Serial Block Face Sem of Biological Structures at Near Isotropic Spatial Resolution using Multiple Beam Energies and Monte Carlo Simulations

Abstract

Serial block face scanning electron microscopy (SBF-SEM) provides nanoscale 3D ultrastructure of entire cells and tissue volumes. In SBF-SEM, an ultramicrotome built into the SEM specimen stage successively removes thin sections from a plastic-embedded, heavy metal-stained specimen. After each cut, the freshly exposed block face is imaged at a low incident electron energy using a backscattered electron detector to provide 3D ultrastructure with a resolution of approximately 5 nm in the plane of the block face and around 25 nm in the perpendicular z-direction, as limited by the slice thickness. We have explored the feasibility of improving the z-resolution in SBF-SEM by recording images at multiple primary beam energies, thus sampling different depths below the block surface.A linear relationship was found between the depth of test structures, generated by Monte Carlo simulations, and the ratio of backscattered image intensities recorded at primary beam energies between 1.4 keV and 6.8 keV. This enabled us to reconstruct the 3D model within a 25-nm surface layer at a z-resolution of around 5 nm. We used a Zeiss Sigma-VP SEM equipped with a Gatan 3View SBF system to acquire 3D data from a specimen consisting of gold spheres embedded in carbon. Experiments were also performed on embedded blocks of stained biological tissues.Although damage of the block under electron irradiation limits the signal to noise ratio, the use of multiple primary beam energies, coupled with a physics-based Monte Carlo model, provides the possibility of obtaining cellular ultrastructure at nearly isotropic 3D spatial resolution.