Dedicated image analysis techniques for three-dimensional reconstruction from serial sections in electron microscopy

This article describes the digital treatments needed to reconstruct spatial information at a 40-nm depth resolution of entire cells from transmission electron microscopic images of serial sections containing laser-induced topographical references. The use of a scanning transmission electron microscope (STEM) allows the acquisition of images with high contrast and good resolution at medium magnification. The scanning of our specimens at video frequencies is an attractive way to link a STEM with an image processing system. The magnetic hysteresis of the spools responsible for the electron scanning induces image deformations that have to be modelized and rectified before registering the images corrected for cutting-induced deformations.