Structured illumination microscopy based on principal component analysis

Abstract

AbstractStructured illumination microscopy (SIM) is one of the powerful super-resolution modalities in bioscience with the advantages of full-field imaging and high photon efficiency. However, artifact-free super-resolution image reconstruction requires precise knowledge about the illumination parameters. The sample- and environment-dependent on-the-fly experimental parameters need to be retrieved a posteriori from the acquired data, posing a major challenge for real-time, long-term live-cell imaging, where low photobleaching, phototoxicity, and light dose are a must. In this work, we present an efficient and robust SIM algorithm based on principal component analysis (PCA-SIM). PCA-SIM is based on the observation that the ideal phasor matrix of a SIM pattern is of rank one, leading to the low complexity, precise identification of noninteger pixel wave vector and pattern phase while rejecting components that are unrelated to the parameter estimation. We demonstrate that PCA-SIM achieves non-iteratively fast, accurate (below 0.01-pixel wave vector and 0.1$$\%$$ % of 2$$\pi$$ π relative phase under typical noise level), and robust parameter estimation at low SNRs, which allows real-time super-resolution imaging of live cells in complicated experimental scenarios where other state-of-the-art methods inevitably fail. In particular, we provide the open-source MATLAB toolbox of our PCA-SIM algorithm and associated datasets. The combination of iteration-free reconstruction, robustness to noise, and limited computational complexity makes PCA-SIM a promising method for high-speed, long-term, artifact-free super-resolution imaging of live cells.