Laser & Optoelectronics Progress, Volume. 59, Issue 6, 0617009(2022)
Recent Advances in Structured Illumination Microscope Super-Resolution Image Reconstruction
Figures & Tables(6)
Fig. 2. Principle of iterative autocorrelation algorithm and comparison of reconstruction results with and without accurate parameter estimation. (a) Original image; (b)(c) principle of iterative autocorrelation algorithm; (d) reconstruction result under wrong spatial frequency (error is about 7.69%); (e) reconstruction result under wrong phase (error is about 8.67%); (f) reconstruction result with accurate parameters
Fig. 3. Quantitative characterization of thefidelity of HiFi-SIM reconstruction[57]
Fig. 4. Comparison of sidelobe artifacts in reconstructed images of Wide-field, fairSIM, TV-SIM, Hessian-SIM, and HiFi-SIM[57]
Table 1. Open-source SIM reconstruction algorithms
View tableTable 1. Open-source SIM reconstruction algorithms
Algorithm Download link Application（benefits） Running platform SIMcheck［ 64 ］https：//github.com/MicronOxford/SIMcheck 1）Assessing the resolution and image quality；2）identification of sources of errors and artefacts in reconstructed images FiJi /ImageJ FairSIM［ 48 ］https：//github.com/fairsim SIM super-resolution reconstruction for all sinusoidal illumination modes FiJi /ImageJ SIMToolbox［ 65 ］http：//mmtg.fel.cvut.cz/SIMToolbox 1）Optical sectioning，classical SIM algorithm；2）support MAP-SIM algorithm［ 50 ］MATLAB OpenSIM［ 23 ］https：//github.com/LanMai/OpenSIM Classical 2D-SIM reconstruction algorithm MATLAB Hessian-SIM［ 51 ］https：//www.nature.com/articles/nbt.4115#Sec21 1）Effective suppression of reconstruction artifacts at low signal-to-noise ratios；2）long-time dynamic imaging MATLAB Sparse-SIM［ 46 ］https：//github.com/WeisongZhao/Sparse-SIM 1）Effective suppression of reconstruction artifacts at low signal-to-noise ratios；2）high spatial resolution（~60 nm） MATLAB HiFi-SIM［ 57 ］https：//doi.org/10.1038/s41377-021-00513-w 1）Effective reduction of reconstruction artifacts；2）effective solution to the problems caused by PSF mismatch MATLAB True-Wiener SIM［ 58 ］https：//github.com/qnano/simnoise 1）Reduction of user adjustable parameters；2）high contrast imaging MATLAB Flat-noise SIM［ 58 ］https：//github.com/qnano/simnoise 1）No user adjustable parameters；2）suppression of structural noise artifacts MATLAB Notch-fitered SIM［ 58 ］https：//github.com/qnano/simnoise 1）No user adjustable parameters；2）higher image contrast than flat-noise SIM MATLAB
Table 2. Deep learning based SIM reconstruction algorithm
View tableTable 2. Deep learning based SIM reconstruction algorithm
Algorithm Network Download link Advantage Biological sample scU-Net［ 78 ］U-Net https：//github.com/drbeiliu/DeepLearning High quality image reconstruction in low signal-to-noise conditions Microtubules；adhesions；mitochondria；F-actin DFCAN/DFGAN［ 79 ］GAN https：//github.com/qc17-THU/DL-SR High quality image reconstruction in low signal-to-noise conditions Clathrin-coated pits；
endoplasmic reticulum；microtubules；F-actin
RED-fairSIM［ 80 ］RED-Net — 1）High quality image reconstruction in low signal-to-noise conditions；2）no image pre-processing required；3）low training costs U2OS cells；tubulin cytoskeleton ML-SIM［ 82 ］RCAN http：//ML-SIM.github.io 1）High quality image reconstruction in low signal-to-noise conditions；2）model is highly generalized Endoplasmic reticulum；cell membrane U-Net-SIM3［ 78 ］U-Net https：//github.com/drbeiliu/DeepLearning Fewer raw images（five-fold reduction） Microtubules；adhesions；mitochondria；F-actin Ref.［ 83 ］cycleGAN — Fewer raw images（three original images） — caGAN［ 84 ］GAN https：//github.com/qc17-THU/DL-SR 1）Halving the number of raw images（axial）；2）high quality image reconstruction in low signal-to-noise conditions Clathrin-coated pits；
endoplasmic reticulum；microtubules；F-actin
Ref.［ 76 ］GAN — 1）Large imaging field of view；
2）wide field images for super resolution
Gene-edited SUM159；drosophila embryos
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Yujun Tang, Linbo Wang, Gang Wen, Hui Li. Recent Advances in Structured Illumination Microscope Super-Resolution Image Reconstruction[J]. Laser & Optoelectronics Progress, 2022, 59(6): 0617009
Paper Information
Category: Medical Optics and Biotechnology
Received: Jan. 4, 2022
Accepted: Feb. 10, 2022
Published Online: Mar. 8, 2022
The Author Email: Hui Li (hui.li@sibet.ac.cn)
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