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 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.

  • The latest ready-to-use JAR file of the plugin can be found here
  • All releases, which might include current beta versions, are 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, doi:10.1038/ncomms10980

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.
  • A tightly integrated combination of SLM-based video-rate SIM imaging and fairSIM reconstruction is coming up.

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.

Contact & Development

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