Structured illumination microscopy image reconstruction algorithm

TL;DR

This paper consolidates the theoretical foundations of structured illumination microscopy (SIM) reconstruction and introduces an open-source tool, OpenSIM, for interactive parameter study and improved image reconstruction.

Contribution

It provides a comprehensive review of SIM reconstruction theory and releases an open-source software for practical experimentation and enhanced understanding.

Findings

Collected essential SIM reconstruction theory in one accessible resource.

Developed and released an interactive open-source SIM reconstruction tool.

Facilitated better understanding and potential improvements in SIM imaging techniques.

Abstract

Structured illumination microscopy (SIM) is a very important super-resolution microscopy technique, which provides high speed super-resolution with about two-fold spatial resolution enhancement. Several attempts aimed at improving the performance of SIM reconstruction algorithm have been reported. However, most of these highlight only one specific aspect of the SIM reconstruction -- such as the determination of the illumination pattern phase shift accurately -- whereas other key elements -- such as determination of modulation factor, estimation of object power spectrum, Wiener filtering frequency components with inclusion of object power spectrum information, translocating and the merging of the overlapping frequency components -- are usually glossed over superficially. In addition, most of the work reported lie scattered throughout the literature and a comprehensive review of the theoretical background is found lacking. The purpose of the present work is two-fold: 1) to collect the essential theoretical details of SIM algorithm at one place, thereby making them readily accessible to readers for the first time; and 2) to provide an open source SIM reconstruction code (named OpenSIM), which enables users to interactively vary the code parameters and study it's effect on reconstructed SIM image.