quantitative Single-Molecule Localization Microscopy is the core of our work.

Digitized Experimental Microscopy

Jun.Prof. Dr. Christian Franke
quantitative Single-Molecule Localization Microscopy is the core of our work.
Image: Christian Franke



  • 2022/04/15: Liju joins us as for his Research Lab work on Pattern Optimization for Structured Illumination. Welcome
  • 2022/04/15: Kedar joins us as for his Research Lab work on 360 degree reconstruction. Welcome
  • 2022/04/07: Friedrich joins us as for his Bachelor Thesis on super-fast Pattern Creation for Structured Illumination. Welcome
  • 2022/04/01: Andrey joins us as a Research Assistant and will work on Computer Vision and Machine Learning for Super-Resolution Microscopy. Welcome
  • 2022/04/01: Lukas joins us as a Research Assistant and for his Bachelor Thesis on super-high resolution imaging of endosomal compartments. Welcome
  • 2022/03/18: Our recent paper on mRNA escape from endosomal recycling tubules, analysed by multi-colour dSTORM in the Journal of Cell Biology is featured in this weeks issue of Science! Wow! #mindblown
  • 2022/03/15: Andreas' paper on "Miniaturization of a coherent monocular structured illumination system for future combination with digital holography" has been accepted in Light: Advanced Manufacturing. Congratulations! Much more to come soon.
  • 2022/03/09: Our straight-forward & accessible-for-all workflow to quantitatively map and analyse the 3D-distribution of (T-) cell surface receptors with #isotropic nanometer resolution, while preserving the native membrane topography is now published in Communications Biology
  • 2020/11/01: First Day in the Office @FSU - #Exciting #NewPI

Seeing is believing. The newly established research group of Christian Franke is focused on the development of advanced optical and computational tools for the quantitative study of (cell-) biological questions. On one side, we work to advance super-resolution microscopy methods like single-molecule localization microscopy (SMLM, e.g. dSTORM, PALM) and random structured illumination microscopy (nanoSpeck3D) to quantitatively study the structure-function relationship of sub-cellular (trafficking) organelles, e.g. endosomes, with three-dimensional nanometer resolution. Here, we create novel hard- and software tools to push the limits of 3D volume, colour and time resolution. For this, we have home-built microscopes in our labs in the Abbeanum and are in close collaboration with the Eggeling group at ZAF and IPHT, providing a large range of complementary microscope setups. Recently, we branched out into macroscopic measurements of 3D volumes by stereophotogrammetry, a project led by Dr. Andreas Stark, also utilizing structured illumination, with which we can now measure objects on the centimeter to micrometer scale, thus bridging dimensions between the macro- and nanoscopic world. TBC

The basic principle of Single-Molecule Localisation Microscopy
What are we doing?
Go Team
Go Team! #TeamRedbeard
Latest #preprints and manuscripts from the Lab.
Old Microscopy Patents
Learning by Doing & Teaching.
Take the Red Pill.
Take the Red Pill.
Fun from the Lab and beyond.
Fun from the Lab and Beyond.
Single-Molecule Blinking of Fluorescent Dyes
Video: Christian Franke

Single-Molecule Blinking of Fluorescent Dyes - Every spot represents a nanometer size dye molecule, imaged in a wide-field microscope onto a EMCCD chip. Detecting single molecules allows us to create super-resolution fluorescence images way beyond the Abbe diffraction limit.

Institute of Applied Optics and Biophysics - Group Experimental Digitized Microscopy
Postal address:
Friedrich-Schiller-Universität Jena
Institut für Angewandte Optik und Biophysik
Max-Wien-Platz 1
07743 Jena