Digital Brain Atlasing

From here it is easy to see that – assuming no distortion in the shape of the brain in the coronal sections – if we stacked and aligned these images we could recover the 3D shape of the brain. This is one approach to 3D atlas construction from 2D data.

What is a 3D digital brain atlas?

1. Volumetric data that provides the brain shape.
   1. The volume is composed of discrete elements (voxels) on a regular grid at 3D locations.
   2. Other modalities mapped to that shape.
2. List of brain regions.
   1. An ID for each region and hierarchical information.
3. Parcellation/delineation of brain regions.
   1. Each voxel has one or more IDs depending on hierarchy and purpose
4. An anatomical coordinate system.
   1. To specify brain orientation, specify locations, and take measurements.

The traditional book form atlases have a long history and still make for a useful reference. Since they are 2D by nature they match well with the viewing of histological section images. But the real brain is a 3D object – if we move to 3D we can view and understand its true shape. Most digital atlases are 3D atlases. We can generate 2D section images by virtually slicing at any angle through the 3D brain volume. With a digital atlas we can map data from many sources into a common 3D space defined by the atlas. With a digital atlas we can do things computationally, which means we can also try to automate our analysis.

Essentially, a 3D atlas can be used to organize neuroscience information from a variety of sources!

Coordinate Systems

When dealing with medical image data we can consider world, anatomical, and image coordinate systems and their relationships. Two common anatomical coordinate systems are the LPS = {from right towards left, from anterior towards posterior, from inferior towards superior} and RAS = {from left towards right, from posterior towards anterior, from inferior towards superior} systems. For example, the R, A, & S axes correspond with the positive  X, Y, & Z axes. We can use stable features of the brain, such as the anterior and posterior commissures, and the mid-sagittal plane (that divides the two hemispheres) to (re)orient the brain orientation to align with these systems.