Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps.

fig1 fig2 MEFS_cryo
Correlative light-electron microscopy image Immunogold labeled section of reovirus-infected dendritic cells Cryo-EM virtual slide of a thin part of an unstained vitrified mouse embryonic fibroblast
Sagittal section of a zebrafish embryo
The thumbnail shows the cartilage in slateblue
, the eye in sienna
, the brain in forestgreen
, the muscles in salmon
,the liver in indianred
, the intestine in darkkhaki
, the pancreas in plum
, the pronephric duct in yellow
, the olfactory pit in limegreen
, and the yolk in turquoise

Click on a image to navigate to the interactive pages with the full virtual slides.

  • [DOI] Ravelli Raimond B. G., Kalicharan Ruby D., Avramut M. Cristina, Sjollema Klaas A., Pronk Joachim W., Dijk Freark, Koster Abraham J., Visser Jeroen T. J., Faas Frank G. A., and Giepmans Ben N. G., “Destruction of Tissue, Cells and Organelles in Type 1 Diabetic Rats Presented at Macromolecular Resolution,” Sci. rep., vol. 3, 2013.
    author = "{Ravelli Raimond B. G.} and {Kalicharan Ruby D.} and {Avramut M. Cristina} and {Sjollema Klaas A.} and {Pronk Joachim W.} and {Dijk Freark} and {Koster Abraham J.} and {Visser Jeroen T. J.} and {Faas Frank G. A.} and {Giepmans Ben N. G.}",
    doi = " 10.1038/srep01804",
    journal = "Sci. Rep.",
    month = "may",
    publisher = "Macmillan Publishers Limited. All rights reserved",
    title = "{Destruction of Tissue, Cells and Organelles in Type 1 Diabetic Rats Presented at Macromolecular Resolution}",
    volume = "3",
    year = "2013"
  • E. H. Williams, P. Carpentier, and T. Misteli, “The jcb dataviewer scales up,” The journal of cell biology, vol. 198, iss. 3, pp. 271-272, 2012.
    title={The JCB DataViewer scales up},
    author={Williams, Elizabeth H and Carpentier, Pamela and Misteli, Tom},
    journal={The Journal of cell biology},
    publisher={Rockefeller Univ Press}
  • F. G. Faas, C. M. Avramut, B. M. van den Berg, M. A. Mommaas, A. J. Koster, and R. B. Ravelli, “Virtual nanoscopy: generation of ultra-large high resolution electron microscopy maps,” The journal of cell biology, vol. 198, iss. 3, pp. 457-469, 2012.
    title={Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps},
    author={Faas, Frank GA and Avramut, M Cristina and van den Berg, Bernard M and Mommaas, A Mieke and Koster, Abraham J and Ravelli, Raimond BG},
    journal={The Journal of cell biology},
    publisher={Rockefeller Univ Press}
  • [DOI] M. J. C. Dane, B. M. van den Berg, C. M. Avramut, F. G. A. Faas, J. van der Vlag, A. L. W. M. M. Rops, R. B. G. Ravelli, B. J. Koster, A. J. van Zonneveld, H. Vink, and T. J. Rabelink, “Glomerular Endothelial Surface Layer Acts as a Barrier against Albumin Filtration,” The american journal of pathology, vol. 182, iss. 5, p. 1532–1540, 2013.
    abstract = "Glomerular endothelium is highly fenestrated, and its contribution to glomerular barrier function is the subject of debate. In recent years, a polysaccharide-rich endothelial surface layer (ESL) has been postulated to act as a filtration barrier for large molecules, such as albumin. To test this hypothesis, we disturbed the \{ESL\} in C57Bl/6 mice using long-term hyaluronidase infusion for 4 weeks and monitored albumin passage using immunolabeling and correlative light-electron microscopy that allows for complete and integral assessment of glomerular albumin passage. \{ESL\} ultrastructure was visualized by transmission electron microscopy using cupromeronic blue and by localization of \{ESL\} binding lectins using confocal microscopy. We demonstrate that glomerular fenestrae are filled with dense negatively charged polysaccharide structures that are largely removed in the presence of circulating hyaluronidase, leaving the polysaccharide surfaces of other glomerular cells intact. Both retention of cationic ferritin in the glomerular basement membrane and systemic blood pressure were unaltered. Enzyme treatment, however, induced albumin passage across the endothelium in 90\% of glomeruli, whereas this could not be observed in controls. Yet, there was no net albuminuria due to binding and uptake of filtered albumin by the podocytes and parietal epithelium. \{ESL\} structure and function completely recovered within 4 weeks on cessation of hyaluronidase infusion. Thus, the polyanionic \{ESL\} component, hyaluronan, is a key component of the glomerular endothelial protein permeability barrier.",
    author = "Dane, Martijn J.C. and van den Berg, Bernard M. and Avramut, M. Cristina and Faas, Frank G.A. and van der Vlag, Johan and Rops, Angelique L.W.M.M. and Ravelli, Raimond B.G. and Koster, Bram J. and van Zonneveld, Anton Jan and Vink, Hans and Rabelink, Ton J.",
    doi = "10.1016/j.ajpath.2013.01.049",
    issn = "0002-9440",
    journal = "The American Journal of Pathology",
    note = "",
    number = "5",
    pages = "1532–1540",
    title = "{Glomerular Endothelial Surface Layer Acts as a Barrier against Albumin Filtration}",
    url = "",
    volume = "182",
    year = "2013"


A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm2 at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.