The fairSIM project

Free Algorithms, Instrumentation and Resources
for Structured Illumination Microscopy

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Structured Illumination Microscopy (SIM) provides a fast and gentle super-resolution approach for fluorescence microscopy. The fairSIM project aims to provide a range of free and open-source tools and resources for scientists working with SIM.

The fairSIM ImageJ / FIJI plugin

We provide an open-source implementation of the reconstruction algorithms used for SIM. It runs as a plugin to the popular image processing software ImageJ and the FIJI package.

Slide explaining SIM

  • The latest ready-to-use JAR file of the plugin can be found here
  • The source code is found in our main repository on github
  • There’s also a quickstart manual for the plugin
  • Screencast videos showing how to reconstruct SIM data

If you use fairSIM for your research or education, please cite our associated publication:

M. Müller, V. Mönkemöller, S. Hennig, W. Hübner, T. Huser Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ, Nature Communications, 7(1), 10980. doi:10.1038/ncomms10980

The fairSIM VIGOR microscope & software

We developed a bespoke, multi-color, video-rate SIM microscope that immediately reconstructs image data on-the-fly.

Figure showing the video-rate SIM in operation

The system is documented here

A. Markwirth, M. Lachetta, V. Mönkemöller, R. Heintzmann, W. Hübner, T. Huser, M. Müller Video-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction. Nature communications, 10(1), 1-11. doi:10.1038/s41467-019-12165-x

Supporting the project

Many research groups developing and applying SIM, as well as imaging facilities running SIM microscopes, profit from and support the fairSIM project.

A list of official support statement can be found here.

Current developments

  • Various recent development (2016–2019) are summarized in this talk from April 2019, given at the ‘Focus on Microscopy’ conference.
  • Support for full 3D reconstruction is in beta. The current implementation can be found in the develop-3D-SIM branch, but there are known bugs compromising axial resolution.
  • Our preprint of a multi-planar SIM system, employing an image splitting prism to simultaneously image multiple focal planes, can be found here on biorxiv.

Reference / test datasets

A number of SIM raw data sets can be found in this repository. They include data from commercial instruments (Delta Vision OMX v4, Zeiss Elyra) and home-build systems. You can reprocude all reconstruction from our original publication.

The reconstruction can be run both using estimated and experimentally determined transfers functions. Both parameter files and optical transfer functions are provided to test this feature.


The EU flag emblem
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreements No. 752080, "FASTR 3D SIM".

Contact & Development

The maintainer and lead developer of the fairSIM project is Marcel Müller