Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

Wei, Zhao; Zhao, Shiqun; Li, Liuju; Huang, Xiaoshuai; Xing, Shijia; Zhang, Yulin; Qiu, Guohua; Han, Zhenqian; Shang, Yingxu; Sun, De‐en; Shan, Chunyan; Wu, Runlong; Gu, Lijun; Zhang, Shuwen; Chen, Riwang; Xiao, Jianguo; Mo, Yanquan; Wang, Jianyong; Ji, Wei; Chen, Xing; Ding, Baoquan; Liu, Yanmei; Mao, Heng; Song, Bei; Tan, Jiubin; Liu, Jian; Li, Haoyu; Chen, Liangyi

doi:10.1038/s41587-021-01092-2

Cited by 211 publications

(160 citation statements)

References 67 publications

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“…Disentangling underlying signals from noisy images before light-field reconstruction could eliminate artifacts and ensure high-fidelity results. Moreover, a recently published work reported that standard Richardson–Lucy deconvolution can recover high-frequency information beyond the spatial frequency limit of the microscope if there is no noise contamination 62 , which inspires us that our method would be helpful for deconvolution algorithms by denoising input images in advance. Single-molecule localization microscopy (SMLM) is also susceptible to noise since the localization precision is fundamentally limited by SNR 3, 63 .…”

Section: Discussionmentioning

confidence: 82%

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

Zhou

et al. 2022

Preprint

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A fundamental challenge in fluorescence microscopy is the inherent photon shot noise caused by the inevitable stochasticity of photon detection. Noise increases measurement uncertainty, degrades image quality, and limits imaging resolution, speed, and sensitivity. To achieve high-sensitivity imaging beyond the shot-noise limit, we provide DeepCAD-RT, a versatile self-supervised method for effective noise suppression of fluorescence time-lapse imaging. We made comprehensive optimizations to reduce its data dependency, processing time, and memory consumption, finally allowing real-time processing on a two-photon microscope. High imaging signal-to-noise ratio (SNR) can be acquired with 10-fold fewer fluorescence photons. Meanwhile, the self-supervised superiority makes it a practical tool in fluorescence microscopy where ground-truth images for training are hard to obtain. We demonstrated the utility of DeepCAD-RT in extensive experiments, including in vivo calcium imaging of various model organisms (mouse, zebrafish larva, fruit fly), 3D migration of neutrophils after acute brain injury, and 3D dynamics of cortical ATP (adenosine 5'-triphosphate) release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with minimal photon budget.

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Section: Discussionmentioning

confidence: 82%

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

Zhou

et al. 2022

Preprint

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“…Furthermore, A-PoD coupled multiplex SRS can be applied to imaging other biomolecules such as nucleic acids, etc.. Recently, various super-resolution techniques have been applied to SRS imaging (11,12,61,62). Nonetheless, the localization method for super-resolution fluorescence microscopy was considered not applicable to Raman imaging.…”

Section: Discussionmentioning

confidence: 99%

Super-resolution stimulated Raman Scattering microscopy with A-PoD

Jang

Fung

et al. 2022

Preprint

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Unlike traditionally-mapped Raman imaging, stimulated Raman scattering (SRS) imaging achieved the capability of imaging metabolic dynamics and a greatly improved signal-noise-ratio. However, its spatial resolution is still limited by the numerical aperture or scattering cross section. To achieve super-resolved SRS imaging, we developed a new deconvolution algorithm Adam optimization-based Pointillism Deconvolution (A-PoD) for SRS imaging, and demonstrated a spatial resolution of 52 nm on polystyrene beads. By changing the genetic algorithm to A-PoD, the image deconvolution process was shortened by more than 3 orders of magnitude, from a few hours to a few seconds. By applying A-PoD to spatially correlated multi-photon fluorescence (MPF) imaging and deuterium oxide (D2O)-probed SRS (DO-SRS) imaging data from diverse samples, we compared nanoscopic distributions of proteins and lipids in cells and subcellular organelles. We successfully differentiated newly synthesized lipids in lipid droplets using A-PoD coupled with DO-SRS. The A-PoD-enhanced DO-SRS imaging method was also applied to reveal the metabolic change in brain samples from Drosophila on different diets. This new approach allows us to quantitatively measure the nanoscopic co-localization of biomolecules and metabolic dynamics in organelles. We expect that the A-PoD algorithm will have a wide range of applications, from nano-scale measurements of biomolecules to processing astronomical images.

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“…The low copy numbers—in contrast to highly abundant cellular RNAs—imply that the crowding of signals beyond the limit of microscopy is unlikely given the current resolution limits of microscopy (lateral resolution: approx. 120 × 120 nm last generation confocal microscopy, wave-length-dependent; 60 × 60 nm sparse deconvolution during real-time microscopy [ 28 ], 20 × 20 nm stimulated emission depletion (STED) microscopy; axial resolution approx. 3-fold).…”

Section: Problems and Significance Of Cccdna And Mrna Visualisationmentioning

confidence: 99%

Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges

Bustamante-Jaramillo

Fingal

Blondot

et al. 2022

Viruses

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Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 1010 virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.

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Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy

Cited by 211 publications

References 67 publications

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

Real-time denoising of fluorescence time-lapse imaging enables high-sensitivity observations of biological dynamics beyond the shot-noise limit

Super-resolution stimulated Raman Scattering microscopy with A-PoD

Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges

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