May 20, 2013

Allen Brain Atlas: Brain Explorer 2!

As a fan of new gadgets and software, especially those related to the brain, I was quite stoked to see that the Allen Institute for Brain Science / Allen Brain Atlas (Seattle, WA) came out with a new version of their Brain Explorer, which is a program that you download and you have the brain at your fingertips!  It is, quite simply, amazing. (link is at bottom of post).

For those who don't know, Brain Explorer (BE) is a software used to visualize neuroanatomical locations in the brain.  It's better than a regular book atlas in that you can move the brain around to get a 3D view.

Now, Brain Explorer 1 is pretty cool.  I've used it before to demonstrate where the hippocampal formation is in a previous blog post (Ingredients of a Hippocampus, bottom two figures).  It nicely shows what structures you want it to show in relation to other structures, and, in the program, you can move the brain around on an X-Y-Z axis to get a real 3D view of it -- enough with the Styrofoam models!  This is really helpful to visualize and spatially pin-point unfamiliar neuroanatomical areas.

What's the upgrade to Brain Explorer 2? A big download of greatness! Read on for that & some pictures...

Now, previously, you could only visualize where structures are, like where the hippocampus is in relation to the basolateral nucleus of the amygdala (left figure).  You can nicely see that those nuclei lay anterior to the (temporal) hippocampus.  Cool, eh?  Now you might be able to infer (but don't rely on inference!) something about function after seeing how close they are in the brain.

Another one: Within the hippocampus, there's a region called the dentate gyrus.  Along with the basolateral nuclei of the amygdala, there's also the anterior amygdala area.  Lying just in front of the hippocampus, is the medial septal area.  As you can see, it appears that there might be a nice little loop connecting the dentate, with the medial septum with the amygdala area; however, we don't know!

 Now, in BE 2, you can visualize afferent and efferent connections of specified brain areas!  For example, in this next figure, I am visualizing the efferent connections of the dentate gyrus.  You can view recurrent collaterals, its dense projections to CA3, but also find some rarer ones.  They may not be monosynaptic connections but may go through the subiculum and out to the other brain areas.  You can change the intensity (say you want to see only the really strong connections to the other area) and also the density (the number of the connections).  Here, I've scaled back on both parameters so you can see better.  Plus, you can color-code connections to show direct / indirect projects, where they originate, where they're going, and probably way more things that I have not discovered, yet.

Showing you the connectivity is HUGE.  I am used to scrambling to find books that tell me it, occasionally visiting Allen Brain Atlas online to see it, or sifting through some articles to see what the efferents and afferents of, say, the hippocamupus are that we know about today.  But, now, I can just visualize it with this program!

It's great fun. Try it out yourself.  It can get quite confusing because a lot of connectivity is known, but what do you expect with billions upon billions of connections?

Just a quick post to let all you neuro-nerds get your connectivity on!

Download Brain Explorer 2 -- yes, they have a Windows and a Mac version

If you don't feel like downloading this huge program, which it is, you can see the more text-based version on their website here ; just add a source and a target and vuala!


  1. Great post! I'm presenting the recent Nature paper (Oh et al) at a journal club next week, but I'd forgotten all about Brain Explorer, I'll be sure to include it.

    1. Thanks... and thanks for reminding me I still have a blog. hehe. I need to start writing again!