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Related Experiment Video

Updated: Jan 11, 2026

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Author Spotlight: Advancing Large-Scale Neural Dynamics Through HD-MEA Technology

Published on: March 8, 2024

Integrative analysis of single-neuron projectomes links connectome, transcriptome, and function in the mouse cortex.

Le Gao¹, Haifang Wang¹, Yu Chen¹

¹Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.

|November 18, 2025

Summary

Researchers mapped nearly 20,000 mouse cortical neurons, revealing 346 subtypes and seven connectivity modules. This detailed brain map links neural structure to gene expression and activity, advancing our understanding of the cortical network.

Keywords:

Neuropixels probe basal ganglia calcium imaging connectome cortex cortical hierarchy cortico-cortical connectivity multimodal analysis single-neuron projectome spatial transcriptome

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Last Updated: Jan 11, 2026

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Published on: March 8, 2024

Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex

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Published on: September 5, 2018

Multi-layer Cortical Ca2+ Imaging in Freely Moving Mice with Prism Probes and Miniaturized Fluorescence Microscopy

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Published on: June 13, 2017

Area of Science:

Neuroscience
Computational Neuroscience
Systems Neuroscience

Background:

The mammalian cortex's complex neural network underlies sensory processing, motor control, and cognition.
Principles of single-neuron connectivity, transcriptome, and activity remain poorly understood.

Purpose of the Study:

To reconstruct the projectomes of approximately 20,000 neurons in the entire mouse cortex.
To identify projection-defined neuronal subtypes and their distributions.
To analyze cortico-cortical and cortico-subcortical connectivity patterns.

Main Methods:

Reconstruction of neuronal projectomes using advanced tracing techniques.
Identification and classification of 346 projection-defined neuronal subtypes.
Analysis of connectivity modules, cortical hierarchy, and topographic maps.

Main Results:

Discovery of 346 region- and layer-specific projection-defined neuronal subtypes.
Unveiling of seven cortico-cortical modules with submodular organization and a high-resolution cortical hierarchy.
Detailed mapping of cortico-subcortical projections, including novel cortico-basal ganglia pathways.
Demonstration of close correlations between connectivity maps, Ca2+ activity, electrical activity, and gene expression.

Conclusions:

The study provides a foundational, fine-grained map of the mouse cortical connectome.
This multimodal analysis links neuronal structure, activity, and gene expression.
The findings offer a new framework for understanding cortical network organization and function.