The fairSIM project: structured illumination microscopes and reconstruction for video-rate imaging

microscopy (SIM) allows for sub-diffraction imaging with low phototoxicity and high frame rates, making it a popular technique for live cell imaging. Current-generation instruments provide video-rate imaging speeds, and thus enable the observation of even fast dynamical processes with sub-diffraction resolution. In 2016, we released a free and open-source implementation of the SIM reconstruction algorithm [1]. Since then, the fairSIM project has been greatly extended in various ways: The reconstruction algorithm itself gained new filter options [2], the 3D data processing [3] implementation is well on its way, and microscope profiling tools such as optical transfer function generation have been added. We also pushed for the development of bespoke SIM microscopes, such as a multi-color version of the SLM-based fastSIM [4] system, a cost-effective DMD-based SIM and a modular, customizable and easily replicable SIM illumination system. All these microscope systems can now be linked to an on-the-fly reconstruction feature, which merges data acquisition and post-processing, and allows the user to obtain an immediate superresolution views of their samples. This is achieved by tight integration of the data acquisition process with a GPU-accelerated implementation of the reconstruction process. On our fastest data acquisition systems (based on [4]), we can achieve 25fps simultaneously on 3 color channels, and provide reconstructed super-resolution images within half a second after data acquisition. Here, we present an overview of the fairSIM project, its applications, features and capabilities, but also its current limitations and ongoing development. We hope to connect groups in need of bespoke, high speed SIM imaging with those developing these methods and algorithms.