Visualizing intraorganellar ultrastructures, dynamics, and interactions with open-access background-free Lock-in-SIM

Wenjie Liu (), Meng Zhang, Wenbin Zhu, Shunyu Xie, Jinfeng Zhang, Shuhao Qian, Zhiyi Liu, Xiu Zheng, Qiuyuan Fang, Wei Yang, Yi Wang, Dazhao Zhu, Jianjie Dong, Xu Liu, Youhua Chen (), Cuifang Kuang, Yu-Hui Zhang () and Lothar Schermelleh ()
Additional contact information
Wenjie Liu: University of Oxford, Department of Biochemistry
Meng Zhang: Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics
Wenbin Zhu: Zhejiang Lab
Shunyu Xie: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Jinfeng Zhang: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Shuhao Qian: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Zhiyi Liu: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Xiu Zheng: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Qiuyuan Fang: Zhejiang University School of Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, Department of Biophysics, Institute of Neuroscience
Wei Yang: Zhejiang University School of Medicine, NHC and CAMS Key Laboratory of Medical Neurobiology, Department of Biophysics, Institute of Neuroscience
Yi Wang: Zhejiang University, Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences
Dazhao Zhu: Zhejiang Lab
Jianjie Dong: Zhangjiang Laboratory
Xu Liu: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Youhua Chen: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Cuifang Kuang: Zhejiang University, State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering
Yu-Hui Zhang: Huazhong University of Science and Technology, MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics
Lothar Schermelleh: University of Oxford, Department of Biochemistry

Nature Communications, 2025, vol. 16, issue 1, 1-14

Abstract: Abstract Structured illumination microscopy (SIM) is a powerful method for fast and gentle live-cell super-resolution imaging. However, its susceptibility to reconstruction artifacts from out-of-focus blur and background imposes substantial barriers to analyze the dynamics of densely packed volumetric intraorganellar ultrastructures that are typically in a size range of SIM’s spatial resolution. To address this limitation, we have developed Lock-in-SIM, an open-access two-dimensional SIM framework that eliminates background and maximizes the recovery of sub-diffraction information with the highest possible frequency extraction. By leveraging the intrinsic modulation differences of volumetric sample structures, Lock-in-SIM enables efficient optical sectioning, extends imaging depth, and improves data fidelity and quantifiability. We demonstrate the superiority of Lock-in-SIM by visualizing various challenging intraorganellar ultrastructures in live cells. Our investigations uncover mechanisms of mitochondrial fission and endoplasmic reticulum-lysosome interactions and provide insights into the intricate yet highly regulated structural remodeling of organelles.

Date: 2025
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DOI: 10.1038/s41467-025-65805-w

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