<scp>High</scp>‐speed volumetric imaging in vivo based on structured illumination microscopy with interleaved reconstruction

Shi, Ruheng; Li, Yuting; Kong, Lingjie

doi:10.1002/jbio.202000513

Cited by 7 publications

(11 citation statements)

References 28 publications

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“…For the in vitro experiments, we achieve optical sectioning using the HiLo method 41 in which two raw images are recorded to reconstruct one optical-sectioning image, decreasing the imaging speed by half. We thus use the refined SIM method with interleaved reconstruction to achieve optical sectioning in the in vivo experiments 42,43 . Briefly, three raw images (I 1 , I 2 and I 3 ), each laterally shifted by a third of the grid period, are acquired.…”

Section: Optical Sectioning Via Structured Illumination and Computati...mentioning

confidence: 99%

“…2 and η is a scaling factor to ensure continuity at the crossover frequency in the Fourier domain 42 . To fill in the missing temporary information among adjacent reconstructed frames, we utilize the interleaved refined reconstruction method 43 in which we slide the time windows to pick up raw images for reconstruction.…”

Section: Optical Sectioning Via Structured Illumination and Computati...mentioning

confidence: 99%

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Random-access wide-field mesoscopy for centimetre-scale imaging of biodynamics with subcellular resolution

Shi,

Chen,

Deng

et al. 2024

Nat. Photon.

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Benefitting from the advantages of high imaging throughput and low cost, wide-field microscopy has become indispensable in biomedical studies. However, it remains challenging to record biodynamics with a large field of view and high spatiotemporal resolution due to the limited space–bandwidth product. Here we propose random-access wide-field (RA-WiFi) mesoscopy for the imaging of in vivo biodynamics over a 163.84 mm2 area with a spatial resolution of ~2.18 μm. We extend the field of view beyond the nominal value of the objective by enlarging the object distance, which leads to a lower field angle, followed by the correction of optical aberrations. We also implement random-access scanning with structured illumination, which enables optical-sectioning capability and high imaging contrast. The multi-plane imaging capability also makes the technique suitable for curved-surface samples. We demonstrate RA-WiFi mesoscopy in multi-modal imaging, including bright-field, dark-field and multi-colour fluorescence imaging. Specifically, we apply RA-WiFi mesoscopy to calcium imaging of cortex-wide neural network activities in awake mice in vivo, under both physiological and pathological conditions. We also show its unique capability in the three-dimensional random access of irregular regions of interest via the biodynamic imaging of mouse spinal cords in vivo. As a compact, low-cost mesoscope with optical-sectioning capability, RA-WiFi mesoscopy will enable broad applications in the biodynamic study of biological systems.

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Section: Optical Sectioning Via Structured Illumination and Computati...mentioning

confidence: 99%

Section: Optical Sectioning Via Structured Illumination and Computati...mentioning

confidence: 99%

Random-access wide-field mesoscopy for centimetre-scale imaging of biodynamics with subcellular resolution

Shi,

Chen,

Deng

et al. 2024

Nat. Photon.

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“…Additionally, motion-related changes to the phase shift can cause artifacts in the reconstructed data if they are not corrected before reconstruction [10]. To adapt this technique for in vivo neural recording, modifications to the reconstruction algorithm have been proposed [11,12]. Refined OS-SIM (rSIM) can be used to reduce signal variance by applying a spatial low-pass filter to each frame after OS-SIM reconstruction [11].…”

Section: Introductionmentioning

confidence: 99%

High-speed in vivo calcium recording using structured illumination with self-supervised denoising

Speed,

Saladrigas,

Teel

et al. 2024

Preprint

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High-speed widefield fluorescence imaging of neural activity in vivo is fundamentally limited by fluctuations in recorded signal due to background contamination and stochastic noise. In this study, we show background and shot noise reduced imaging of the ultrafast genetically encoded Ca2+ indicator GCaMP8f in CA1 pyramidal neurons using periodic structured illumination (SI) with computational image reconstruction. We implement a novel HiLo reconstruction, termed pseudo-HiLo (pHiLo), for high frame rate recording and compare this new technique to interleaved optical sectioning structured illumination microscopy (OS-SIM) and pseudo-widefield (pWF) reconstruction. We quantify the performance of each reconstruction by evaluating contrast, transient peak-to-noise ratio (PNR) and pair-wise correlation coefficients between ΔF/F time courses extracted from individual in-focus cells. We additionally incorporate a self-supervised deep learning method for real-time noise suppression (DeepCAD-RT) into our data preprocessing pipeline. At 500 Hz frame rates, we demonstrate an 84% increase in PNR using the denoised pHiLo reconstruction compared to pWF. Utilizing DeepCAD-RT, we show significant PNR improvements using both structured illumination (SI) reconstruction methods with OS-SIM showing a 59% increase in PNR after denoising. Both pHiLo and OS-SIM reconstructions result in a ~65% decrease in mean correlation coefficient of the ΔF/F time courses between ROIs in comparison with pWF, indicating the potential to remove background fluorescent transients from out of focus cells.

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“…Therefore, the traditional SIM needs to take three consecutive images to recover a single optical sectioned image, which is even slower than HiLo. However, inspired from the periodicity of the sine function, SIM has the potential to restore the original imaging speed ( Shi et al, 2021 ). When we switch the SIM illumination patterns continually, the phases of all patterns are physically continuous too.…”

Section: Introductionmentioning

confidence: 99%

Background inhibited and speed-loss-free volumetric imaging in vivo based on structured-illumination Fourier light field microscopy

et al. 2022

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Benefiting from its advantages in fast volumetric imaging for recording biodynamics, Fourier light field microscopy (FLFM) has a wide range of applications in biomedical research, especially in neuroscience. However, the imaging quality of the FLFM is always deteriorated by both the out-of-focus background and the strong scattering in biological samples. Here we propose a structured-illumination and interleaved-reconstruction based Fourier light field microscopy (SI-FLFM), in which we can filter out the background fluorescence in FLFM without sacrificing imaging speed. We demonstrate the superiority of our SI-FLFM in high-speed, background-inhibited volumetric imaging of various biodynamics in larval zebrafish and mice in vivo. The signal-to-background ratio (SBR) is improved by tens of times. And the volumetric imaging speed can be up to 40 Hz, avoiding artifacts caused by temporal under-sampling in conventional structured illumination microscopy. These suggest that our SI-FLFM is suitable for applications of weak fluorescence signals but high imaging speed requirements.

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High‐speed volumetric imaging in vivo based on structured illumination microscopy with interleaved reconstruction

Cited by 7 publications

References 28 publications

Random-access wide-field mesoscopy for centimetre-scale imaging of biodynamics with subcellular resolution

Random-access wide-field mesoscopy for centimetre-scale imaging of biodynamics with subcellular resolution

High-speed in vivo calcium recording using structured illumination with self-supervised denoising

Background inhibited and speed-loss-free volumetric imaging in vivo based on structured-illumination Fourier light field microscopy

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