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Updated: May 8, 2026

A Scanning Electron Microscopy-Compatible Optical Imaging Method for Mesoscopic All-Cell Brain Mapping

A Scanning Electron Microscopy-Compatible Optical Imaging Method for Mesoscopic All-Cell Brain Mapping

Published on: February 20, 2026

Pan-Optical Shadow Imaging of Brain Microanatomy.

Yulia Dembitskaya^1,2, Kosuke Okuda^1,2, Thibault Brugiere¹

¹Interdisciplinary Institute for Neuroscience, CNRS UMR 5297 and University of Bordeaux, Bordeaux, France.

Methods in Molecular Biology (Clifton, N.J.)

|May 6, 2026

Summary

This summary is machine-generated.

Shadow imaging provides high-resolution visualization of brain microarchitecture by labeling the extracellular space. This technique offers a flexible approach to study neural circuits in various models, including those relevant to neurological diseases.

Keywords:

Brain extracellular space Brain microstructure In vivo brain imaging Microglia imaging Organotypic and acute brain slices Pan-optical tissue imaging Shadow imaging Super-resolution microscopy Two-photon microscopy

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Last Updated: May 8, 2026

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Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

Micron-scale Resolution Optical Tomography of Entire Mouse Brains with Confocal Light Sheet Microscopy

Published on: October 8, 2013

Area of Science:

Neuroscience
Microscopy
Biophysics

Background:

Understanding brain microarchitecture is crucial for neuroscience.
Existing methods often require cell-type-specific labeling, limiting unbiased analysis.
The SUper-resolution SHadow Imaging (SUSHI) technique offers a novel approach.

Purpose of the Study:

To present comprehensive protocols for implementing shadow imaging in diverse biological models.
To enable high-resolution, unbiased visualization of brain microarchitecture.
To facilitate the study of neural circuits in health and disease.

Main Methods:

Developed the SUper-resolution SHadow Imaging (SUSHI) technique.
Adapted SUSHI for acute slices, organotypic cultures, and in vivo mouse brains.
Utilized multiple imaging modalities including 2-photon, STED, and confocal microscopy.
Included protocols for fixed tissue using extracellular matrix labeling.

Main Results:

Demonstrated SUSHI's capability for panoramic, high-resolution visualization of brain microarchitecture.
Showcased SUSHI's utility in live brain tissue without cell-type-specific labeling.
Extended SUSHI to in vivo applications using confocal and light-sheet microscopy.
Provided detailed protocols for sample preparation, dye delivery, and data acquisition.

Conclusions:

Shadow imaging offers a flexible and scalable method for resolving structural interplay in neural tissue.
This technique is applicable to diverse experimental models, including those relevant to neurological diseases.
SUSHI enhances the accessibility and utility of nanoscale imaging in neuroscience research.