Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform

Ruijie Cao; Yaning Li; Xin Chen; Xichuan Ge; Meiqi Li; Meiling Guan; Yiwei Hou; Yunzhe Fu; Xinzhu Xu; Christophe Leterrier; Shan Jiang; Baoxiang Gao; Peng Xi

doi:10.1038/s41592-023-01958-0

Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform

Nat Methods. 2023 Aug;20(8):1183-1186. doi: 10.1038/s41592-023-01958-0. Epub 2023 Jul 20.

Authors

Ruijie Cao^{1

2}, Yaning Li^{1

2}, Xin Chen^{1

2}, Xichuan Ge³, Meiqi Li^{1

2}, Meiling Guan^{1

2}, Yiwei Hou^{1

2}, Yunzhe Fu^{1

2}, Xinzhu Xu^{1

2}, Christophe Leterrier⁴, Shan Jiang⁵, Baoxiang Gao³, Peng Xi^{6

7}

Affiliations

¹ Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
² National Biomedical Imaging Center, Peking University, Beijing, China.
³ Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environment Science, Hebei University, Baoding, China.
⁴ Aix-Marseille Université, CNRS, INP UMR7051, NeuroCyto, Marseille, France.
⁵ Institute of Biomedical Engineering, Beijing Institute of Collaborative Innovation, Beijing, China.
⁶ Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China. xipeng@pku.edu.cn.
⁷ National Biomedical Imaging Center, Peking University, Beijing, China. xipeng@pku.edu.cn.

Abstract

Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Image Processing, Computer-Assisted / methods
Lighting* / methods
Microscopy* / methods