title: Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ.
abstract: Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses.
authors.affiliation: Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany.
authors.forename: Marcel
authors.initials: M
authors.lastname: Müller
authors.affiliation: Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany.
authors.forename: Viola
authors.initials: V
authors.lastname: Mönkemöller
authors.affiliation: Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Hennig
authors.affiliation: Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Hübner
authors.affiliation: Biomolecular Photonics, Department of Physics, University of Bielefeld, 33615 Bielefeld, Germany.|Department of Internal Medicine and NSF Center for Biophotonics, University of California, Davis, Sacramento, California 95817, USA.
authors.forename: Thomas
authors.identifier: http://orcid.org/0000-0003-2348-7416
authors.initials: T
authors.lastname: Huser