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
- 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.
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.
- 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.
- OMX LSEC Membrane 680nm
- OMX LSEC Actin 525nm
- 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
- Datasets for the VIGOR live SIM reconstruction can be found on Zenodo.
Contact & Development
The maintainer and lead developer of the fairSIM project is Marcel Müller