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Three-photon microscopy: an emerging technique for deep intravital brain imaging
Robert Prevedel1,2,3,4, Júlia Ferrer Ortas5,6, Jason N D Kerr7
1Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. prevedel@embl.de.
Nature Reviews. Neuroscience
|June 20, 2025
Summary
Three-photon microscopy allows high-resolution imaging deep within the brain, overcoming limitations of previous methods. This breakthrough enables new investigations into neural circuits and brain diseases in previously inaccessible regions.
Area of Science:
- Neuroscience
- Biomedical Imaging
- Cellular Biology
Background:
- Two-photon microscopy advanced in vivo brain imaging but is limited to superficial cortical layers.
- Accessing deep brain structures is crucial for understanding higher-order functions and pathologies.
- Existing imaging techniques have limitations in visualizing deep neural circuits and cellular dynamics.
Purpose of the Study:
- To review the transformative impact of three-photon microscopy on neuroscience research.
- To highlight its capability in visualizing deep brain structures and cellular processes.
- To discuss applications in studying neural circuits, glial biology, and neuroimmune interactions.
Main Methods:
- Utilizing three-photon microscopy for minimally invasive, high-resolution in vivo brain imaging.
- Applying the technology to visualize deep cortical and subcortical regions in model organisms.
- Examining advancements in imaging neural circuits, glial cells, and disease mechanisms.
Main Results:
- Three-photon microscopy provides unprecedented access to deep brain structures for cellular observation.
- The technology facilitates detailed investigation of neural circuit dynamics in vivo.
- It enables the study of glial biology and neuroimmune interactions in previously inaccessible areas.
Conclusions:
- Three-photon microscopy is revolutionizing neuroscience by enabling deep brain exploration.
- It offers new possibilities for understanding brain function, pathology, and disease mechanisms.
- Continued technical innovation promises further advancements in visualizing the living brain.

