electron microscopy (TEM) in intact cardiac muscles, and electron tomography (ET) combined with sub-tomographic averaging. Results: TEM shows that cardiomyocyte ultrastructure is relatively well maintained under the total deletion of cMyBP-C from the heart and due to the expression of constitutive phosphorylation of cMyBP-C. However, the constitutive expression of non-PKA-phosphorylatable cMyBP-C leads to both sarcomeric disarray and mitochondria disruption. Longitudinal views of the average 3D reconstructions employing ET illustrate the surface density features of thick filaments. In the WT, two projection masses can be identified originating from cMyBP-C. Both the absence of cMyBP-C and the presence of constitutive non-phosphorylatable cMyBP-C seem to be associated with poorer structural preservation of the thick filaments. Conclusions: This study shows that cMyBP-C constitutive phosphorylation effectively preserves the intracellular arrangement of cardiac myocytes. However, non-PKA-phosphorylatable cMyBP-C leads to a dramatic overall decrease of tissue organization which is much more deleterious than the total deletion of cMyBP-C. This finding provides a structural explanation for cardiac dysfunction in this sample. This study shows that chemically fixed samples can be used for ET to reveal 3D structural information of thick filaments. Results obtained by using this methodology are in good agreement with previous studies using isolated filament approaches. However, in order to obtain higher resolution, advanced methods of sample processing will be required.

Aerosols affect the climate system through various physical processes as they can scatter and absorb solar radiation, emit thermal radiation, or act as cloud condensation nuclei that modify the cloudiness coverage, changing then its albedo. Carbonaceous solid aerosols resulting either from anthropogenic processes or biomass burning are one of the most significant contributors to global climate change [1] with respect to their impact on radiative forcing. They are constituted by tiny primary spherules having a diameter typically ranging from a few nanometers to dozens nanometers. These spherules are aggregated to form particles of larger sizes (0.1 to 1 micrometre) showing a complex morphology (Figure 1) that plays an important role on their radiative and transport properties. These soot aggregates are commonly characterized from 2D transmission electron microscopy (TEM) images and their 3D shape is then deduced from TEM projections assuming geometrical models of spheres, cylinders or spheroids. In order to check the validity of the 2D to 3D transition of these geometrical models we investigated bright field (BF) TEM tomography and directly determine 3D soot morphological characteristics. To be suitable for tomographic reconstruction, images of the tilt series must fulfill the projection requirement and BF TEM images of amorphous specimen, which are dominated by mass‐thickness contrast, can satisfy this assumption. We show in this work that attention must be paid on the influence of defocus, responsible of the appearance of Fresnel fringes, which do not answer the projection requirement and can lead to artefacts that do not ensure a realistic reconstruction of soot aggregates. To do so, we analyse the effect of defocus both on real and numerical soot particles. Thus the same real soot aggregate is reconstructed (with the SIRT algorithm) from different tilt series obtained at different defocus values. Its surface area and volume are determined by using the Amira software suite after a segmentation step based on the method of Adachi et al [2]. The same procedure (reconstruction, segmentation, surface area measurement) is then applied on an amorphous numerical particle, which is generated using a tight binding model [3] processed with the Nanofabric software developed by Y.Lebouar. Projection series are simulated with the EMS software based on the multislice method [4]. Both experimental and numerical approaches show that defocus drastically modifies the intensity profile of primary particles along their diameter and subsequently affects the shape of the reconstructed aggregate (Figure 2) and leads to overestimated values of their surface area and volume.

ABSTRACTPrimary Ciliary Dyskinesia (PCD) is a heterogeneous genetic condition characterized by dysfunction of motile cilia. Patients suffer from chronic infection and inflammation of the upper and lower respiratory tract. Diagnosis of PCD is confirmed by identification of a hallmark defect of ciliary ultrastructure or by identification of biallelic pathogenic mutations in a known PCD gene. Since the first description of PCD in 1976, assessment of ciliary ultrastructure by transmission electron microscopy (TEM) has been central to diagnosis and research. Electron tomography is a technique whereby a series of transmission electron micrographs are collected at different angles and reconstructed into a single 3D model of a specimen. Electron tomography provides improved spatial information and resolution compared to a single micrograph. Research by electron tomography has revealed new insight into ciliary ultrastructure and consequently ciliary function at a molecular and cellular level. Gene discovery studies in PCD have utilized electron tomography to define the structural consequences of variants in cilia genes. Modern transmission electron microscopes capable of electron tomography are increasingly being installed in clinical laboratories. This presents the possibility for the use of tomography technique in a diagnostic setting. This review describes the electron tomography technique, the contribution tomography has made to the understanding of basic cilia structure and function and finally the potential of the technique for use in PCD diagnosis.

This review of the development and current status of electron tomography deals mainly with the mathematical and algorithmic aspects. After a very brief description of the role of electron tomography in structural biology, we turn our attention to the derivation of the forward operator. Starting from the Schrödinger equation, the electron–specimen interaction is modelled as a diffraction tomography problem and the picture is completed by adding a description of the optical system of the transmission electron microscope. The first-order Born approximation enables one to explicitly express the intensity for any finite wavenumber in terms of the propagation operator acting on the specimen convolved with a point spread function, derived from the optics in the transmission electron microscope. Next, we focus on the difficulties that cause the reconstruction problem to be quite challenging. Special emphasis is put on explaining the extremely low signal-to-noise ratio in the data combined with the incomplete data problems, which lead to severe ill-posedness. The next step is to derive the standard phase contrast model used in the electron tomography community. The above-mentioned expression for the intensity generalizes the standard phase contrast model which can be obtained by replacing the propagation operator by its high-energy limit, the x-ray transform, as the wavenumber tends to infinity. The importance of more carefully including the wave nature of the electron–specimen interaction is supported by performing an asymptotic analysis of the intensity as the wavenumber tends to infinity. Next we provide an overview of the various reconstruction methods that have been employed in electron tomography and we conclude by mentioning a number of open problems. Besides providing an introduction to electron tomography written in the ‘language of inverse problems’, the authors hope to raise interest among experts in integral geometry and regularization theory for the mathematical and algorithmic difficulties that are encountered in electron tomography.

Primary ciliary dyskinesia with normal ultrastructure: three-dimensional tomography detects absence of DNAH11.

Tomography is an efficient tool to probe the 3 dimensional (3D) structure of materials. In the laboratory, a device has been developed to perform electron tomography in an environmental scanning electron microscopy (ESEM). The configuration of Scanning Transmission Electron Microscopy (STEM) in Environmental Scanning Electron Microscopy (ESEM) provides a novel approach for the characterization of the 3D structure of materials and optimizes a compromise between the resolution level of a few nm and the large tomogram due to the high thickness of transparency. Moreover, STEM allows the observation in 2D of wet samples in an ESEM by finely controlling the sample temperature and the water pressure of the sample environment. It has been recently demonstrated that it was possible to acquire image series of hydrated objects and thus to attain 3D characterization of wet samples. In order to get reliable and quantitative data, the present study deals with the simulation of electron-matter interactions. From such simulation on the MCM-41 material, we determine the minimum quantity of water layer which can be detected on wet materials.

Electron tomography (ET) is a method for three-dimensional (3-D) reconstruction of single, transparent objects from a series of images (i.e., a tilt series) recorded with a transmission electron microscope (EM) (Fig. 4.1). The method is related to the procedures used in medical tomography. The 3-D reconstructions are usually computed from the digitized tilt series after a radial weighting scheme has been applied to the Fourier-transformed data. The ET method can be used to reconstruct in 3-D any object that is transparent enough for projection imaging with the transmission EM. This means that specimens of biological origin are usually available for ET 3-D reconstruction, whereas, e.g., colloidal gold particles are not. An ET-calculated 3-D map could be based on projections from objects that have been visualized by EM in several different ways, i.e., from stained or unstained objects, objects visualized at different energy loss levels or objects embedded in different media. The combined analysis of the 3-D structure, imaged in different ways, could thus become very informative. The general applicability also means that it is not restricted to symmetrical or regularly arranged objects, nor to objects with preferred orientations on a support grid. In its present state, the ET method allows reproducible 3-D reconstructions of single molecular objects, with a resolution in the range of 5 nm, of complex cellular specimens. For isolated objects, free of interfering cellular substances, a somewhat higher resolution can be achieved. The ET method covers the intermediate resolution range where there is no other physical technique available to analyze single molecular complexes.