Biopolis Dresden Imaging Platform

Special Techniques

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Extended resolution

In 1873 Ernst Abbe defined the so-called "diffraction barrier": the spatial resolution limit attainable with conventional light microscopy as follows. Resolution is the light wavelength divided by twice the numerical aperture of the lens. A reasonable approximation to that is the full width half maximum (FWHM) of the point spread function of an optical system; the image of a point source of light. For example, a widefield microscope with a high numerical aperture (NA) objective (eg. 1.4), using a wavelength within the visible spectrum (eg. 550 nm), would give a resolution of about 200 nm.

However, in recent years different light microscopy techniques have been developed to work around this limit and to image and resolve features smaller than the diffraction barrier. 


Here you can find more about the history and technical concepts of superresolution.

In this lecture, Prof. Xiaowei Zhuang surveys a variety of recent methods that achieve higher  resolution than is possible with conventional microscopy with  diffraction-limited optics. These include different types of patterned  illumination (e.g. STED and SIM microscopy) or techniques that build up  an image by stochastically switching on single fluorescent molecules and  localizing each molecule with high spatial precision (STORM, PALM,  FPALM).

In  the following, we aim to give you a brief overview of the  super resolution techniques accessible to you on the campus and lead you to further interesting readings about them.

Further reading: 

Reviews about supper resolution techniques: 


One of the best known superresolution techniques is STimulated Emission Depletion (STED) microscopy. Besides the normal, exciting laser beam this techniques uses a second, doughnut shaped beam around the focus point with which to selectively deplete fluorphores. With this approach the actual excited area is minimized, thus increasing the achived resolution beyond the diffraction barrier.

As a result of the development of this technique, Stefan Hell was awarded the Nobel Prize in Chemistry in 2014.



Here,  Stefan Hell, who invented many of the methods allowing a resolution  beyond the diffraction barrier, gives an  introduction to these  super-resolution microscopy techniques, and a  detailed discussion of  two such techniques: STED (Stimulated Emission  Depletion) and RESOLFT  (REversible Saturable OpticaL Fluorescence  Transitions).


Find here an introduction to the STED concept. Includes an interactive Java Tutoial.


This tutorial explains the principles of STED super-resolution  microscopy - from the underlying photo physical processes to the  integration into a confocal laser scanning microscope.


Picoquant explains STED and introduces their implementation of it.


Find out more about the fundamentals of STED.


Here you can find a very detailed explanation of the principles of PALM and its possible applications.

In this lecture Prof. Xiaowei Zhuang begins by explaining that the resolution of  traditional light microscopy is about 200 nm due to the diffraction of  light. This diffraction limit has long hampered the ability of  scientists to visualize individual proteins and sub-cellular structures.  The recent development of sub-diffraction limit, or super resolution,  microscopy techniques, such as STORM, allows scientists to obtain  beautiful images of individual labeled proteins in live cells. In Part 2  of her talk, Zhuang gives two examples of how her lab has used STORM;  first to study the chromosome organization of E. coli and second, to  determine the molecular architecture of a synapse:

Find here a basic description to the PALM concept. Includes an interactive Java Tutorial.

During their 20-years friendship, nobel prize winning Eric Betzig and Hess worked together and  separately, in academia and industry, before eventually joining forces  to develop the first super-high-resolution PALM microscope. They tell us  the story of this journey and emphasize how their unusual and varied  backgrounds provided the skills to complete the project: Betzig and Hess

Find here another basic description to the PALM concept. Includes an interactive Java Tutoial.

Structured Illumination (3D SIM)

In confocal-like structured illumination systems such as Apotome, Optigrid, DSD, and indeed point scanning and spinning disk confocal systems, structured illumination is primarily used to increase image contrast.  Further benefits of even higher contrast and doubled resolution are possible using a 3D structured illumination pattern of light projected into the sample. 

This 3D structured illumination results in the formation of Moiré patterns: Interference fringes between the light pattern and the sample fluorescence distribution. Multiple images are required such that the light covers all the sample over the image series. The diffraction limited patterns contain doubled resolution information that can be retrieved by the mathematical trick of Heterodyning, a very common method in engineering and signal processing. The processing consist of two parts: extracting the higher resolution information from the interference fringes, and applying a deconvolution based on the system's PSF, and results in a reconstructed image with very high contrast (particularly in the usually poor axial, z direction) and doubled resolution in all axes.

3D-SIM out-performs point scanning confocal in speed, sensitivity, contrast and resolution for samples where the 3D light pattern is not disturbed by the sample, such as bacteria, yeast, and mammalian cell monolayers and even thick sections when mounted in high refractive index media. 

Sample preparation tips: 

  • All Fluorophores can be used for 3D SIM, but it is recommended to match the lasers available on the systems
  • Use high precision #1.5 coverslips
  • Use mounting media without DAPI such as Vectashield or Prolong Diamond
  • Use samples with high labelling density and low background
  • Optimize the fixation (e.g. y adding a small percentage of glutaraldehyde, fixation at 37°C)
  • Reduce the refractive index mismatch by choosing correct immersion oil (OMX)



OMX stands for Optical Microscope eXperimental, and came out of the Sedat lab in California, with hardware and image reconstruction software licenses to Applied Precision for the DeltaVision range of microscopes, then bought by GE Healthcare. 
The traditional microscope stand, built around a human's eyes and hands was discarded, and instead the microscope was redesigned around having multiple cameras and a fixed inverted objective lens and nano motion xyz sample stage. This was to optimise the OMX for modern high performance biological fluorescence microscopy: Simultaneous multicolour widefield imaging with deconvolution and specifically, very high performance 3D-SIM. 
Ring TIRF is also available on the OMX as a module. OMX has a second generation patterned light engine called Blaze. This makes live cell imaging with 3D-SIM possible, compared to the first generation slow, unstable mechanical pattern generators. 

Structured Illumination TIRF Microscopy (2D-TIRF-SIM)

Combining TIRF with 2D-SIM both increases contrast, and can double spatial resolution.


Further reading: 

online tutorials: 

SIM original publication


Sample preparation