Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy DOI Creative Commons
Elise Delage, Thomas Guilbert, F Yates

et al.

The Journal of Cell Biology, Journal Year: 2023, Volume and Issue: 222(11)

Published: Oct. 17, 2023

In parallel with the development of tissue-clearing methods, over last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, experience technique is not always up expectations. response a survey specific challenges associated sample clearing labeling, image acquisition, data analysis, we have critically assessed recent literature characterize difficulties inherent applied cleared biological samples propose solutions overcome them. This review aims provide interested primer for pipeline, from preparation analysis. Importantly, believe that issues could be avoided better anticipation analysis requirements, which should kept mind while optimizing acquisition parameters.

Language: Английский

More than double the fun with two-photon excitation microscopy DOI Creative Commons
Peter Luu, Scott E. Fraser, Falk Schneider

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: March 26, 2024

Abstract For generations researchers have been observing the dynamic processes of life through lens a microscope. This has offered tremendous insights into biological phenomena that span multiple orders time- and length-scales ranging from pure magic molecular reorganization at membrane immune cells, to cell migration differentiation during development or wound healing. Standard fluorescence microscopy techniques offer glimpses such in vitro, however, when applied intact systems, they are challenged by reduced signal strengths signal-to-noise ratios result deeper imaging. As remedy, two-photon excitation (TPE) takes special place, because it allows us investigate vivo, their natural environment, even living animal. Here, we review fundamental principles underlying TPE aimed basic advanced users interested adopting for intravital We focus on applications neurobiology, present current trends towards faster, wider imaging, discuss combination with photon counting technologies metabolic imaging spectroscopy, as well highlight outstanding issues drawbacks application these methodologies.

Language: Английский

Citations

16
Imagining the future of optical microscopy: everything, everywhere, all at once DOI Creative Commons
Harikrushnan Balasubramanian, Chad M. Hobson, Teng‐Leong Chew

et al.

Communications Biology, Journal Year: 2023, Volume and Issue: 6(1)

Published: Oct. 28, 2023

The optical microscope has revolutionized biology since at least the 17

Language: Английский

Citations

32
Live-cell imaging in the deep learning era DOI Creative Commons
Joanna W. Pylvänäinen, Estibaliz Gómez‐de‐Mariscal, Ricardo Henriques

et al.

Current Opinion in Cell Biology, Journal Year: 2023, Volume and Issue: 85, P. 102271 - 102271

Published: Oct. 27, 2023

Live imaging is a powerful tool, enabling scientists to observe living organisms in real time. In particular, when combined with fluorescence microscopy, live allows the monitoring of cellular components high sensitivity and specificity. Yet, due critical challenges (i.e., drift, phototoxicity, dataset size), implementing analyzing resulting datasets rarely straightforward. Over past years, development bioimage analysis tools, including deep learning, changing how we perform imaging. Here briefly cover important computational methods aiding carrying out key tasks such as drift correction, denoising, super-resolution imaging, artificial labeling, tracking, time series analysis. We also recent advances self-driving microscopy.

Language: Английский

Citations

28
Fluorescence microscopy: A statistics-optics perspective DOI
Mohamadreza Fazel, Kristin S. Grußmayer, Boris Ferdman

et al.

Reviews of Modern Physics, Journal Year: 2024, Volume and Issue: 96(2)

Published: June 5, 2024

For centuries, human fascination with the living world motivated development of tools for visualizing life's events at spatiotemporal scales beyond our visual range. While all optical microscopes use light to probe object interest, fluorescence can discern between and background molecular scale. At this scale, stochastic properties are fundamental interpreting microscopy data. Accordingly quantitative methods that enable such interpretation necessitate perspective statistical concepts. The physical-optical principles governing formation fluorescent images modeling these while accounting stochasticity measurements reviewed.

Language: Английский

Citations

11
An end-to-end workflow for nondestructive 3D pathology DOI
Kevin W. Bishop, Lindsey A. Barner,

Qinghua Han

et al.

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(4), P. 1122 - 1148

Published: Jan. 23, 2024

Language: Английский

Citations

10
Imaging of cellular dynamics from a whole organism to subcellular scale with self-driving, multiscale microscopy DOI
Stephan Daetwyler, Hanieh Mazloom-Farsibaf, Felix Zhou

et al.

Nature Methods, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 12, 2025

Language: Английский

Citations

1
Frontiers in artificial intelligence‐directed light‐sheet microscopy for uncovering biological phenomena and multiorgan imaging DOI Creative Commons
Enbo Zhu,

Yan‐Ruide Li,

Samuel Margolis

et al.

View, Journal Year: 2024, Volume and Issue: 5(5)

Published: Sept. 3, 2024

Light-sheet fluorescence microscopy (LSFM) introduces fast scanning of biological phenomena with deep photon penetration and minimal phototoxicity. This advancement represents a significant shift in 3-D imaging large-scale tissues 4-D (space + time) small live animals. The large data associated LSFM requires efficient acquisition analysis the use artificial intelligence (AI)/machine learning (ML) algorithms. To this end, AI/ML-directed is an emerging area for multi-organ tumor diagnostics. review will present development highlight various configurations designs multi-scale imaging. Optical clearance techniques be compared effective reduction light scattering optimal deep-tissue further depict diverse range research translational applications, from organisms to diagnosis. In addition, address reconstruction, including application convolutional neural networks (CNNs) generative adversarial (GANs). summary, advancements have enabled post-imaging reconstruction analyses, underscoring LSFM's contribution advancing fundamental research.

Language: Английский

Citations

6
Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues DOI Open Access
Adam K. Glaser, Jayaram Chandrashekar, Joshua Vasquez

et al.

Published: Oct. 23, 2023

Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure cells tissues at sub-diffraction resolutions near single molecule sensitivity, driving discoveries diverse fields biology, including neuroscience. Biological is organized over scales nanometers to centimeters. Harnessing molecular imaging across three-dimensional samples on this scale requires new types microscopes with larger view working distance, as well higher throughput. We present a expansion-assisted selective plane illumination microscope (ExA-SPIM) diffraction-limited aberration-free performance large field (85 mm 2 ) distance (35 mm). Combined clearing expansion methods, allows nanoscale centimeter-scale samples, entire mouse brains, high contrast without sectioning. illustrate ExA-SPIM by reconstructing individual neurons brain, cortico-spinal macaque motor cortex, tracing axons human white matter.

Language: Английский

Citations

13
Plug-and-play DPC-based quantitative phase microscope DOI Creative Commons
Tao Peng, Zeyu Ke, Hao Wu

et al.

Biomedical Optics Express, Journal Year: 2024, Volume and Issue: 15(3), P. 1785 - 1785

Published: Feb. 7, 2024

Point-of-care testing (POCT) plays an increasingly important role in biomedical research and health care. Quantitative phase microscopes (QPMs) with good contrast, no invasion, labeling, high speed automation could be effectively applied for POCT. However, most QPMs are fixed on the optical platform bulky size, lack of timeliness, which remained challenging POCT solutions. In this paper, we proposed a plug-and-play QPM multimode imaging based quantitative differential contrast (qDPC) method. The system employs programmable LED array as light source uses GPU to accelerate calculation, can realize multi-contrast six modes. Accurate measurement real-time implemented by qDPC algorithms targets samples. A 3D electric control is designed mechanical field view focusing without manual operations. experimental results verify robustness performance setup. Even rookie finish scheme applications at scene using compact size 140 × 165 250 mm 3 .

Language: Английский

Citations

5
Mesoscopic oblique plane microscopy via light-sheet mirroring DOI Creative Commons
Stephan Daetwyler, Bo-Jui Chang, Bingying Chen

et al.

Optica, Journal Year: 2023, Volume and Issue: 10(11), P. 1571 - 1571

Published: Oct. 18, 2023

Understanding the intricate interplay and inter-connectivity of biological processes across an entire organism is important in various fields biology, including cardiovascular research, neuroscience, developmental biology. Here, we present a mesoscopic oblique plane microscope (OPM) that enables whole imaging with high speed while revealing fine details such as endothelial nuclei. A microprism underneath sample enhances axial resolution optical sectioning through total internal reflection light sheet. Through rapid refocusing sheet, depth extended up to threefold keeping constant. Using low magnification objectives large field view, realize over volume 3.7mm×1.5mm×1mm ∼2.3µm lateral ∼9.2µm resolution. Applying OPM, demonstrate vivo toto zebrafish vasculature its nuclei, blood flow dynamics at 12 Hz acquisition rate, resulting quantitative map organism.

Language: Английский

Citations

12