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Educator Spotlight: Using the Allen Brain Map to Teach Data Science

Access individual lesson plans and a full-term data science course modeled around the open data featured in the Allen Brain Map.

About these resources:

These lesson plans walk students through rich datasets that explore electrophysiology, mouse brain connectivity, and visual perception. This collection of resources includes three lesson plans intended for undergraduates/college students who are studying neuroscience and/or data science. Each lesson plan can be completed within a single class period and is suitable for in-person, hybrid, or virtual learning. It is recommended for students to have some prior experience with Python. These lessons were authored by Ashley Juavinett, PhD of the University of California, San Diego.  

In addition to authoring the three lessons, Ashley Juavinett has also made the materials publicly available for her Neural Data Science course that features data from the Allen Institute for Brain Science. Juavinett’s course is project-based. Students will use computational notebooks to perform exploratory data analyses and to test hypotheses in large neuroscience datasets, including the differences between unique neuron types, leveraging text mining of the neuroscience literature, and human neuroimaging analyses.  

full data science course

Lesson plans:

Three researchers sit at electrophysiology rigs.

Defining Cell Types by Their Electrophysiology

Take a look at whole-cell patch clamp recordings from mice and human cells in order to compare cell types.
View lesson plan
Mouse Brain Connectivity

Mouse Brain Connectivity

Analyze viral tracing experiments in transgenic mice to investigate whether certain areas of the brain are connected.
View lesson plan
A visualization of a large-scale model of a mouse visual cortex brain circuit, built at the Allen Institute and containing 230,000 neuron building-block models, recently published in the journal Neuron. Image courtesy of Sergey Gratiy, Ph.D.

Visual Perception in a Mouse

Analyze two-photon calcium imaging data to investigate how different cell types in the mouse encode visual information.
View lesson plan


  • Ashley Juavinett, PhD

Science Programs at Allen Institute