title: SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy.
abstract: SIMToolbox is an open-source, modular set of functions for MATLAB equipped with a user-friendly graphical interface and designed for processing two-dimensional and three-dimensional data acquired by structured illumination microscopy (SIM). Both optical sectioning and super-resolution applications are supported. The software is also capable of maximum a posteriori probability image estimation (MAP-SIM), an alternative method for reconstruction of structured illumination images. MAP-SIM can potentially reduce reconstruction artifacts, which commonly occur due to refractive index mismatch within the sample and to imperfections in the illumination.
  
  
  METHODS
  SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox.
  
  
  BACKGROUND
  ghagen@uccs.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: First Faculty of Medicine, Charles University in Prague, Prague 12800, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Křížek
authors.affiliation: Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague 16627, Czech Republic, Laboratoire d'Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne CH-1015, Switzerland and.
authors.forename: Tomáš
authors.initials: T
authors.lastname: Lukeš
authors.affiliation: First Faculty of Medicine, Charles University in Prague, Prague 12800, Czech Republic.
authors.forename: Martin
authors.initials: M
authors.lastname: Ovesný
authors.affiliation: Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Prague 16627, Czech Republic.
authors.forename: Karel
authors.initials: K
authors.lastname: Fliegel
authors.affiliation: UCCS center for the BioFrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA.
authors.forename: Guy M
authors.initials: GM
authors.lastname: Hagen
mesh_terms: D008841:Actin Cytoskeleton / Q000648:ultrastructure*; D005453:Fluorescence; D056945:Hep G2 Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D021621:Imaging, Three-Dimensional / Q000379:methods; D008029:Lighting / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D012984:Software