Fast reconstruction algorithm for structured illumination microscopy

AbstractStructured illumination microscopy (SIM) is a well-established fluorescence imaging technique, which can increase spatial resolution by up to a factor of two. This article reports on a new way to extend the capabilities of structured illumination microscopy, by combining ideas from the fields of illumination engineering and nanophotonics. In this technique, plasmonic arrays of hexagonal symmetry are illuminated by two obliquely incident beams originating from a single laser. The resulting interference between the light grating and plasmonic grating creates a wide range of spatial frequencies above the microscope passband, while still preserving the spatial frequencies of regular SIM. To systematically investigate this technique and to contrast it with regular SIM and localized plasmon SIM, we implement a rigorous simulation procedure, which simulates the near-field illumination of the plasmonic grating and uses it in the subsequent forward imaging model. The inverse problem, of obtaining a super-resolution (SR) image from multiple low-resolution images, is solved using a numerical reconstruction algorithm while the obtained resolution is quantitatively assessed. The results point at the possibility of resolution enhancements beyond regular SIM, which rapidly vanishes with the height above the grating. In an initial experimental realization, the existence of the expected spatial frequencies is shown and the performance of compatible reconstruction approaches is compared. Finally, we discuss the obstacles of experimental implementations that would need to be overcome for artifact-free SR imaging.

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High-fidelity structured illumination microscopy by point-spread-function engineering

Light Science & Applications ◽

10.1038/s41377-021-00513-w ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Gang Wen ◽

Simin Li ◽

Linbo Wang ◽

Xiaohu Chen ◽

Zhenglong Sun ◽

...

Keyword(s):

Point Spread Function ◽

Super Resolution ◽

Reconstruction Algorithm ◽

High Fidelity ◽

Structured Illumination ◽

Structured Illumination Microscopy ◽

Imaging Tool ◽

Point Spread ◽

Spread Function ◽

Point Spread Function Engineering

AbstractStructured illumination microscopy (SIM) has become a widely used tool for insight into biomedical challenges due to its rapid, long-term, and super-resolution (SR) imaging. However, artifacts that often appear in SIM images have long brought into question its fidelity, and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly seen artifacts without loss of fine structures and improve the axial sectioning for samples with strong background. In particular, HiFi-SIM is not sensitive to the commonly used PSF and reconstruction parameters; hence, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.

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Super-Resolution Imaging by Dual Iterative Structured Illumination Microscopy

10.1101/2021.05.12.443720 ◽

2021 ◽

Author(s):

Anna Loeschberger ◽

Yauheni Novikau ◽

Ralf Netz ◽

Marie-Christin Spindler ◽

Ricardo Benavente ◽

...

Keyword(s):

Three Dimensional ◽

Brain Slices ◽

Super Resolution ◽

Reconstruction Algorithm ◽

Living Cells ◽

Structured Illumination ◽

Structured Illumination Microscopy ◽

Spatiotemporal Resolution ◽

Coated Pits ◽

Resolution Imaging

Three-dimensional (3D) multicolor super-resolution imaging in the 50-100 nm range in fixed and living cells remains challenging. We extend the resolution of structured illumination microscopy (SIM) by an improved nonlinear iterative reconstruction algorithm that enables 3D multicolor imaging with improved spatiotemporal resolution at low illumination intensities. We demonstrate the performance of dual iterative SIM (diSIM) imaging cellular structures in fixed cells including synaptonemal complexes, clathrin coated pits and the actin cytoskeleton with lateral resolutions of 60-100 nm with standard fluorophores. Furthermore, we visualize dendritic spines in 70 micrometer thick brain slices with an axial resolution < 200 nm. Finally, we image dynamics of the endoplasmatic reticulum and microtubules in living cells with up to 255 frames/s.

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Tiled Reconstruction Improves Structured Illumination Microscopy

10.1101/2020.01.06.895318 ◽

2020 ◽

Cited By ~ 1

Author(s):

David P. Hoffman ◽

Eric Betzig

Keyword(s):

Super Resolution ◽

Reconstruction Algorithm ◽

Live Cell ◽

Structured Illumination ◽

Structured Illumination Microscopy ◽

Resolution Imaging

AbstractStructured illumination microscopy (SIM) is widely used for fast, long-term, live-cell super-resolution imaging. However, SIM images can contain substantial artifacts if the sample does not conform to the underlying assumptions of the reconstruction algorithm. Here we describe a simple, easy to implement, process that can be combined with any reconstruction algorithm to alleviate many common SIM reconstruction artifacts and briefly discuss possible extensions.

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Structured Illumination Microscopy Image Reconstruction Algorithm

IEEE Journal of Selected Topics in Quantum Electronics ◽

10.1109/jstqe.2016.2521542 ◽

2016 ◽

Vol 22 (4) ◽

pp. 50-63 ◽

Cited By ~ 39

Author(s):

Amit Lal ◽

Chunyan Shan ◽

Peng Xi

Keyword(s):

Image Reconstruction ◽

Reconstruction Algorithm ◽

Structured Illumination ◽

Structured Illumination Microscopy ◽

Image Reconstruction Algorithm ◽

Microscopy Image

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HiFi-SIM: reconstructing high-fidelity structured illumination microscope images

10.1101/2020.07.16.204875 ◽

2020 ◽

Author(s):

Gang Wen ◽

Simin Li ◽

Linbo Wang ◽

Xiaohu Chen ◽

Zhenglong Sun ◽

...

Keyword(s):

Super Resolution ◽

Reconstruction Algorithm ◽

High Fidelity ◽

Structured Illumination ◽

Structured Illumination Microscopy ◽

Microscopy Technique ◽

Imaging Tool ◽

Point Spread ◽

Spread Function ◽

Fine Structures

Structured illumination microscopy (SIM) has been a widely-used super-resolution (SR) fluorescence microscopy technique, but artifacts often appear in reconstructed SR images which reduce its fidelity and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly-seen artifacts without loss of fine structures and improve the axial sectioning. Since results of HiFi-SIM are not sensitive to used PSF and reconstruction parameters, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.

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