scholarly journals A versatile compressed sensing scheme for faster and less phototoxic 3D fluorescence microscopy

2017 ◽  
Author(s):  
Maxime Woringer ◽  
Xavier Darzacq ◽  
Christophe Zimmer ◽  
Mustafa Mir
Keyword(s):  
Fluorescence Microscopy ◽  
Compressed Sensing ◽  
Light Exposure ◽  
Three Dimensional ◽  
Light Sheet ◽  
Computational Imaging ◽  
Acquisition Time ◽  
Trade Offs ◽  
Fold Reduction ◽  
3D Fluorescence Microscopy

AbstractThree-dimensional fluorescence microscopy based on Nyquist sampling of focal planes faces harsh trade-offs between acquisition time, light exposure, and signal-to-noise. We propose a 3D compressed sensing approach that uses temporal modulation of the excitation intensity during axial stage sweeping and can be adapted to fluorescence microscopes without hardware modification. We describe implementations on a lattice light sheet microscope and an epifluorescence microscope, and show that images of beads and biological samples can be reconstructed with a 5-10 fold reduction of light exposure and acquisition time. Our scheme opens a new door towards faster and less damaging 3D fluorescence microscopy.OCIS codes: (110.1758) Computational imaging; (170.2520) Fluorescence microscopy; (170.6900) Three-dimensional microscopy.

scholarly journals Network-enabled efficient image restoration for 3D microscopy of turbid biological specimens

2020 ◽  
Author(s):  
Le Xiao ◽  
Chunyu Fang ◽  
Yarong Wang ◽  
Tingting Yu ◽  
Yuxuan Zhao ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Image Restoration ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Science Research ◽  
Light Sheet ◽  
Cell Nuclei ◽  
Two Photon ◽  
Photon Excitation ◽  
3D Fluorescence Microscopy

AbstractThough three-dimensional (3D) fluorescence microscopy has been an essential tool for modern life science research, the light scattering by biological specimens fundamentally prevents its more widespread applications in live imaging. We hereby report a deep-learning approach, termed ScatNet, that enables reversion of 3D fluorescence microscopy from high-resolution targets to low-quality, light-scattered measurements, thereby allowing restoration for a single blurred and light-scattered 3D image of deep tissue, with achieving improved resolution and signal-to-noise ratio. Our approach can computationally extend the imaging depth for current 3D fluorescence microscopes, without the addition of complicated optics. Combining ScatNet approach with cutting-edge light-sheet fluorescence microscopy, we demonstrate that the image restoration of cell nuclei in the deep layer of live Drosophila melanogaster embryos at single-cell resolution. Applying our approach to two-photon excitation microscopy, we could improve the signal and resolution of neurons in mouse brain beyond the photon ballistic region.

scholarly journals Breaking the limit of 3D fluorescence microscopy by dual-stage-processing network

2018 ◽  
Author(s):  
Hao Zhang ◽  
Yuxuan Zhao ◽  
Chunyu Fang ◽  
Guo Li ◽  
Meng Zhang ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Single Cell ◽  
Science Research ◽  
Light Sheet ◽  
Diffraction Limit ◽  
Acquisition Time ◽  
Cell Organelles ◽  
Volume Rate ◽  
Dual Stage ◽  
3D Fluorescence Microscopy

AbstractAlthough three-dimensional (3D) fluorescence microscopy is an essential tool for life science research, the fundamentally-limited optical throughput, as reflected in the compromise between speed and resolution, so far prevents further movement towards faster, clearer, and higher-throughput applications. We herein report a dual-stage mutual-feedback deep-learning approach that allows gradual reversion of microscopy degradation from high-resolution targets to low-resolution images. Using a single blurred-and-pixelated 3D image as input, our trained network infers a 3D output with notably higher resolution and improved contrast. The performance is better than conventional 1-stage network approaches. It pushes the throughput limit of current 3D fluorescence microscopy in three ways: notably reducing the acquisition time for accurate mapping of large organs, breaking the diffraction limit for imaging subcellular events with faster lower-toxicity measurement, and improving temporal resolution for capturing instantaneous biological processes. Combining our network approach with light-sheet fluorescence microscopy, we demonstrate the imaging of vessels and neurons in the mouse brain at single-cell resolution and with a throughput of 6 minutes for a whole brain. We also image cell organelles beyond the diffraction limit at a 2-Hz volume rate, and map neuronal activities of freely-moving C. elegans at single-cell resolution and 30-Hz volume rate.

scholarly journals Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

2017 ◽  
Author(s):  
Martin Weigert ◽  
Uwe Schmidt ◽  
Tobias Boothe ◽  
Andreas Müller ◽  
Alexandr Dibrov ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Image Restoration ◽  
Light Exposure ◽  
Axial Direction ◽  
Isotropic Resolution ◽  
Biological Phenomena ◽  
Trade Offs ◽  
Under Sampling ◽  
Key Driver ◽  
Photon Exposure

Fluorescence microscopy is a key driver of discoveries in the life-sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how image restoration based on deep learning extends the range of biological phenomena observable by microscopy. On seven concrete examples we demonstrate how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to 10-fold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times higher frame-rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, Fiji, and Knime.

Three-Dimensional Live Imaging of Filamentous Fungi with Light Sheet-Based Fluorescence Microscopy (LSFM)

2017 ◽  
pp. 19-31 ◽  
Author(s):  
Francesco Pampaloni ◽  
Laura Knuppertz ◽  
Andrea Hamann ◽  
Heinz D. Osiewacz ◽  
Ernst H. K. Stelzer
Keyword(s):  
Fluorescence Microscopy ◽  
Filamentous Fungi ◽  
Three Dimensional ◽  
Light Sheet ◽  
Live Imaging

Tissue-culture light sheet fluorescence microscopy (TC-LSFM) allows long-term imaging of three-dimensional cell cultures under controlled conditions

2014 ◽  
Vol 6 (10) ◽  
pp. 988-998 ◽  
Author(s):  
Francesco Pampaloni ◽  
Ulrich Berge ◽  
Anastasios Marmaras ◽  
Peter Horvath ◽  
Ruth Kroschewski ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Fluorescence Microscopy ◽  
Fluorescence Imaging ◽  
Cell Cultures ◽  
Three Dimensional ◽  
Light Sheet ◽  
Controlled Conditions ◽  
Light Sheet Fluorescence Microscopy ◽  
Dimensional Cell

This novel system for the long-term fluorescence imaging of live three-dimensional cultures provides minimal photodamage, control of temperature, CO2, pH, and media flow.

scholarly journals A Review on Dual-Lens Fluorescence Microscopy for Three-Dimensional Imaging

2020 ◽  
Vol 8 ◽  
Author(s):  
Xiaoyan Li ◽  
Yubing Han ◽  
Wenjie Liu ◽  
Cuifang Kuang ◽  
Xu Liu ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
3D Imaging ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Super Resolution ◽  
Light Sheet ◽  
Animal Cells ◽  
3D Images ◽  
Single Lens ◽  
Model Animal

Three-dimensional (3D) imaging using dual-lens fluorescence microscopies is popular in observing fluorescently labeled biological samples, such as mammalian/model animal cells, tissues, and embryos. Specifically, dual-lens super-resolution fluorescence microscopy methods using two opposing objective lenses allow significantly higher axial resolution and better signal to noise ratio than traditional single-lens counterparts, and thus distinguish more details in 3D images of fine intracellular structures. For 3D imaging of thick tissues and entire embryos, dual-lens light-sheet fluorescence microscopy methods using two objective lenses, either orthogonal or non-orthogonal, to achieve selective plane illumination, can meet the requirements, and thus can be used to observe embryo development and structures of interest in thick tissues. This review summarizes both dual-lens fluorescence microscopy methods, including their principles, configurations, and 3D imaging applications, providing a guideline for biological laboratories with different 3D imaging needs.

scholarly journals Light-Sheet Fluorescence Microscopy with Scanning Non-diffracting Beams

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hosein Kafian ◽  
Meelad Lalenejad ◽  
Sahar Moradi-Mehr ◽  
Shiva Akbari Birgani ◽  
Daryoush Abdollahpour
Keyword(s):  
Fluorescence Microscopy ◽  
Spatial Coherence ◽  
Three Dimensional ◽  
Light Sheet ◽  
Tissue Imaging ◽  
Wide Field ◽  
Self Healing ◽  
Main Challenge ◽  
Cancer Tumor ◽  
Light Sheet Fluorescence Microscopy

Abstract Light-sheet fluorescence microscopy (LSFM) has now become a unique tool in different fields ranging from three-dimensional (3D) tissue imaging to real-time functional imaging of neuronal activities. Nevertheless, obtaining high-quality artifact-free images from large, dense and inhomogeneous samples is the main challenge of the method that still needs to be adequately addressed. Here, we demonstrate significant enhancement of LSFM image qualities by using scanning non-diffracting illuminating beams, both through experimental and numerical investigations. The effect of static and scanning illumination with several beams are analyzed and compared, and it is shown that scanning 2D Airy light-sheet is minimally affected by the inhomogeneities in the samples, and provides higher contrasts and uniform resolution over a wide field-of-view, due to its reduced spatial coherence, self-healing feature and longer penetration depth. Further, the capabilities of the illumination scheme is utilized for both single-and double-wavelength 3D imaging of large and dense mammospheres of cancer tumor cells as complex inhomogeneous biological samples.

Three-dimensional imaging on a chip using optofluidics light-sheet fluorescence microscopy

Lab on a Chip ◽  
2021 ◽  
Author(s):  
Erick Vargas Ordaz ◽  
Sergey Gorelick ◽  
Harrison York ◽  
Bonan Liu ◽  
Michelle L. Halls ◽  
...  
Keyword(s):  
Fluorescence Microscopy ◽  
Fluorescence Imaging ◽  
Three Dimensional ◽  
Light Sheet ◽  
Three Dimensional Imaging ◽  
Cellular Organelle ◽  
Resolution Imaging ◽  
Light Sheet Fluorescence Microscopy

Volumetric, sub-micron to micron level resolution imaging is necessary to assay phenotypes or characteristics at the sub-cellular/organelle scale. However, three-dimensional fluorescence imaging of cells is typically low throughput or compromises...

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