Researching | High-fidelity CUDA-based 3DSIM parallel reconstruction method

Advanced Imaging, Volume. 2, Issue 4, 041001(2025)

High-fidelity CUDA-based 3DSIM parallel reconstruction method Editors' Pick

Hongyu Wang^1,2, Ruijie Cao¹, Wenyi Wang³, Yaning Li⁴, and Peng Xi^1,3、*

Author Affiliations

¹College of Future Technology, Peking University, Beijing, China

²School of Artificial Intelligence, Shenyang University of Technology, Shenyang, China

³Airy Technologies Co., Ltd., Beijing, China

⁴Beijing Institute of Space Mechanics and Electricity, China Academy of Space Technology, Beijing, China

show less

Full Text Get PDF

Figures&Tables (7)

References (31)

Paper Information

References(31)

[1] et alThree-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J., 94, 4957(2008). https://doi.org/10.1529/biophysj.107.120345

[2] et alStructured illumination microscopy image reconstruction algorithm. IEEE J. Quantum Electron., 22, 50(2016). https://doi.org/10.1109/JSTQE.2016.2521542

[3] et alSuper-resolution 3D microscopy of live whole cells using structured illumination. Nat. Methods, 8, 1044(2011). https://doi.org/10.1038/nmeth.1734

[4] et alHigh spatiotemporal resolution structured illumination microscopy: principle, instrumentation, and applications. Photonics Insights, 4, R01(2025). https://doi.org/10.3788/PI.2025.R01

[5] et alSuperresolution structured illumination microscopy reconstruction algorithms: a review. Light Sci. Appl., 12, 172(2023). https://doi.org/10.1038/s41377-023-01204-4

[6] et alFast reconstruction and optical-sectioning three-dimensional structured illumination microscopy. The Innovation, 6, 100757(2025). https://doi.org/10.1016/j.xinn.2024.100757

[7] et alTime-lapse two-color 3D imaging of live cells with doubled resolution using structured illumination. Proc. Natl Acad. Sci. USA, 109, 5311(2012). https://doi.org/10.1073/pnas.1119262109

[8] GPU-accelerated real-time reconstruction in Python of three-dimensional datasets from structured illumination microscopy with hexagonal patterns. Philos. Trans. R. Soc. A, 379, 20200162(2021). https://doi.org/10.1098/rsta.2020.0162

[9] et alVideo-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction. Nat. Commun., 10, 4315(2019). https://doi.org/10.1038/s41467-019-12165-x

[10] et alUltra-high spatio-temporal resolution imaging with parallel acquisition-readout structured illumination microscopy (PAR-SIM). Light Sci. Appl., 13, 125(2024). https://doi.org/10.1038/s41377-024-01464-8

[11] et alDark-based optical sectioning assists background removal in fluorescence microscopy. Nat. Methods, 22, 1299(2025). https://doi.org/10.1038/s41592-025-02667-6

[12] et alDeep learning enables structured illumination microscopy with low light levels and enhanced speed. Nat. Commun., 11, 1934(2020). https://doi.org/10.1038/s41467-020-15784-x

[13] et alHigh-fidelity structured illumination microscopy by point-spread-function engineering. Light Sci. Appl., 10, 70(2021). https://doi.org/10.1038/s41377-021-00513-w

[14] et alEvent-driven acquisition for content-enriched microscopy. Nat. Methods, 19, 1262(2022). https://doi.org/10.1038/s41592-022-01589-x

[15] et alSubcellular three-dimensional imaging deep through multicellular thick samples by structured illumination microscopy and adaptive optics. Nat. Commun., 12, 3148(2021). https://doi.org/10.1038/s41467-021-23449-6

[16] et alThree-dimensional resolution doubling in wide-field fluorescence microscopy by structured illumination. Biophys. J., 94, 4957(2008). https://doi.org/10.1529/biophysj.107.120345

[17] et alStructured illumination microscopy with noise-controlled image reconstructions. Nat. Methods, 18, 821(2021). https://doi.org/10.1038/s41592-021-01167-7

[18] et alThree-dimensional structured illumination microscopy with enhanced axial resolution. Nat. Biotechnol., 41, 1307(2023). https://doi.org/10.1038/s41587-022-01651-1

[19] et alOpen-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform. Nat. Methods, 20, 1183(2023). https://doi.org/10.1038/s41592-023-01958-0

[20] et alAn LED-based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction. Plos One, 17, e0273990(2022). https://doi.org/10.1371/journal.pone.0273990

[21] et alSpectrum-optimized direct image reconstruction of super-resolution structured illumination microscopy. PhotoniX, 4, 19(2023). https://doi.org/10.1186/s43074-023-00092-6

[22] et alPhase optimisation for structured illumination microscopy. Opt. Express, 21, 2032(2013). https://doi.org/10.1364/OE.21.002032

[23] et alParameter estimation of the structured illumination pattern based on principal component analysis (PCA): PCA-SIM[J]. Light Sci. Appl., 12, 41(2023). https://doi.org/10.1038/s41377-022-01043-9

[24] et alPhase-shift estimation in sinusoidally illuminated images for lateral superresolution. J. Opt. Soc. Am. A, 26, 413(2009). https://doi.org/10.1364/JOSAA.26.000413

[25] et alLateral superresolution using a posteriori phase shift estimation for a moving object: experimental results. J. Opt. Soc. Am. A, 27, 1770(2010). https://doi.org/10.1364/JOSAA.27.001770

[26] Non-iterative determination of pattern phase in structured illumination microscopy using auto-correlations in Fourier space. Opt. Express, 21, 24692(2013). https://doi.org/10.1364/OE.21.024692

[27] et alImage recombination transform algorithm for superresolution structured illumination microscopy. J. Biomed. Opt., 21, 96009(2016). https://doi.org/10.1117/1.JBO.21.9.096009

[28] et alFast-structured illumination microscopy based on dichotomy–correlation parameter estimation (dCOR-SIM). ACS Photonics, 11, 1887(2024). https://doi.org/10.1021/acsphotonics.3c01845

[29] et alOptically sectioned in vivo imaging with speckle illumination HiLo microscopy. J. Biomed. Opt., 16, 016014(2011). https://doi.org/10.1117/1.3528656

[30] Data for ‘High-fidelity CUDA-based 3DSIM parallel reconstruction method’. https://figshare.com/projects/Data_for_High-fidelity_CUDA-based_3DSIM_parallel_reconstruction_method_/249950

[31] https://github.com/clslzwhy/Cu-SIM.

Tools

Get Citation

Copy Citation Text

Hongyu Wang, Ruijie Cao, Wenyi Wang, Yaning Li, Peng Xi, "High-fidelity CUDA-based 3DSIM parallel reconstruction method," Adv. Imaging 2, 041001 (2025)

Download Citation

EndNote(RIS)BibTex Plain Text

Set citation alerts for article

Save article for my favorites

Paper Information

Category: Research Article

Received: Mar. 14, 2025

Accepted: Jun. 4, 2025

Published Online: Jul. 11, 2025

The Author Email: Peng Xi (xipeng@pku.edu.cn)

DOI:10.3788/AI.2025.10002

Topics

laser devices and laser physics

Lasers and Laser Optics

laser manufacturing

Instrumentation, Measurement and Metrology