Conventional bright-field electron tomographic tilt series are obtained by collecting electrons that have traversed a specimen illuminated by a broad beam. Using this approach, the thickness is limited by the severe image blurring that occurs when electrons that have undergone multiple energy losses are focused by the objective lens of the microscope. Furthermore, the maximum area of the image is limited by the depth-of-field of the objective lens, so that only part of the sample is in focus at high tilt angles. Tomographic reconstruction using STEM with a tightly focused electron probe can overcome some of the limitations imposed by tomographic reconstruction using conventional TEM. First, because the incident STEM probe can be focused at any point in a specimen, large areas are imaged in focus even for high tilt angles. Second, because in STEM there are no image-forming lenses after the specimen, the resolution attainable in images of thick specimens is not further degraded by electrons that have suffered multiple energy losses. The most commonly applied STEM approach makes use of an annular dark-field detector to collect electrons that are scattered to high angles. However, the dark-field STEM technique is not well-suited to imaging thick biological specimens because of the limited depth of field defined by the large convergence angle of the incident electron probe. A tenfold or higher increase in depth of field is possible by adjusting the microscope optics to decrease the convergence semi-angle to approximately 12 mrad. Another limiting feature of dark-field STEM as applied to imaging thick specimens is the severe degradation in spatial resolution that occurs toward the bottom surface of a section because of beam broadening. In contrast, we found that much higher spatial resolution can be obtained by collecting only those electrons that are scattered to low angles, that is, by using an axial bright-field detector. Electrons that undergo multiple elastic scattering are substantially displaced from the point of incidence of the STEM probe and have, on average, larger net scattering angles. A large fraction of these electrons can thus be excluded from images recorded with an axial detector, leading to an improvement in spatial resolution toward the bottom surface of thick specimens. We quantified this unexpected improvement in resolution using Monte Carlo electron-trajectory simulations. We have applied axial bright-field STEM tomography to reconstruct one-micrometer thick unstained sections of plastic-embedded beta cells from mouse pancreatic islets of Langerhans. The reconstructions have enabled us to visualize features in the beta cells, such as insulin granules, mitochondria and Golgi stacks, throughout the entire specimen volume. This more comprehensive view of the cell volume provides information about the organization of organelles, which is not attainable using conventional tomography approaches. We have also used the technique to visualize synaptic spines in cultured slices of rat hippocampus. It has been possible for the first time to visualize entire post-synaptic densities and to assess differences in ultrastructure that occur when certain important proteins such as PSD-95 are knocked down. In other experiments, it has been feasible to characterize entire ribbon synapses in rat retina and to visualize the precise organization of secretory vesicles within those structures. In another application, we are applying STEM tomography to determine the three-dimensional arrangement of the complex membrane systems that are present in blood platelets, including the open canalicular system, dense tubules, and secretory granules. Collecting STEM tomograms from whole platelets provides a new way to visualize the structural changes that occur on activation of platelets that have been prepared by rapid freezing and freeze-substitution. Thus we have demonstrated the feasibility and advantages of STEM using axial detection for imaging thick sections at a spatial resolution around 5 to 10 nm, which is comparrable to the spatial resolution of conventional electron tomography from thinner sections (typically 3 to 8 nm). Most modern electron microscopes can be operated in STEM mode and can be readily equipped with a bright-field detector, which is anticipated to facilitate implementation of the technique. The demand for high-resolution, large-volume imaging of biological specimens has been addressed so far by the large-scale application of conventional electron tomography of thin sections. Our current work suggests that it will be possible to reconstruct intact organelles, intracellular pathogens and even entire mammalian cells through serial thick-section tomography.

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National Institute of Biomedical Imaging and Bioengineering
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Graydon, Cole W; Zhang, Jun; Oesch, Nicholas W et al. (2014) Passive diffusion as a mechanism underlying ribbon synapse vesicle release and resupply. J Neurosci 34:8948-62
Glushakova, Svetlana; Mazar, Julia; Hohmann-Marriott, Martin F et al. (2009) Irreversible effect of cysteine protease inhibitors on the release of malaria parasites from infected erythrocytes. Cell Microbiol 11:95-105
Hohmann-Marriott, Martin F; Sousa, Alioscka A; Azari, Afrouz A et al. (2009) Nanoscale 3D cellular imaging by axial scanning transmission electron tomography. Nat Methods 6:729-31
Sousa, A A; Hohmann-Marriott, M F; Zhang, G et al. (2009) Monte Carlo electron-trajectory simulations in bright-field and dark-field STEM: implications for tomography of thick biological sections. Ultramicroscopy 109:213-21