allen brain atlas


Background: In our recent issue, Hongkui Zeng and colleagues present the first brain-wide, mesoscale connectome for a mammalian species — the laboratory mouse — based on cell-type-specific tracing of axonal projections.

Design challenge: This amazing visualization obviously took a lot of work. This from Zeng on how it was created:

“This image shows the brain-wide axonal projection patterns from 21 distinct cortical areas (differentially color coded). This represents 21 mapping experiments selected from the Allen Mouse Brain Connectivity Atlas to sample the entire cortex. High resolution images from each experiment are quantified and co-registered into a common 3-D reference space using automated methods. Each of the viral tracer injection sites (source regions), which are in the right hemisphere only, is indicated by a cluster of round spheres. The connectivity paths are created by virtual tractography, namely, each sampled target location (squares) is computationally traced through the highest signal density path back to the injection site. The 3-D visualization is generated using the Brain Explorer® program.”

-Kelly Krause