3D Brain Anatomy: The Allen Brain Atlas

The Allen Brain Atlas is an incredible tool that lives up to the term “Big Data”.  The atlas combines neuroscience images from labs all over the world, and makes them easily accessible to everyone! I highly recommend it to anyone interested in the differences in gene expression throughout the different regions of the brain.  You can explore both a human and a mouse brain on their website!

NEW Mind Game – Brain Kick: The Motor Cortex

First, though, you might want to get up to speed on the major brain regions of the brain.  Brain anatomy can seem overly complex, but is a symptom of the many distinct regions that all work together to make sense of our world.  3D brain anatomy adds another layer of complexity!  Here are some of the best YouTube videos I have found for understanding the anatomy of the human brain, and also how brain anatomy relates to brain function.

For more advanced 3D brain anatomy visualization, scroll to the bottom of the page.

The Cortex and it’s Functions


The Brain’s Central Information Hub: The fornix and the corpus callosum



Detailed 3D brain anatomy: the Allen Brain Atlas

The Allen Brain Atlas was created by the Allen Institute for Brain Science.  It can take you through cross-sections of the human and mouse brain and also maps out genes across each brain region in the mouse brain.  This is the  best way to see the anatomy of the brain in 3D.  You can filter for gene expression, and compare across the thousands of experiments compiled in the app.

Introduction Video:



Advanced Usage Video:


If you’re more less interested in 3D brain anatomy and would rather explore the body, check out the The Database Center for Life Science  here.

That’s also where I got the spinning brain animation, licensed under CC Attribution-Share Alike 2.1 Japan.


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