Spectrum-optimized direct image reconstruction of super-resolution structured illumination microscopy

Abstract

Super-resolution structured illumination microscopy (SR-SIM) has become a widely used nanoscopy technique for rapid, long-term, and multi-color imaging of live cells. Precise but troublesome determination of the illumination pattern parameters is a prerequisite for Wiener-deconvolution-based SR-SIM image reconstruction. Here, we present a direct reconstruction SIM algorithm (direct-SIM) with an initial spatial-domain reconstruction followed by frequency-domain spectrum optimization. Without any prior knowledge of illumination patterns and bypassing the artifact-sensitive Wiener deconvolution procedures, resolution-doubled SR images could be reconstructed by direct-SIM free of common artifacts, even for the raw images with large pattern variance in the field of view (FOV). Direct-SIM can be applied to previously difficult scenarios such as very sparse samples, periodic samples, very small FOV imaging, and stitched large FOV imaging.

Surpassing Light Inhomogeneities in Structured-Illumination Microscopy with FlexSIM

“…Complementary comparisons are provided in Figures S7–S9. One can see that FlexSIM performs as well as the best-in-class HiFi-SIM [22] and JSFR-SIM [24] methods while outperforming other algorithms. In particular, due to the proposed weighted-least-squares datafidelity term, including an OTF attenuation strategy, FlexSIM strongly attenuates out-of-focus signal as well as typical associated artifacts.…”

“…From a numerical standpoint, the importance and popularity of SIM can be measured by the growing number of reconstruction software packages [16]. These include, among open-source packages: SIMToolbox [17]; FairSIM [18]; OpenSIM [19]; Hessian-SIM [20]; DL-SIM [21]; HiFi-SIM [22]; ML-SIM [23]; JSFR-SIM [24]; Direct-SIM [25]; rDL-SIM [26]; or Open-3DSIM [27].…”

High-speed autopolarization synchronization modulation three-dimensional structured illumination microscopy

“…SIM can be mainly categorized into two types: two-dimensional structured illumination microscopy (2DSIM) [5][6][7][8] and three-dimensional structured illumination microscopy (3DSIM). [9][10][11] 2DSIM, also known as traditional SIM, extends the resolution beyond the diffraction limit by a factor of 2 in the x − o − y plane by utilizing 2D patterned illumination and subsequent reconstruction algorithms 7,[12][13][14][15][16] 2DSIM has emerged as a powerful imaging technique that facilitates rapid and time-lapse visualization of diverse biological processes. However, because the illumination pattern of 2DSIM is not modulated axially, its axial resolution is the same as that of wide-field microscopy, leading to significant reconstruction errors when imaging thick specimens with defocus background.…”

Super-Resolution Imaging of Neuronal Structures with Structured Illumination Microscopy

“…As shown here, SIM is accomplished with a standard fluorescence microscope with some additional required elements, whereas other approaches such as light-sheet microscopy require more specialized setups. There is an increasing interest in the methods and applications of SIM, with the field seeing many recent (2022–2023) improvements [ 31 , 32 , 33 , 34 , 35 , 36 , 37 ], including new methods involving deep learning approaches [ 38 , 39 ].…”