Exploring pathways in the brain

Explore open access datasets on neuroanatomy, gene expression, and brain connectivity

resource type /

Lesson Plan

topic /

neuroscience

published / March 2, 2026

audience /

Graduate

Undergraduate

Histological cross-section of human ear and cerebellum tissue stained with purple dye

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Kaitlyn Casimo

Manager, Education & Engagement

About this lesson:

This lesson is built around a student worksheet where students are guided through two open access resources: the Allen Mouse Brain Atlas (gene expression) and the Allen Mouse Brain Connectivity Atlas (images of axonal projections). Through this activity, students explore neuroanatomical atlases and the connections between gene expression and brain region functions. An optional extension activity challenges students to explore a research question of their choice exploring connectivity between brain regions.

What is the Allen Mouse Brain Atlas?

The database consists of a comprehensive review of gene expression across the healthy adult mouse brain. Over 20,000 gene expression levels were surveyed across the whole mouse brain and in situ hybridization (ISH) was used to record gene expression.

Mouse Brain Atlas

What is the Allen Mouse Brain Connectivity Atlas?

This database consists of images of axonal projections labeled by viral (rAAV) tracers and visualized using serial two-photon tomography.

Mouse Brain Connectivity Atlas

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Reading Resources:

Neural network visualization with interconnected nodes and branching red and blue pathways

Five unsolved mysteries about the brain

Can we understand our own brains? We have a long way to go, neuroscientists say. Read the article here.

Brain cross-section with anatomical regions labeled including cortex, thalamus, hippocampus, and cerebellum.

Lein et al. (2007)

Genome-wide atlas of gene expression in the adult mouse brain. Read the article here.

Data visualization from connectome publication in Nature

Oh et al. (2007)

A mesoscale connectome of the mouse brain. Read the article here.

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Materials

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Student worksheet

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Colorful cross-section of a mouse brain showing neural tissue with pink, blue, and orange regions.

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