Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Three-Dimensional Microscopy in Microbiology

Three-Dimensional Microscopy in Microbiology

Three-dimensional imaging techniques are essential in cell biology, allowing researchers to visualize intricate cellular structures with high resolution. Two prominent methods, Differential Interference Contrast Microscopy (DIC) and Confocal Scanning Laser Microscopy (CSLM), provide distinct advantages for imaging live and thick specimens, respectively.Differential Interference Contrast MicroscopyDIC microscopy enhances contrast in transparent, unstained samples by converting phase...

Confocal Fluorescence Microscopy

Confocal Fluorescence Microscopy

Confocal microscopy is an advanced microscopic technique. The prime advantage of the confocal microscope over other microscopy techniques is its ability to block the out-of-focus light from the illuminated samples using pinholes. It is widely used with fluorescence optics to obtain high-resolution, sharp contrast images. Unlike optical microscopes, confocal microscopes use a focused beam of light laser to scan the entire sample surface at different z-planes. These microscopes are, therefore,...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Efficient Separation of Single-Stranded DNA of Various Lengths for Applications in Bioimaging, Gene Editing, and Nanostructures.

ACS applied materials & interfaces·2025

Same author

Mouse Forebrain Region Features and Cholinergic Neurons Subtyping: Integrated Analysis with Spatial Multi-omics.

Genomics, proteomics & bioinformatics·2025

Same author

Marker-free drift correction for 3D RNA imaging via spatiotemporal clustering and imputation.

Optics express·2025

Same author

Designing a Hybrid Chain Reaction Probe for Multiplex Transcripts Assay with High-Level Imaging.

ACS nano·2023

Same author

Three-dimensional mapping of hepatic lymphatic vessels and transcriptome profiling of lymphatic endothelial cells in healthy and diseased livers.

Theranostics·2023

Same author

Cryo-fluorescence micro-optical sectioning tomography for volumetric imaging of various whole organs with subcellular resolution.

iScience·2022

Search research articles

Related Experiment Video

Updated: Sep 13, 2025

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Published on: October 29, 2019

Tilted thick light-sheet microscopy with context-aware 3D localization for RNA imaging in intact 50 μm-thick

Lin Cai, Qihang Song, Dongjian Cao

|July 30, 2025

Summary

We developed a new 3D RNA imaging technique for thick brain sections, enabling large-area coverage for precise neuron typing and whole-brain transcriptomics.

More Related Videos

En face Cryosectioning of Mouse Retina for High-dimensional Spatial Molecular Analysis

En face Cryosectioning of Mouse Retina for High-dimensional Spatial Molecular Analysis

Published on: July 8, 2025

A Guide to Build a Highly Inclined Swept Tile Microscope for Extended Field-of-view Single-molecule Imaging

A Guide to Build a Highly Inclined Swept Tile Microscope for Extended Field-of-view Single-molecule Imaging

Published on: April 8, 2019

Related Experiment Videos

Last Updated: Sep 13, 2025

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Three-dimensional Imaging of Bacterial Cells for Accurate Cellular Representations and Precise Protein Localization

Published on: October 29, 2019

En face Cryosectioning of Mouse Retina for High-dimensional Spatial Molecular Analysis

En face Cryosectioning of Mouse Retina for High-dimensional Spatial Molecular Analysis

Published on: July 8, 2025

A Guide to Build a Highly Inclined Swept Tile Microscope for Extended Field-of-view Single-molecule Imaging

A Guide to Build a Highly Inclined Swept Tile Microscope for Extended Field-of-view Single-molecule Imaging

Published on: April 8, 2019

Area of Science:

Neuroscience
Microscopy
Molecular Biology

Background:

Accurate neuron typing requires 3D imaging of intact brain sections.
Existing RNA imaging methods face limitations in balancing imaging area and section thickness.
Challenges persist in achieving high-resolution, large-area RNA imaging in thick tissues.

Purpose of the Study:

To develop an advanced RNA imaging method for 3D neuron typing in thick brain sections.
To overcome the limitations of conventional RNA imaging techniques regarding area coverage and section thickness.
To enable high-resolution, large-scale transcriptomic analysis in the brain.

Main Methods:

Introduced tilted thick light-sheet microscopy with a 45° illumination geometry.
Integrated a context-aware 3D astigmatic localization algorithm with continuous frame filtering.
Enabled multiplexed RNA imaging in 50 μm-thick tissue sections across centimeter-scale regions.

Main Results:

Achieved optical-interference-free imaging in 50 μm-thick samples.
Recovered submicron resolution by pinpointing fluorescence in situ hybridization (FISH) spots within volumetric excitation.
Demonstrated the capability for layer-spanning neuronal distribution and region-specific expression gradient analysis.

Conclusions:

The developed platform resolves the trade-off between imaging depth and spatial coverage for RNA imaging.
Advances whole-brain transcriptomics and 3D neuron typing capabilities.
Provides a novel approach for deciphering brain-wide cellular architectures.