SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy

Bioinformatics. 2016 Jan 15;32(2):318-20. doi: 10.1093/bioinformatics/btv576. Epub 2015 Oct 6.


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


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actin Cytoskeleton / ultrastructure*
  • Fluorescence*
  • Hep G2 Cells
  • Humans
  • Image Processing, Computer-Assisted
  • Imaging, Three-Dimensional / methods
  • Lighting / methods*
  • Microscopy, Fluorescence / methods*
  • Software*