Volume scanning electron microscopy for imaging biological ultrastructure

Biol Cell. 2016 Nov;108(11):307-323. doi: 10.1111/boc.201600024. Epub 2016 Aug 12.


Electron microscopy (EM) has been a key imaging method to investigate biological ultrastructure for over six decades. In recent years, novel volume EM techniques have significantly advanced nanometre-scale imaging of cells and tissues in three dimensions. Previously, this had depended on the slow and error-prone manual tasks of cutting and handling large numbers of sections, and imaging them one-by-one with transmission EM. Now, automated volume imaging methods mostly based on scanning EM (SEM) allow faster and more reliable acquisition of serial images through tissue volumes and achieve higher z-resolution. Various software tools have been developed to manipulate the acquired image stacks and facilitate quantitative analysis. Here, we introduce three volume SEM methods: serial block-face electron microscopy (SBEM), focused ion beam SEM (FIB-SEM) and automated tape-collecting ultramicrotome SEM (ATUM-SEM). We discuss and compare their capabilities, provide an overview of the full volume SEM workflow for obtaining 3D datasets and showcase different applications for biological research.

Keywords: Brain/nervous system; Cellular imaging; Electron microscopy; Systems biology.

Publication types

  • Review

MeSH terms

  • Animals
  • Brain / ultrastructure*
  • Histocytological Preparation Techniques / methods
  • Humans
  • Image Processing, Computer-Assisted / methods
  • Microscopy, Electron, Scanning / methods*
  • Microtomy / methods