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Successful optimization of reconstruction parameters in structured illumination microscopy – A practical guide

Journal article
Authors C. Karras
Maria Smedh
R. Förster
Hendrik Deschout
Julia Fernandez-Rodriguez
R. Heintzmann
Published in Optics Communications
Volume 436
Pages 69-75
ISSN 0030-4018
Publication year 2019
Published at Core Facilities, Centre for Cellular Imaging
Pages 69-75
Language en
Keywords Fluorescence microscopy, Image reconstruction, Parameter estimation, Structured illumination microscopy, Super resolution, Optical resolving power, Optical transfer function, Apodization function, Image artifacts, Parameter optimization, Reconstructed image, Reconstruction parameters, Structured illumination microscopies (SIM)
Subject categories Atom and Molecular Physics and Optics


The impact of the different reconstruction parameters in super-resolution structured illumination microscopy (SIM) on image artifacts is carefully analyzed. These parameters comprise the Wiener filter parameter, an apodization function, zero-frequency suppression and modifications of the optical transfer function. A detailed investigation of the reconstructed image spectrum is concluded to be suitable for identifying artifacts. For this purpose, two samples, an artificial test slide and a more realistic biological system, were used to characterize the artifact classes and their correlation with the image spectra as well as the reconstruction parameters. In addition, a guideline for efficient parameter optimization is suggested and the implementation of the parameters in selected up-to-date processing packages (proprietary and open-source) is depicted. © 2018 The Authors

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