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bioRxiv · 10.1101/402115

Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide

Karras, C.·Smedh, M.·Foerster, R.·Deschout, H.·Fernandez-Rodriguez, J.·Heintzmann, R.
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Abstract

The impact of the different reconstruction parameters in super-resolution structured illumination microscopy (SIM) onto artifacts is carefully analyzed. They 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.

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Karras, C., Smedh, M., Foerster, R., Deschout, H., Fernandez-Rodriguez, J., Heintzmann, R.. 2018-08-29. Successful optimization of reconstruction parameters in structured illumination microscopy - a practical guide. https://doi.org/10.1101/402115

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