Connecting the Dots in your Brain

A new era in neuroscience is upon us: you can now cut through a brain and expose its different parts without ever leaving your computer.  Online brain atlases are collections of many thin slices through brain tissue that are stained to show specific brain structures.  Atlases like BrainNavigator (available online at http://www.brainnav.com/home) and the Allen Brain Atlas (http://www.brain-map.org/) are organized primarily to be researcher-friendly, but they are straightforward enough for students to use.  Presently, there are brain atlases for human, rhesus monkey, mouse, and infant mouse brains.  Each brain atlas is organized by animal, brain structure, and areas that express related genes.  By combining these different functions, researchers can see where in the brain particular genes are expressed and relate them to each other in real, 3D space.

To make a brain atlas, scientists averaged super-thin 2D slices of brains from many subjects and stacked them together to make a 3D model of a brain.  Since each individual brain is slightly different, some generalization has to be made when determining the level of detail of the brain. Apart from genetic differences, each person’s brain is slightly different just by having lived a different life and having different experiences.  Everyone’s brain has slightly different connections, or synapses, that represent differing memories, beliefs, and intelligence levels (Seung).  With the right stain, connections between neurons can be mapped, too.  Like dropping watercolor paint on a napkin traces the pattern on the paper, cell staining methods reveal patterns in the long projections between neurons.  Even though some slight differences exist, scientists assume that the major tracts of connections between brain structures that are responsible for thought and sensation are essentially the same in everyone.  By staining the interior of specific neurons or groups of neurons and seeing where the stain travels, scientists can show what brain regions interconnect, and how strongly they are coupled.  This principle forms the basis for building a connectome, which is a map of all the connections between brain cells.  Brain atlases are not detailed enough at this stage to show all the connections in the human brain yet.  Once the connectome is fully mapped, one great application of the brain atlases would be to overlay major connecting tracts of axons into the 3D brain atlases already available.  Scientists can then infer what might be responsible for mental deficits in people with brain damage (Toga et al.)

A brain atlas with major connections from the connectome would be supremely useful for scientists.  The ultimate goal of mapping the connectome is to superimpose the connections between neurons on the brain navigation maps already in use.  Since we can’t often cut open live human brains to access these deeper regions of the brain, the 3D Brain Navigator provides an ideal alternative for scientists and students to explore the impacts of various types of brain damage (Toga et al.).  When planning experiments, a standard brain atlas would be useful as well.  To measure electrical activity in live neurons, neuroscientists use tiny electrodes stuck in brain cells.  To reach deeper cells, though, the electrode must pass through several layers of cells on the surface.  By manipulating a 3D image of the brain in BrainNavigator, scientists can plan where to stick the electrode with minimal damage to other parts of the brain.  It is also difficult to judge electrode depth in a live brain.  With BrainNavigator, scientists can calculate the estimated depth of their target structure to eliminate a lot of guesswork when they are in the brain (Hamilton). 

It’s simple to look at 3D brain atlases.  Downloading the software takes about a minute, and the picture quality is good.  By selecting any number of specific structures, it’s easy to compare spatial relationships and relative sizes of parts of the brain. With the addition of connections between neurons, online brain atlases will give the best possible picture of brain anatomy to date.