Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)

Jiaming Qian; Weiyi Xia; Yuxia Huang; Jing Feng; Qian Chen; Chao Zuo

doi:10.1038/s41377-025-01979-8

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Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)

Original Articles

- Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)
- Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)
- Light: Science & Applications 2025年14卷第10期页码：3170-3181
- Affiliations：
  
  1.Smart Computational Imaging (SCI) Laboratory, Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
  2.Smart Computational Imaging Research Institute (SCIRI) of Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
  3.Jiangsu Key Laboratory of Spectral Imaging & Intelligent Sense, Nanjing University of Science and Technology, Nanjing, Jiangsu Province 210094, China
- Author bio：
  
  Qian Chen (chenqian@njust.edu.cn)
  Chao Zuo (zuochao@njust.edu.cn)
- Funds：
- DOI：10.1038/s41377-025-01979-8
  中图分类号：
- 收稿：2024-12-31，
  
  修回：2025-06-07，
  
  录用：2025-07-22，
  
  网络出版：2025-09-01，
  
  纸质出版：2025-10-31
- Accepted：
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Jiaming Qian, Weiyi Xia, Yuxia Huang, 等. Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)[J]. Light: Science & Applications, 2025,14(10):3170-3181.

Qian, J. M. et al. Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM). Light: Science & Applications, 14, 3170-3181 (2025).
Jiaming Qian, Weiyi Xia, Yuxia Huang, 等. Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM)[J]. Light: Science & Applications, 2025,14(10):3170-3181. DOI： 10.1038/s41377-025-01979-8.

Qian, J. M. et al. Principal component analysis for three-dimensional structured illumination microscopy (PCA-3DSIM). Light: Science & Applications, 14, 3170-3181 (2025). DOI： 10.1038/s41377-025-01979-8.

摘要

Abstract

Three-dimensional structured illumination microscopy (3DSIM) is an essential super-resolution imaging technique for visualizing volumetric subcellular structures at the nanoscale

capable of doubling both lateral and axial resolution beyond the diffraction limit. However

high-quality 3DSIM reconstruction is often hindered by uncertainties in experimental parameters

such as optical aberrations and fluorescence density heterogeneity. Here

we present PCA-3DSIM

a novel 3DSIM reconstruction framework that extends principal component analysis (PCA) from two-dimensional (2D) to three-dimensional (3D) super-resolution microscopy. To further compensate spatial nonuniformities of illumination parameters

PCA-3DSIM can be implemented in an adaptive tiled-block manner. By segmenting raw volumetric data into localized subsets

PCA-3DSIM enables accurate parameter estimation and effective interference rejection for high-fidelity

artifact-free 3D super-resolution reconstruction

with the inherent efficiency of PCA supporting the tiled reconstruction with limited computational burden. Experimental results demonstrate that PCA-3DSIM provides reliable reconstruction performance and improved robustness across diverse imaging scenarios

from custom-built platforms to commercial systems. These results establish PCA-3DSIM as a flexible and practical tool for super-resolved volumetric imaging of subcellular structures

with broad potential applications in biomedical research.

关键词

Keywords

references

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