Exploring pathways in the brain

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

Details

Topics: Neuroscience
Audience: Advanced undergraduate students, introductory graduate students
Databases: Allen Mouse Brain Atlas, Allen Mouse Brain Connectivity Atlas
Resource type: Lesson

Materials

Instructor guide

Student worksheet

Download materials

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