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Exploring Pathways in the Brain

This unit advances students’ understanding of neuroanatomy, explores the relationship between gene expression and brain region function, and guides students through developing their own experimental questions about brain connectivity.

About this lesson:

The content of this lesson develops students’ understanding of neuroanatomy, explores the relationship between gene expression and brain region function, and guides students through developing their own experimental questions about brain connectivity. It also introduces open research questions in the world of neuroscience. Students are guided through a data set that is under active development and are encouraged to consider current and future research questions.

This lesson is divided into three sections of increasing difficulty and complexity, which build on each other. Depending on the level of their students and needs of the course, instructors may choose to use only Section 1 (suitable for introductory college neuroscience/some very advanced high schoolers), Sections 1 and 2 (suitable for introductory to intermediate college students), or the full lesson of Sections 1-3 (suitable for intermediate to advanced college and graduate students).

The datasets used in this unit come from the Allen Brain Map, a group of open datasets encompassing gene expression in the brain, visual behavior, properties of neurons, neural development, and more. Students will learn what kind of data is collected in research settings and begin learning how it can be used.

The full lesson plan includes learning objectives, a teacher guide, suggested timing, and student worksheets.

Lesson Materials

Reading Resources:

Human brain cells

Five unsolved mysteries about the brain

Can we understand our own brains? We have a long way to go, neuroscientists say.
Allen Mouse Brain Atlas Gene Expression

Lein, E, et al. Nature (2007)

Genome-wide atlas of gene expression in the adult mouse brain.
Data visualization from connectome publication in Nature

Oh, SW, et al. Nature (2007)

A mesoscale connectome of the mouse brain
Screenshot of Brain Facts 3D brain visualization tool

Brain Facts 3D Brain

Visualization tool. Imagery by Society for Neuroscience.
Science art showing brain connectivity

A new high-resolution map of how the brain is wired

Systematic tracing of how neurons connect reveals mammalian brain’s ‘org chart’ of possible information flow

Open neuroscience data resources:

Allen Mouse Brain Connectivity Database

A high-resolution map of neural connections in the mouse brain

NIH gene database

Information from a wide range of species

Allen Brain Map reference atlases

The Allen Institute for Brain Science has generated multiple reference atlases

Allen Mouse Brain Atlas

A genome-wide, high-resolution atlas of gene expression throughout the adult mouse brain

Allen Human Brain Atlas

A unique multimodal atlas of the human brain, integrating anatomic and genomic information