3D imaging by serial block face scanning electron microscopy for materials science using ultramicrotomy

Sample preparation and data collection for serial block face scanning electron microscopy of mammalian cell monolayers

Volume electron microscopy encompasses a set of electron microscopy techniques that can be used to examine the ultrastructure of biological tissues and cells in three dimensions. Two block face techniques, focused ion beam scanning electron microscopy (FIB-SEM) and serial block face scanning electron microscopy (SBF-SEM) have often been used to study biological tissue samples. More recently, these techniques have been adapted to in vitro tissue culture samples. Here we describe step-by-step protocols for two sample embedding methods for in vitro tissue culture cells intended to be studied using SBF-SEM. The first focuses on cell pellet embedding and the second on en face embedding. En face embedding can be combined with light microscopy, and this CLEM workflow can be used to identify specific biological events by light microscopy, which can then be imaged using SBF-SEM. We systematically outline the steps necessary to fix, stain, embed and image adherent tissue culture cell monolayers by SBF-SEM. In addition to sample preparation, we discuss optimization of parameters for data collection. We highlight the challenges and key steps of sample preparation, and the consideration of imaging variables.

Serial Block-Face Scanning Electron Microscopy (SBF-SEM) of Biological Tissue Samples

Serial block-face scanning electron microscopy (SBF-SEM) allows for the collection of hundreds to thousands of serially-registered ultrastructural images, offering an unprecedented three-dimensional view of tissue microanatomy. While SBF-SEM has seen an exponential increase in use in recent years, technical aspects such as proper tissue preparation and imaging parameters are paramount for the success of this imaging modality. This imaging system benefits from the automated nature of the device, allowing one to leave the microscope unattended during the imaging process, with the automated collection of hundreds of images possible in a single day. However, without appropriate tissue preparation cellular ultrastructure can be altered in such a way that incorrect or misleading conclusions might be drawn. Additionally, images are generated by scanning the block-face of a resin-embedded biological sample and this often presents challenges and considerations that must be addressed. The accumulation of electrons within the block during imaging, known as "tissue charging," can lead to a loss of contrast and an inability to appreciate cellular structure. Moreover, while increasing electron beam intensity/voltage or decreasing beam-scanning speed can increase image resolution, this can also have the unfortunate side effect of damaging the resin block and distorting subsequent images in the imaging series. Here we present a routine protocol for the preparation of biological tissue samples that preserves cellular ultrastructure and diminishes tissue charging. We also provide imaging considerations for the rapid acquisition of high-quality serial-images with minimal damage to the tissue block.

Development of protocols for the first serial block-face scanning electron microscopy (SBF SEM) studies of bone tissue

There is an unmet need for a high-resolution three-dimensional (3D) technique to simultaneously image osteocytes and the matrix in which these cells reside. In serial block-face scanning electron microscopy (SBF SEM), an ultramicrotome mounted within the vacuum chamber of a microscope repeatedly sections a resin-embedded block of tissue. Backscattered electron scans of the block face provide a stack of high-resolution two-dimensional images, which can be used to visualise and quantify cells and organelles in 3D. High-resolution 3D images of biological tissues from SBF SEM have been exploited considerably to date in the neuroscience field. However, non-brain samples, in particular hard biological tissues, have appeared more challenging to image by SBF SEM due to the difficulties of sectioning and rendering the samples conductive. We have developed and propose protocols for bone tissue preparation using SBF SEM, for imaging simultaneously soft and hard bone tissue components in 3D. We review the state of the art in high-resolution imaging of osteocytes, provide a historical perspective of SBF SEM, and we present first SBF SEM proof-of-concept studies for murine and human tissue. The application of SBF SEM to hard tissues will facilitate qualitative and quantitative 3D studies of tissue microstructure and ultrastructure in bone development, ageing and pathologies such as osteoporosis and osteoarthritis.

Helical fibrillar microstructure of tendon using serial block-face scanning electron microscopy and a mechanical model for interfibrillar load transfer

Tendon's hierarchical structure allows for load transfer between its fibrillar elements at multiple length scales. Tendon microstructure is particularly important, because it includes the cells and their surrounding collagen fibrils, where mechanical interactions can have potentially important physiological and pathological contributions. However, the three-dimensional (3D) microstructure and the mechanisms of load transfer in that length scale are not known. It has been postulated that interfibrillar matrix shear or direct load transfer via the fusion/branching of small fibrils are responsible for load transfer, but the significance of these mechanisms is still unclear. Alternatively, the helical fibrils that occur at the microstructural scale in tendon may also mediate load transfer; however, these structures are not well studied due to the lack of a three-dimensional visualization of tendon microstructure. In this study, we used serial block-face scanning electron microscopy to investigate the 3D microstructure of fibrils in rat tail tendon. We found that tendon fibrils have a complex architecture with many helically wrapped fibrils. We studied the mechanical implications of these helical structures using finite-element modelling and found that frictional contact between helical fibrils can induce load transfer even in the absence of matrix bonding or fibril fusion/branching. This study is significant in that it provides a three-dimensional view of the tendon microstructure and suggests friction between helically wrapped fibrils as a mechanism for load transfer, which is an important aspect of tendon biomechanics.

Investigation of Three-Dimensional Structure and Pigment Surrounding Environment of a TiO₂ Containing Waterborne Paint

Serial block-face scanning electron microscopy (SBFSEM) has been used to investigate the three-dimensional (3D) structure of a cured waterborne paint containing TiO₂ pigment particles, and the surrounding environment of the TiO₂ pigment particles in the cured paint film was also discussed. The 3D spatial distribution of the particles in the paint film and their degree of dispersion were clearly revealed. More than 55% of the measured TiO₂ particles have volumes between 1.0 × 10⁶ nm³ and 1.0 × 10⁷ nm³. From the obtained 3D images, we proposed that there are three different types of voids in the measured cured waterborne paint film: voids that exist in the cured paint themselves, voids produced by particle shedding, and voids produced by quasi-liquid phase evaporation during measurement. Among these, the latter two types of voids are artefacts caused during SBFSEM measurement which provide evidence to support that the pigment particles in the cured paint/coating films are surrounding by quasi-liquid environment rather than dry solid environment. The error caused by particle shedding to the statistical calculation of the TiO₂ particles was corrected in our analysis. The resulting 3D structure of the paint, especially the different voids are important for further systematic research, and are critical for understanding the real environment of the pigment particles in the cured paint films.

Methodological Improvements With Conductive Materials for Volume Imaging of Neural Circuits by Electron Microscopy

Recent advancements in electron microscope volume imaging, such as serial imaging using scanning electron microscopy (SEM), have facilitated the acquisition of three-dimensional ultrastructural information of biological samples. These advancements help build a comprehensive understanding of the functional structures in entire organelles, cells, organs and organisms, including large-scale wiring maps of neural circuitry in various species. Advanced volume imaging of biological specimens has often been limited by artifacts and insufficient contrast, which are partly caused by problems in staining, serial sectioning and electron beam irradiation. To address these issues, methods of sample preparation have been modified and improved in order to achieve better resolution and higher signal-to-noise ratios (SNRs) in large tissue volumes. These improvements include the development of new embedding media for electron microscope imaging that have desirable physical properties such as less deformation in the electron beam and higher stability for sectioning. The optimization of embedding media involves multiple resins and filler materials including biological tissues, metallic particles and conductive carbon black. These materials alter the physical properties of the embedding media, such as conductivity, which reduces specimen charge, ameliorates damage to sections, reduces image deformation and results in better ultrastructural data. These improvements and further studies to improve electron microscope volume imaging methods provide options for better scale, quality and throughput in the three-dimensional ultrastructural analyses of biological samples. These efforts will enable a deeper understanding of neuronal circuitry and the structural foundation of basic and higher brain functions.

Multi-modal plasma focused ion beam serial section tomography of an organic paint coating

Pigment distributions have a critical role in the corrosion protection properties of organic paint coatings, but they are difficult to image in 3D over statistically significant volumes and at sufficiently high spatial resolutions required for detailed analysis. Here we report, for the first time, large volume analytical serial sectioning tomography of an organic composite coating using a xenon Plasma Focused Ion Beam (PFIB) combined with secondary electron imaging, energy dispersive X-ray (EDX) spectrum imaging (SI) and electron backscattered diffraction (EBSD). Together these techniques provide a comprehensive quantitative description of the physical orientation and distribution of the pigments within a model marine ballast tank coating, as well as their crystallographic and elemental characterisation. Polymers and organic materials are challenging because of their propensity for ion beam damage and possible beam heating effects. Our novel, optimised block preparation technique permits automated data acquisition with minimal operator intervention, and can have significant applications for the structural and chemical characterisation of a wide range of organic materials. Our results revealed that the paint contained 7.5 vol% aluminium flakes and 25 vol% quartz particles. The aluminium flakes were oriented parallel to the substrate surface, which is beneficial in terms of the corrosion protection capability of the coating.

Three-dimensional imaging and analysis of the internal structure of SAPO-34 zeolite crystals

SAPO-34 is widely used as a catalyst for important industrial reactions, such as the methanol-to-olefin (MTO) reaction and selective catalytic reduction (SCR) of nitrogen oxides (NO_x). The internal structure of SAPO-34 has a great influence on the catalytic performance. Two-dimensional (2D) images of the SAPO-34 particle surfaces from scanning electron microscopy (SEM) show clearly well-faceted cube morphologies, which suggest they should be quite uniform perfect crystals. However, Bragg coherent X-ray diffraction imaging (BCDI) of the SAPO-34 particles shows a rich internal structure existing within these crystals. In this work, we investigated the internal structure of a SAPO-34 zeolite by serial block-face scanning electron microscopy (SBFSEM). The internal structure observed in the backscattered electron (BSE) micrographs from SBFSEM and the energy dispersive spectroscopy (EDS) measurements is found to be consistent with the BCDI results. From the three-dimensional (3D) structural images of SAPO-34 crystals obtained by SBFSEM, the domains within the individual SAPO-34 were visualized and quantified.

This work studies the inter-structure of a SAPO-34 particle by Bragg coherent X-ray diffraction imaging and serial-block-face scanning electron microscopy.

Time-lapse lab-based x-ray nano-CT study of corrosion damage

An experimental protocol (workflow) has been developed for time-lapse x-ray nanotomography (nano-CT) imaging of environmentally driven morphological changes to materials. Two case studies are presented. First, the leaching of nanoparticle corrosion inhibitor pigment from a polymer coating was followed over 14 days, while in the second case the corrosion damage to an AA2099 aluminium alloy was imaged over 12 hours. The protocol includes several novel aspects relevant to nano-CT with the use of a combination of x-ray absorption and phase contrast data to provide enhanced morphological and composition information, and hence reveal the best information to provide new insights into the changes of different phases over time. For the pigmented polymer coating containing nominally strontium aluminium polyphosphate, the strontium-rich components within the materials are observed to leach extensively whereas the aluminium-rich components are more resistant to dissolution. In the case of AA2099 it is found that the initial grain boundary corrosion is driven by the presence of copper-rich phases and is then followed by the corrosion of grains of specific orientation.