Computer-Controlled Transmission Electron Microscopy: Automated Tomography

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.

Electron tomography is a mature 3D nanocharacterisation technique with applications to almost all classes of materials. It offers 3D resolution at the nanometre level, or better, in volumes of a few hundred nanometres—precisely the playground of the nanoscientist. Electron tomography is especially suited for uncovering the links between structure and properties in systems that show complex 3D character. This chapter offers a comprehensive introduction to the technique, from its mathematical background to practical experimental issues and from tomographic reconstruction to quantitative analysis of 3D volumes. Being angled more towards the physical scientist, this chapter concentrates on the particular challenges of acquiring tomographic data from systems in physical, chemical and materials science using the panoply of imaging techniques available in the modern transmission electron microscope (TEM). These include scanning TEM (STEM), dark-field TEM and chemically sensitive 3D imaging via electron energy loss spectroscopy (EELS) and energy-dispersive X-ray (EDX) spectroscopy. The chapter concludes by examining emerging areas such as atomic-resolution 3D imaging and scanning confocal electron microscopy (SCEM).

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.

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

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.

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.

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.

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

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.

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

To assess the use of three-dimensional (3D) imaging methods to quantify the changes in soft- and hard-tissues in cleft patients after cleft-related treatment during growth. PubMed, EMBASE, Web of Science and the Cochrane Library were searched up to 1 June 2018. Included publications were those using 3D imaging to quantify soft- and hard-tissue changes after cleft-related treatments in patients with any type of cleft, during growth. Data extraction and qualitative analysis were performed by two reviewers. The methodological quality of each study was reviewed using the QUADAS-2 tool. From 4 databases, 2315 articles were found. Full texts of 422 articles were analyzed and finally 12 articles were included for qualitative analysis. CT was performed in the majority of studies for hard-tissue quantification. Stereophotogrammetry, Laser scanner and 3D digitizer were identified as viable methods to quantify both soft- and hard-tissue changes, depending on whether the scan was made of the facial surface or the cast surface. Most studies conducted imaging analysis without registration between multitemporal images, which is the reason why they did not fulfil the inclusion criteria. Although several imaging modalities have the potential to quantify cleft-related treatment follow-up, there is an urgent need to assess the imaging methods and related analyses allowing to standardise a 3D imaging protocol to quantify hard- and soft-tissue treatment follow-up.

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).

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.

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.