Multibeam Serial Scanning Electron Microscopy Volume Alignment

Technological advances in electron microscopy (EM) have made the acquisition of cubic-millimeter and larger-sized volumes with 10 nm or less pixel resolution tractable. Multibeam Scanning EM imaging of multiple areas allows for fast image acquisition of petabyte-sized datasets from thousands of serial sections, in our case deposited on silicon wafers. Thus, single image tiles of relatively small areas must be computationally aligned in 2D (within single z-slices) and 3D (between z-slices), correcting for potential section distortions, and then blended together. Due to its immense computational costs, the alignment process poses a major bottleneck as the first step in large-scale 3D reconstructions. Here we present our image alignment and blending procedures for reconstructing large 3D volumes from small 2D images. The alignment pipeline takes advantage both of traditional image processing and machine vision echniques. The pipeline aims for an alignment that is sufficient for human annotation but that also minimizes alignment run time