Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: implications for tomography of thick biological sections

Ultrastructure and Nanoporosity of Human Bone Shown with Correlative On-Axis Electron and Spectroscopic Tomographies

Mineralized collagen fibrils are the building block units of bone at the nanoscale. While it is known that collagen fibrils are mineralized both inside their gap zones (intra-fibrillar mineralization) and on their outer surfaces (extra-fibrillar mineralization), a clear visualization of this architecture in three dimensions (3D), combining structural and compositional information over large volumes, but without compromising the resolution, remains challenging. In this study, we demonstrate the use of on-axis Z-contrast electron tomography (ET) with correlative energy-dispersive X-ray spectroscopy (EDX) tomography to examine rod-shaped samples with diameters up to 700 nm prepared from individual osteonal lamellae in the human femur. Our work mainly focuses on two aspects: (i) low-contrast nanosized circular spaces ("holes") observed in sections of bone oriented perpendicular to the long axis of a long bone, and (ii) extra-fibrillar mineral, especially in terms of morphology and spatial relationship with respect to intra-fibrillar mineral and collagen fibrils. From our analyses, it emerges quite clearly that most "holes" are cross-sectional views of collagen fibrils. While this had been postulated before, our 3D reconstructions and reslicing along meaningful two-dimensional (2D) cross-sections provide a direct visual confirmation. Extra-fibrillar mineral appears to be composed of thin plates that are interconnected and span over several collagen fibrils, confirming that mineralization is cross-fibrillar, at least for the extra-fibrillar phase. EDX tomography shows mineral signatures (Ca and P) within the gap zones, but the signal appears weaker than that associated with the extra-fibrillar mineral, pointing toward the existence of dissimilarities between the two types of mineralization.

Non-classical crystallization of CeO2 by means of in situ electron microscopy

During in situ liquid-phase electron microscopy (LP-EM) observations, the application of different irradiation dose rates may considerably alter the chemistry of the studied solution and influence processes, in particular growth pathways. While many processes have been studied using LP-EM in the last decade, the extent of the influence of the electron beam is not always understood and comparisons with corresponding bulk experiments are lacking. Here, we employ the radiolytic oxidation of Ce3+ in aqueous solution as a model reaction for the in situ LP-EM study of the formation of CeO2 particles. We compare our findings to the results from our previous study where a larger volume of Ce3+ precursor solution was subjected to γ-irradiation. We systematically analyze the effects of the applied irradiation dose rates and the induced diffusion of Ce ions on the growth mechanisms and the morphology of ceria particles. Our results show that an eight orders of magnitude higher dose rate applied during homogeneous electron-radiation in LP-EM compared to the dose rate using gamma-radiation does not affect the CeO2 particle growth pathway despite the significant higher Ce3+ to Ce4+ oxidation rate. Moreover, in both cases highly ordered structures (mesocrystals) are formed. This finding is explained by the stepwise formation of ceria particles via an intermediate phase, a signature of non-classical crystallization. Furthermore, when irradiation is applied locally using LP scanning transmission electron microscopy (LP-STEM), the higher conversion rate induces Ce-ion concentration gradients affecting the CeO2 growth. The appearance of branched morphologies is associated with the change to diffusion limited growth.

Transmission electron microscopy of thick polymer and biological specimens

We explore the properties of elastic and inelastic scattering in a thick organic specimen, together with the mechanisms that provide contrast in a transmission electron microscope (TEM) and scanning-transmission electron microscope (STEM). Experimental data recorded from amorphous carbon are used to predict the bright-field image intensity, mass-thickness contrast and dose-limited resolution as a function of thickness, objective-aperture size, and primary-electron energy E₀. Combining this information with estimates of chromatic aberration, objective-aperture diffraction and beam broadening in the specimen, we calculate the achievable TEM and STEM resolution to be around 4 nm at E₀ = 300 keV (or below 3 nm at MeV energies) for a 10 µm-diameter objective aperture and 1 - 2 µm thickness of hydrated biological tissue. The 3 MeV resolution for a 10-μm tissue sample is probably closer to 10 nm. We also comment on the error involved in quadrature addition of resolution factors, when one or more of the point-spread functions are non-Gaussian.

The influence of chromatic aberration on the dose-limited spatial resolution of transmission electron microscopy

The effect of chromatic aberration (CC) on the spatial resolution in transmission electron microscopy (TEM) was studied in thick specimens in which the sample becomes the limiting factor in the resolution. The sample influences the energy spread of the electron beam, allows only a limited electron dose, and modulates electron scattering events. The experimental set-up consisted of a thin silicon nitride membrane and a silicon wedge containing gold nanoparticles. The resolution was measured as a function of electron dose and sample thickness for different sample configurations and for different microscopy modalities including regular TEM, energy filtered TEM (EFTEM) and CC-corrected TEM. Comparison with an analytical model aided the understanding of the experimental data applied over varied conditions. The general trend for all microscopy modalities was a transition from a noise-limited resolution at low electron dose to a CC-limited resolution at high-dose in the absence of beam blurring. EFTEM required an accurate energy slit offset and an optimal energy spread to energy-slit width ratio to surpass regular TEM. The key advantage of CC correction appeared to be the best possible resolution for larger sample thickness at low electron dose outperforming EFTEM by about fifty percent. Several hypothetical sample configurations relevant to liquid phase electron microscopy were evaluated as well to demonstrate the capabilities of the analytical model and to determine the most optimal microscopy modality for this type of experiment. The analytical model included an automated optimization of the EFTEM settings and may aid in optimizing the sample-limited resolution for experimental analysis and planning.

A Study of Membrane Impact on Spatial Resolution of Liquid In Situ Transmission Electron Microscope

Microchip technology with electron transparent membranes is a key component for in situ liquid transmission electron microscope (TEM) characterization. The membranes can significantly influence the TEM imaging spatial resolution, not only due to introducing additional material layers but also due to the associated bulging. The membrane bulging is largely defined by the membrane materials, thickness, and short dimension. The impact of the membrane on the spatial resolution, especially the extent of its bulging, was systematically investigated through the impact on the signal-to-noise ratio, chromatic aberration, and beam broadening. The optimization of the membrane parameters is the key component when designing the in situ TEM liquid cell. The optimal membrane thickness of 50 nm was found which balances the impact of membrane bulging and membrane thickness. Beyond this, the short membrane window dimension and the chip nominal spacing should be minimized. However, these two parameters have practical limitations in regards to chip handling.

Tomographic Collection of Block-Based Sparse STEM Images: Practical Implementation and Impact on the Quality of the 3D Reconstructed Volume

The reduction of the electron dose in electron tomography of biological samples is of high significance to diminish radiation damages. Simulations have shown that sparse data collection can perform efficient electron dose reduction. Frameworks based on compressive-sensing or inpainting algorithms have been proposed to accurately reconstruct missing information in sparse data. The present work proposes a practical implementation to perform tomographic collection of block-based sparse images in scanning transmission electron microscopy. The method has been applied on sections of chemically-fixed and resin-embedded Trypanosoma brucei cells. There are 3D reconstructions obtained from various amounts of downsampling, which are compared and eventually the limits of electron dose reduction using this method are explored.

A New and Unexpected Spatial Relationship Between Interaction Volume and Diffraction Pattern in Electron Microscopy in Transmission

The finding of this study is that the interaction volume in electron microscopy in transmission is well ordered laterally, with a remarkable and unexpected consequence being that lateral subsections of the interaction volume produce subsections of the Kikuchi diffraction pattern. It makes the microstructure of samples directly visible in Kikuchi patterns. This is first illustrated with polycrystalline Ti-10Al-25Nb with an on-axis transmission Kikuchi diffraction set-up in a scanning electron microscope. It is then shown via a Monte Carlo simulation and a large-angle convergent-beam electron diffraction experiment that this phenomenon finds its origin in the nature of the differential elastic and quasi-elastic cross sections. This phenomenon is then quantified by a careful image analysis of Kikuchi patterns recorded across a vertical interface in a silicon sample specifically designed and fabricated. A Monte Carlo simulation reproducing all the geometric parameters is conducted. Experiments and simulations match very well qualitatively, but with a slight quantitativity gap. The specificity of the thermal diffuse scattering cross-section, not available in the simulation, is thought to be responsible for this gap. Beside Kikuchi diffraction, the case of diffraction spots and diffuse background present in the pattern is also discussed.

Considerations for imaging thick, low contrast, and beam sensitive samples with liquid cell transmission electron microscopy

Transmission electron microscopy of whole cells is hindered by the inherently large thickness and low atomic contrast intrinsic of cellular material. Liquid cell transmission electron microscopy allows samples to remain in their native hydrated state and may permit visualizing cellular dynamics in-situ. However, imaging biological cells with this approach remains challenging and identifying an optimal imaging regime using empirical data would help foster new advancements in the field. Recent questions about the role of the electron beam inducing morphological changes or damaging cellular structure and function necessitates further investigation of electron beam-cell interactions, but such comparisons are complicated by variability in imaging techniques used across various studies currently present in literature. The necessity for using low electron fluxes while imaging biological samples requires finding an imaging strategy which produces the strongest contrast and signal to noise ratio for the electron flux used. Here, we experimentally measure and evaluate signal to noise ratios and damage mechanisms between liquid and cryogenic samples of intact cells using multiple electron imaging modalities all on the same instrument and with equivalent beam parameters to standardize the comparison. We also discuss considerations for optimal electron microscopy imaging conditions for future studies on whole cells within liquid environments.

Quantification and optimization of ADF-STEM image contrast for beam-sensitive materials

Many functional materials are difficult to analyse by scanning transmission electron microscopy (STEM) on account of their beam sensitivity and low contrast between different phases. The problem becomes even more severe when thick specimens need to be investigated, a situation that is common for materials that are ordered from the nanometre to micrometre length scales or when performing dynamic experiments in a TEM liquid cell. Here we report a method to optimize annular dark-field (ADF) STEM imaging conditions and detector geometries for a thick and beam-sensitive low-contrast specimen using the example of a carbon nanotube/polymer nanocomposite. We carried out Monte Carlo simulations as well as quantitative ADF-STEM imaging experiments to predict and verify optimum contrast conditions. The presented method is general, can be easily adapted to other beam-sensitive and/or low-contrast materials, as shown for a polymer vesicle within a TEM liquid cell, and can act as an expert guide on whether an experiment is feasible and to determine the best imaging conditions.

Comparison of 3D cellular imaging techniques based on scanned electron probes: Serial block face SEM vs. Axial bright-field STEM tomography

Microscopies based on focused electron probes allow the cell biologist to image the 3D ultrastructure of eukaryotic cells and tissues extending over large volumes, thus providing new insight into the relationship between cellular architecture and function of organelles. Here we compare two such techniques: electron tomography in conjunction with axial bright-field scanning transmission electron microscopy (BF-STEM), and serial block face scanning electron microscopy (SBF-SEM). The advantages and limitations of each technique are illustrated by their application to determining the 3D ultrastructure of human blood platelets, by considering specimen geometry, specimen preparation, beam damage and image processing methods. Many features of the complex membranes composing the platelet organelles can be determined from both approaches, although STEM tomography offers a higher ∼3 nm isotropic pixel size, compared with ∼5 nm for SBF-SEM in the plane of the block face and ∼30 nm in the perpendicular direction. In this regard, we demonstrate that STEM tomography is advantageous for visualizing the platelet canalicular system, which consists of an interconnected network of narrow (∼50-100 nm) membranous cisternae. In contrast, SBF-SEM enables visualization of complete platelets, each of which extends ∼2 µm in minimum dimension, whereas BF-STEM tomography can typically only visualize approximately half of the platelet volume due to a rapid non-linear loss of signal in specimens of thickness greater than ∼1.5 µm. We also show that the limitations of each approach can be ameliorated by combining 3D and 2D measurements using a stereological approach.

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.

Graphene-supporting films and low-voltage STEM in SEM toward imaging nanobio materials without staining: Observation of insulin amyloid fibrils

Utilization of graphene-supporting films and low-voltage scanning transmission electron microscopy (LV-STEM) in scanning electron microscopy (SEM) is shown to be an effective means of observing unstained nanobio materials. Insulin amyloid fibrils, which are implicated as a cause of type II diabetes, are formed in vitro and observed without staining at room temperature. An in-lens cold field-emission SEM, equipped with an additional homemade STEM detector, provides dark field (DF)-STEM images in the low energy range of 5-30keV, together with secondary electron (SE) images. Analysis based on Lenz's theory is used to interpret the experimental results. Graphene films, where the fibrils are deposited, reduce the background level of the STEM images compared with instances when conventional amorphous carbon films are used. Using 30keV, which is lower than that for conventional TEM (100-300keV), together with low detection angles (15-55mrad) enhances the signals from the fibrils. These factors improve image quality, which enables observation of thin fibrils with widths of 7-8nm. STEM imaging clearly reveals a twisted-ribbon structure of a fibril, and SE imaging shows an emphasized striped pattern of the fibril. The LV-STEM in SEM enables acquisition of two types of images of an identical fibril in a single instrument, which is useful for understanding the structure. This study expands the application of SEM to other systems of interest, which is beneficial to a large number of users. The method in this study can be applied to the observation of various nanobio materials and analysis of their native structures, thus contributing to research in materials and life sciences.

Biological application of Compressed Sensing Tomography in the Scanning Electron Microscope

The three-dimensional tomographic reconstruction of a biological sample, namely collagen fibrils in human dermal tissue, was obtained from a set of projection-images acquired in the Scanning Electron Microscope. A tailored strategy for the transmission imaging mode was implemented in the microscope and proved effective in acquiring the projections needed for the tomographic reconstruction. Suitable projection alignment and Compressed Sensing formulation were used to overcome the limitations arising from the experimental acquisition strategy and to improve the reconstruction of the sample. The undetermined problem of structure reconstruction from a set of projections, limited in number and angular range, was indeed supported by exploiting the sparsity of the object projected in the electron microscopy images. In particular, the proposed system was able to preserve the reconstruction accuracy even in presence of a significant reduction of experimental projections.

The influence of structure depth on image blurring of micrometres-thick specimens in MeV transmission electron imaging

This study investigates the influence of structure depth on image blurring of micrometres-thick films by experiment and simulation with a conventional transmission electron microscope (TEM). First, ultra-high-voltage electron microscope (ultra-HVEM) images of nanometer gold particles embedded in thick epoxy-resin films were acquired in the experiment and compared with simulated images. Then, variations of image blurring of gold particles at different depths were evaluated by calculating the particle diameter. The results showed that with a decrease in depth, image blurring increased. This depth-related property was more apparent for thicker specimens. Fortunately, larger particle depth involves less image blurring, even for a 10-μm-thick epoxy-resin film. The quality dependence on depth of a 3D reconstruction of particle structures in thick specimens was revealed by electron tomography. The evolution of image blurring with structure depth is determined mainly by multiple elastic scattering effects. Thick specimens of heavier materials produced more blurring due to a larger lateral spread of electrons after scattering from the structure. Nevertheless, increasing electron energy to 2MeV can reduce blurring and produce an acceptable image quality for thick specimens in the TEM.

Intensity distribution analysis of cathodoluminescence using the energy loss distribution of electrons

We present an intensity distribution analysis of cathodoluminescence (CL) excited with a focused electron beam in a luminescent thin film. The energy loss distribution is applied to the developed analysis method in order to determine the arrangement of the dipole locations along the path of the electron traveling in the film. Propagating light emitted from each dipole is analyzed with the finite-difference time-domain (FDTD) method. CL distribution near the film surface is evaluated as a nanometric light source. It is found that a light source with 30 nm widths is generated in the film by the focused electron beam. We also discuss the accuracy of the developed analysis method by comparison with experimental results. The analysis results are brought into good agreement with the experimental results by introducing the energy loss distribution.

Liquid scanning transmission electron microscopy: imaging protein complexes in their native environment in whole eukaryotic cells

Scanning transmission electron microscopy (STEM) of specimens in liquid, so-called Liquid STEM, is capable of imaging the individual subunits of macromolecular complexes in whole eukaryotic cells in liquid. This paper discusses this new microscopy modality within the context of state-of-the-art microscopy of cells. The principle of operation and equations for the resolution are described. The obtained images are different from those acquired with standard transmission electron microscopy showing the cellular ultrastructure. Instead, contrast is obtained on specific labels. Images can be recorded in two ways, either via STEM at 200 keV electron beam energy using a microfluidic chamber enclosing the cells, or via environmental scanning electron microscopy at 30 keV of cells in a wet environment. The first series of experiments involved the epidermal growth factor receptor labeled with gold nanoparticles. The labels were imaged in whole fixed cells with nanometer resolution. Since the cells can be kept alive in the microfluidic chamber, it is also feasible to detect the labels in unfixed, live cells. The rapid sample preparation and imaging allows studies of multiple whole cells.

Specifications for hard condensed matter specimens for three-dimensional high-resolution tomographies

Tomography is a standard and invaluable technique that covers a large range of length scales. It gives access to the inner morphology of specimens and to the three-dimensional (3D) distribution of physical quantities such as elemental composition, crystalline phases, oxidation state, or strain. These data are necessary to determine the effective properties of investigated heterogeneous media. However, each tomographic technique relies on severe sampling conditions and physical principles that require the sample to be adequately shaped. For that purpose, a wide range of sample preparation techniques is used, including mechanical machining, polishing, sawing, ion milling, or chemical techniques. Here, we focus on the basics of tomography that justify such advanced sample preparation, before reviewing and illustrating the main techniques. Performances and limits are highlighted, and we identify the best preparation technique for a particular tomographic scale and application. The targeted tomography techniques include hard X-ray micro- and nanotomography, electron nanotomography, and atom probe tomography. The article mainly focuses on hard condensed matter, including porous materials, alloys, and microelectronics applications, but also includes, to a lesser extent, biological considerations.

Development and application of STEM for the biological sciences

The design of the scanning transmission electron microscope (STEM), as conceived originally by Crewe and coworkers, enables the highly efficient and flexible collection of different elastic and inelastic signals resulting from the interaction of a focused probe of incident electrons with a specimen. In the present paper we provide a brief review for how the STEM today can be applied towards a range of different problems in the biological sciences, emphasizing four main areas of application. (1) For three decades, the most widely used STEM technique has been the mass determination of proteins and other macromolecular assemblies. Such measurements can be performed at low electron dose by collecting the high-angle dark-field signal using an annular detector. STEM mass mapping has proven valuable for characterizing large protein assemblies such as filamentous proteins with a well-defined mass per length. (2) The annular dark-field signal can also be used to image ultrasmall, functionalized nanoparticles of heavy atoms for labeling specific amino-acid sequences in protein assemblies. (3) By acquiring electron energy loss spectra (EELS) at each pixel in a hyperspectral image, it is possible to map the distributions of specific bound elements like phosphorus, calcium and iron in isolated macromolecular assemblies or in compartments within sectioned cells. Near single atom sensitivity is feasible provided that the specimen can tolerate a very high incident electron dose. (4) Electron tomography is a new application of STEM that enables three-dimensional reconstruction of micrometer-thick sections of cells. In this technique a probe of small convergence angle gives a large depth of field throughout the thickness of the specimen while maintaining a probe diameter of <2 nm; and the use of an on-axis bright-field detector reduces the effects of beam broadening and thus improves the spatial resolution compared to that attainable by STEM dark-field tomography.

The probe profile and lateral resolution of scanning transmission electron microscopy of thick specimens

Lateral profiles of the electron probe of scanning transmission electron microscopy (STEM) were simulated at different vertical positions in a micrometers-thick carbon sample. The simulations were carried out using the Monte Carlo method in CASINO software. A model was developed to fit the probe profiles. The model consisted of the sum of a Gaussian function describing the central peak of the profile and two exponential decay functions describing the tail of the profile. Calculations were performed to investigate the fraction of unscattered electrons as a function of the vertical position of the probe in the sample. Line scans were also simulated over gold nanoparticles at the bottom of a carbon film to calculate the achievable resolution as a function of the sample thickness and the number of electrons. The resolution was shown to be noise limited for film thicknesses less than 1 μm. Probe broadening limited the resolution for thicker films. The validity of the simulation method was verified by comparing simulated data with experimental data. The simulation method can be used as quantitative method to predict STEM performance or to interpret STEM images of thick specimens.

Electron microscopy of specimens in liquid

Imaging samples in liquids with electron microscopy can provide unique insights into biological systems, such as cells containing labelled proteins, and into processes of importance in materials science, such as nanoparticle synthesis and electrochemical deposition. Here we review recent progress in the use of electron microscopy in liquids and its applications. We examine the experimental challenges involved and the resolution that can be achieved with different forms of the technique. We conclude by assessing the potential role that electron microscopy of liquid samples can play in areas such as energy storage and bioimaging.

Note: direct measurement of the point-to-point resolution for microns-thick specimens in the ultrahigh-voltage electron microscope

We report on a direct measurement method and results of the point-to-point resolution for microns-thick amorphous specimens in the ultrahigh-voltage electron microscope (ultra-HVEM). We first obtain the ultra-HVEM images of nanometer gold particles with different sizes on the top surfaces of the thick epoxy-resin specimens. Based on the Rayleigh criterion, the point-to-point resolution is then determined as the minimum distance between centers of two resolvable tangent gold particles. Some values of resolution are accordingly acquired for the specimens with different thicknesses at the accelerating voltage of 2 MV, for example, 18.5 nm and 28.4 nm for the 5 μm and 8 μm thick epoxy-resin specimens, respectively. The presented method and results provide a reliable and useful approach to quantifying and comparing the achievable spatial resolution for the thick specimens imaged in the mode of transmission electron including the scanning transmission electron microscope.

Simulating STEM imaging of nanoparticles in micrometers-thick substrates

Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.

Simulating STEM imaging of nanoparticles in micrometers-thick substrates

Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark-field detector was generated. The simulations were carried out using the Monte Carlo method in the CASINO software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal series showed the effect of beam broadening on the spatial resolution and on the signal-to-noise ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial for the design of equipment, or for the analysis of the composition of a certain specimen.

Dual-axis electron tomography of biological specimens: Extending the limits of specimen thickness with bright-field STEM imaging

The absence of imaging lenses after the specimen in the scanning transmission electron microscope (STEM) enables electron tomography to be performed in the STEM mode on micrometer-thick plastic-embedded specimens without the deleterious effect of chromatic aberration, which limits spatial resolution and signal-to-noise ratio in conventional TEM. Using Monte Carlo calculations to simulate electron scattering from gold nanoparticles situated at the top and bottom surfaces of a plastic section, we assess the optimal acquisition strategy for axial bright-field STEM electron tomography at a beam-energy of 300keV. Dual tilt-axis STEM tomography with optimized axial bight-field detector geometry is demonstrated by application to micrometer-thick sections of beta cells from mouse pancreatic islet. The quality of the resulting three-dimensional reconstructions is comparable to that obtained from much thinner (0.3-micrometer) sections using conventional TEM tomography. The increased range of specimen thickness accessible to axial STEM tomography without the need for serial sectioning enables the 3-D visualization of more complex and larger subcellular structures.

Intracellular membrane traffic at high resolution

Membrane traffic between organelles is essential for a multitude of processes that maintain cell homeostasis. Many steps in these tightly regulated trafficking pathways take place in microdomains on the membranes of organelles, which require analysis at nanometer resolution. Electron microscopy (EM) can visualize these processes in detail and is mainly responsible for our current view of morphology on the subcellular level. This review discusses how EM can be applied to solve many questions of intracellular membrane traffic, with a focus on the endosomal system. We describe the expansion of the technique from purely morphological analysis to cryo-immuno-EM, correlative light electron microscopy (CLEM), and 3D electron tomography. In this review we go into some technical details of these various techniques. Furthermore, we provide a full protocol for immunolabeling on Lowicryl sections of high-pressure frozen cells as well as a detailed description of a simple CLEM method that can be applied to answer many membrane trafficking questions. We believe that these EM-based techniques are important tools to expand our understanding of the molecular details of endosomal sorting and intracellular membrane traffic in general.

Nanoscale 3D cellular imaging by axial scanning transmission electron tomography

Electron tomography provides three-dimensional structural information about supramolecular assemblies and organelles in a cellular context but image degradation, caused by scattering of transmitted electrons, limits applicability in specimens thicker than 300 nm. We show that scanning transmission electron tomography of 1000 nm thick samples using axial detection provides resolution comparable to conventional electron tomography. The method is demonstrated by reconstructing a human erythrocyte infected with the malaria parasite Plasmodium falciparum.