Cluster of Excellence –
University of Freiburg

Toolbox Imaging Platform

In the Toolbox Imaging Platform a wide range of microscopes and software are available for the development of imaging methods .

Our staff is working side by side with external users to develop the design of their experiments and perform the analysis. Here you can find a list of our present equipment and expertise.


Fluorescence and confocal microscopy can be used for testing the results of a large number of procedures, here we include some of the most common types of acquisition, however you are strongly encouraged to contact the Toolbox members to further explore the feasibility of your projects on our facilities.

  • Immunocytochemistry on fixed cells, tissues, small organisms
  • Fluorescent targets localization in subcellular compartments,
  • Colocalization studies
  • Time-lapse acquisitions in different modes 
  • Topographic imaging of surfaces at sub-nanometre resolution by Atomic Force Microscopy (AFM)
  • Protein-protein interaction tests (PLA, FRET)
  • Testing cell viability after exposure to nanoparticles/chemicals

Take a tour of our facility and feel free to get in contact with our staff at for further information and discussion of your needs.



  An upright fluorescence microscope equipped with 4x to 100x objectives for conventional bright-field, DIC and epi fluorescence modes. A C2 confocal scanner can be mounted on this microscope with three laser lines (488nm, 561nm and 638nm) to observe specimens in confocal microscopy.


 This macro confocal system allows a wider observation area with respect to normal confocal microscopy, capturing a maximum field of view larger than 1cm, therefore enabling observation of small animals, embrios, larvae and monitoring of their development over time. The C2 confocal scanning unit is attached to three lasers (488nm, 561nm and 638nm) to observe specimens in fluorescence confocal microscopy. The large working distance of the AZ100, allows deeper confocal imaging than conventional microscopes in thick samples. The same lens can be combined with multiple optical magnifications (1x to 8x), enabling the capture of images from the whole multicellular organism down to single cells in the same acquisition.


The A1 confocal microscope is an advanced instrument equipped with both a normal galvano-scanner and a resonant one for faster image acquisition (up to 30 frames per second) a TIRF unit and 6 different wavelenghts to illuminate pretty much any type of specimen. The additional components such as the incubation chamber enable to achieve constant conditions of temperature and CO2 for prolonged live cells acquisitions. This microscope is suitable for all types of confocal fluorescence microscopy acquisition, and especially suitable for kinetics and live cells imaging. It is additionally equipped with a TIRF illumination module and an ANDOR camera with high efficiency of photon detection for TIRF imaging.

ATOMIC FORCE MICROSCOPE – JPK NANOWIZARD 3                                


AFM imaging can be applied to a variety of measurements ranging from imaging single molecules, polymers, nanoparticles, and materials to electrical, optical, electrochemical and mechanical measurements in air and liquid environments.


    “Stochastic Optical Reconstruction Microscopy” is a super-resolution microscopy technique that provides dramatically enhanced resolution, approximately 10 times better than that of conventional optical microscopes. This technique is capable of multi-spectral two-dimensional and three-dimensional nanoscopy, with lateral resolution to approximately 20nm and axial resolution to approximately 50nm, allowing investigation of molecular interactions close to the single molecule level. The microscope is equipped with a motorized TIRF Illumination unit that allows selective illumination of the membrane of cells adhering on the glass coverslip.

Methods available


  • Imaging in bright-field and wide-field epifluorescence
  • Differential Interference Contrast (DIC)
  • Confocal microscopy
  • Total Internal Reflection (TIRF)
  • Super-resolution (STORM) mode
  • AFM imaging in contact and tapping mode



Dr. Thomas Schubert

BIOSS - Toolbox

Schänzlestr. 18

79104 Freiburg