UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: SIMToolbox, example data and the online documentation are freely accessible at http://mmtg.fel.cvut.cz/SIMToolbox. CONTACT: ghagen@uccs.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

1st Faculty of Medicine Charles University Prague Prague 12800 Czech Republic

Department of Radioelectronics Faculty of Electrical Engineering Czech Technical University Prague Prague 16627 Czech Republic

Department of Radioelectronics Faculty of Electrical Engineering Czech Technical University Prague Prague 16627 Czech Republic Laboratoire d'Optique Biomédicale École Polytechnique Fédérale de Lausanne Lausanne CH 1015 Switzerland and

UCCS center for the BioFrontiers Institute University of Colorado at Colorado Springs Colorado Springs CO 80918 USA

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