Bayesian deep-learning structured illumination microscopy enables reliable super-resolution imaging with uncertainty quantification

Tao Liu, Jiahao Liu, Dong Li () and Shan Tan ()
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Tao Liu: Huazhong University of Science and Technology
Jiahao Liu: Huazhong University of Science and Technology
Dong Li: Tsinghua University
Shan Tan: Huazhong University of Science and Technology

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract The objective of optical super-resolution imaging is to acquire reliable sub-diffraction information on bioprocesses to facilitate scientific discovery. Structured illumination microscopy (SIM) is acknowledged as the optimal modality for live-cell super-resolution imaging. Although recent deep learning techniques have substantially advanced SIM, their transparency and reliability remain uncertain and under-explored, often resulting in unreliable results and biological misinterpretation. Here, we develop Bayesian deep learning (BayesDL) for SIM, which enhances the reconstruction of densely labeled structures while enabling the quantification of super-resolution uncertainty. With the uncertainty, BayesDL-SIM achieves high-fidelity distribution-informed SIM imaging, allowing for the communication of credibility estimates to users regarding the model outcomes. We also demonstrate that BayesDL-SIM boosts SIM reliability by identifying and preventing erroneous generalizations in various model misuse scenarios. Moreover, the BayesDL uncertainty shows versatile utilities for daily super-resolution imaging, such as error estimation, data acquisition evaluation, etc. Furthermore, we demonstrate the effectiveness and superiority of BayesDL-SIM in live-cell imaging, which reliably reveals F-actin dynamics and the reorganization of the cell cytoskeleton. This work lays the foundation for the reliable implementation of deep learning-based SIM methods in practical applications.

Date: 2025
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DOI: 10.1038/s41467-025-60093-w

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