Correlative 3D imaging of whole mammalian cells with light and electron microscopy

Gavin E. Murphy, Kedar Narayan, Bradley C. Lowekamp, Lisa M. Hartnell, Jurgen A W Heymann, Jing Fu, Sriram Subramaniam

Research output: Contribution to journalArticlepeer-review

67 Scopus citations


We report methodological advances that extend the current capabilities of ion-abrasion scanning electron microscopy (IA-SEM), also known as focused ion beam scanning electron microscopy, a newly emerging technology for high resolution imaging of large biological specimens in 3D. We establish protocols that enable the routine generation of 3D image stacks of entire plastic-embedded mammalian cells by IA-SEM at resolutions of ∼10-20 nm at high contrast and with minimal artifacts from the focused ion beam. We build on these advances by describing a detailed approach for carrying out correlative live confocal microscopy and IA-SEM on the same cells. Finally, we demonstrate that by combining correlative imaging with newly developed tools for automated image processing, small 100 nm-sized entities such as HIV-1 or gold beads can be localized in SEM image stacks of whole mammalian cells. We anticipate that these methods will add to the arsenal of tools available for investigating mechanisms underlying host-pathogen interactions, and more generally, the 3D subcellular architecture of mammalian cells and tissues.

Original languageEnglish (US)
Pages (from-to)268-278
Number of pages11
JournalJournal of Structural Biology
Issue number3
StatePublished - Dec 2011
Externally publishedYes


  • Correlative light electron microscopy
  • Focused ion beam scanning electron microscopy
  • HIV
  • Ion-abrasion scanning electron microscopy
  • T cells

ASJC Scopus subject areas

  • Structural Biology


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