Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering

Lin, Haonan; Seitz, Scott; Tan, Yuying; Lugagne, Jean-Baptiste; Wang, Le; Ding, Guangrui; He, Hongjian; Rauwolf, Tyler J.; Dunlop, Mary J.; Connor, John H.; Porco, Jr., John A.; Tian, Lei; Cheng, Ji-Xin

doi:10.1038/s41592-024-02575-1

Title: Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering

Journal Article · 15 January 2025 · Nature Methods

DOI: https://doi.org/10.1038/s41592-024-02575-1 · OSTI ID:2503949

^[1]; Seitz, Scott ^[2]; Tan, Yuying ^[1];

^[1]; Wang, Le ^[1]; Ding, Guangrui ^[1]; He, Hongjian ^[1]; Rauwolf, Tyler J. ^[1];

^[1]; Connor, John H. ^[2]; Porco, Jr., John A. ^[1];

^[1];

^[1]

Boston University, MA (United States)
Boston University Chobanian & Avedisian School of Medicine, MA (United States)

Nanoscopic imaging of cell metabolism is hindered by the incompatibility of small metabolites with fluorescent dyes and the limited resolution of imaging mass spectrometry. We present ultrasensitive reweighted visible stimulated Raman scattering (URV-SRS), a label-free vibrational nanoscopy technique that enables multiplexed detection of metabolic nanostructures within cells. We developed an extensively chirped spectral focusing visible SRS microscope that achieves a detection limit of 4,000 molecules and introduced a self-supervised learning-based denoiser to robustly suppress non-independent SRS noise by over 7.2 dB. The instrumentation-based signal enhancement and computation-based noise suppression synergistically improved the detection sensitivity by 50 times over near-infrared SRS. Leveraging this enhanced sensitivity, we further pushed the resolution to nanoscopic levels by introducing Fourier reweighting to amplify sub-100 nm spatial frequencies previously overwhelmed by noise. Validated by Fourier ring correlation, URV-SRS achieves a lateral resolution of 86 nm in cellular imaging. Here, we applied URV-SRS to elucidate the reprogramming of metabolic nanostructures associated with virus replication in Vero E6 host cells and to compositionally delineate subcellular fatty acid synthesis in engineered Escherichia coli, demonstrating its capability towards nanoscopic spatial metabolomics.

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Research Organization:: Boston University, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0019387

OSTI ID:: 2503949

Journal Information:: Nature Methods, Journal Name: Nature Methods Journal Issue: 5 Vol. 22; ISSN 1548-7091

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Title: Label-free nanoscopy of cell metabolism by ultrasensitive reweighted visible stimulated Raman scattering

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