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
- 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
- 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.
- OMX LSEC Membrane 680nm
- OMX 200nm-Tetraspecks 680nm
- OMX U2OS Actin 525nm
- OMX U2OS Mitotracker 600nm
- OMX U2OS Tubulin 525nm
- SLM-SIM 200nm-Tetraspeck 680nm
- TIRF-SIM Tubulin 525nm
- Zeiss Actin 515nm (512x512 px crop)
- Zeiss Actin 515nm
- Zeiss Mito 620nm (512x512 px crop)
- Zeiss Mito 620nm
Contact & Development
The maintainer and lead developer of the fairSIM project is Marcel Müller