Rainer Kaufmann



Rainer has a strong background in the development of new methods in the field of super-resolution single molecule localization microscopy and is currently working in a joint project between Micron and Kay Grünewald's lab (based in STRUBI) on correlative light and electron microscopy (CLEM).

His main focus of interest lies on super-resolution fluorescence cryo-microscopy, a field which has just been opened up (Chang et al. (2014) Nat. Methods; Kaufmann et al. (2014) Nano Lett.), and the correlation of this technique with electron cryo-microscopy. Imaging vitrified (fast frozen) samples allows studying fine structural details in their native cellular context, which cannot be accessed in living cells, or which are affected by chemical fixation methods.

Rainer is also working together with Errin Johnson, who is running the electron microscopy facility at the Dunn School for Pathology, to develop new methods in the field of super-resolution CLEM of resin embedded samples using cryofixation and freeze substitution. This technique presents a compromise that lies in between the ultimate structural preservation of imaging vitrified samples under cryo-conditions and room temperature imaging of chemically fixed samples.



  • Kong, Y., Janssen, B.J., Malinauskas, T., Vangoor, V.R., Coles, C.H., Kaufmann, R., Ni, T., Gilbert, R.J., Padilla-Parra, S., Pasterkamp, R.J. and Jones, E.Y., 2016. Structural basis for plexin activation and regulation. Neuron, 91(3), pp.548-560.
  • Wegel, E., Göhler, A., Lagerholm, B.C., Wainman, A., Uphoff, S., Kaufmann, R. and Dobbie, I.M., 2016. Imaging cellular structures in super-resolution with SIM, STED and Localisation Microscopy: A practical comparison. Scientific Reports, 6, p.27290.
  • Wolff, G., Hagen, C., Grünewald, K. and Kaufmann, R., 2016. Towards correlative super‐resolution fluorescence and electron cryo‐microscopy. Biology of the Cell.


  • Ball G, Demmerle J, Kaufmann R, Davis I, Dobbie IM, Schermelleh L. SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy. Sci Rep. 2015 Nov 3;5:15915.
  • Errin Johnson, Elena Seiradake, E. Yvonne Jones, Ilan Davis, Kay Grunewald & Rainer Kaufmann (2015) Correlative in-resin super-resolution and electron microscopy using standard fluorescent proteins. Scientific Reports 5; 9583.
  • Zhang Y, Máté G, Müller P, Hillebrandt S, Krufczik M, Bach M, Kaufmann R, Hausmann M, Heermann DW. Radiation induced chromatin conformation changes analysed by fluorescent localization microscopy, statistical physics, and graph theory. PLoS One. 2015 Jun 4;10(6):e0128555.


  • R. Kaufmann, C. Hagen, K. Grünewald (2014) Fluorescence cryo-microscopy: current challenges and prospects. Current Opinion in Chemical Biology, 20, 86-91.
  • R. Kaufmann, P. Schellenberger, E. Seiradake, I. Dobbie, E. Y. Jones, I. Davis, C. Hagen, K. Grünewald (2014) Super-Resolution Microscopy using Standard Fluorescent Proteins in Intact Cells under Cryo-Conditions. Nano Letters, 14 (7), 4171-4175.
  • C. Cremer, R. Kaufmann, M. Gunkel, F. Polanski, P. Müller, R. Dierkes , S. Degenhard, C. Wege, M. Hausmann, U. Birk (2014) Application perspectives of localization microscopy in virology. Histochemistry and Cell Biology, 142, 43-59.
  • Müller P, Lemmermann NA, Kaufmann R, Gunkel M, Paech D, Hildenbrand G, Holtappels R, Cremer C, Hausmann M. Spatial distribution and structural arrangement of a murine cytomegalovirus glycoprotein detected by SPDM localization microscopy. Histochem Cell Biol. 2014 Feb 7.
  • Wang Q, Dierkes R, Kaufmann R, Cremer C. Quantitative analysis of individual hepatocyte growth factor receptor clusters in influenza A virus infected human epithelial cells using localization microscopy. Biochim Biophys Acta. 2014 Apr;1838(4):1191-8.


  • Schellenberger P1, Kaufmann R, Siebert CA, Hagen C, Wodrich H, Grünewald K. High-precision correlative fluorescence and electron cryo microscopy using two independent alignment markers. Ultramicroscopy. 2013 Oct 19.
  • Elena Seiradake, Andreas Schaupp, Daniel del Toro Ruiz, Rainer Kaufmann, Nikolaos Mitakidis, Karl Harlos, A Radu Aricescu, Rüdiger Klein & E Yvonne Jones. Structurally encoded intraclass differences in EphA clusters drive distinct cell responses. Nature Structural Molecular Biology 20(8) 958-966. 2013 Jun 30.


  • Huber O, Brunner A, Maier P, Kaufmann R, Couraud PO, Cremer C, Fricker G. Localization Microscopy (SPDM) Reveals Clustered Formations of P-Glycoprotein in a Human Blood-Brain Barrier Model. PLoS One. 2012;7(9):e44776. Epub 2012 Sep 12.
  • Kaufmann R, Cremer C, Gall JG. Superresolution imaging of transcription units on newt lampbrush chromosomes. Chromosome Res. 2012 Aug 15.
  • Kaufmann R, Piontek J, Grüll F, Kirchgessner M, Rossa J, Wolburg H, Blasig IE, Cremer C. Visualization and quantitative analysis of reconstituted tight junctions using localization microscopy. PLoS One. 2012;7(2):e31128. Epub 2012 Feb 2.


  • Cremer C, Kaufmann R, Gunkel M, Pres S, Weiland Y, Müller P, Ruckelshausen T, Lemmer P, Geiger F, Degenhard S, Wege C, Lemmermann NA, Holtappels R, Strickfaden H, Hausmann M. Superresolution imaging of biological nanostructures by spectral precision distance microscopy. Biotechnol J. 2011 Sep;6(9):1037-51.
  • Kaufmann R, Müller P, Hildenbrand G, Hausmann M, Cremer C. Analysis of Her2/neu membrane protein clusters in different types of breast cancer cells using localization microscopy. J Microsc. 2011 Apr;242(1):46-54.


  • Müller P, Schmitt E, Jacob A, Hoheisel J, Kaufmann R, Cremer C, Hausmann M. COMBO-FISH Enables High Precision Localization Microscopy as a Prerequisite for Nanostructure Analysis of Genome Loci. Int J Mol Sci. 2010 Oct 21;11(10):4094-105.
  • Bohn M, Diesinger P, Kaufmann R, Weiland Y, Müller P, Gunkel M, von Ketteler A, Lemmer P, Hausmann M, Heermann DW, Cremer C. Localization microscopy reveals expression-dependent parameters of chromatin nanostructure. Biophys J. 2010 Sep 8;99(5):1358-67.
  • Kaufmann R, Müller P, Hausmann M, Cremer C. Imaging label-free intracellular structures by localisation microscopy. Micron. 2010 May 28.


  • Lemmer P, Gunkel M, Weiland Y, Müller P, Baddeley D, Kaufmann R, Urich A, Eipel H, Amberger R, Hausmann M, Cremer C. Using conventional fluorescent markers for far-field fluorescence localization nanoscopy allows resolution in the 10-nm range. J Microsc. 2009 Aug;235(2):163-71.
  • Gunkel M, Erdel F, Rippe K, Lemmer P, Kaufmann R, Hörmann C, Amberger R, Cremer C. Dual color localization microscopy of cellular nanostructures. Biotechnol J. 2009 Jun;4(6):927-38.


  • P. Lemmer, M. Gunkel, D. Baddeley, R. Kaufmann, A. Urich, Y. Weiland, J. Reymann, P. Müller, M. Hausmann, C. Cremer. SPDM: light microscopy with single-molecule resolution at the nanoscale. Applied Physics B October 2008, Volume 93, Issue 1, pp 1-12.