DeveloperGuide.md

Preprocessing

map from prep a to prep b

Register Annotated Brains

align_annotated_brains_v6.ipynb

This uses the class Aligner.

Build/Update Atlas from globally aligned brains.

• Compute mean centroid of each structure in co-aligned space.
• Rectify co-aligned space to define the canonical atlas space.
• Compute mean shape of each structure (only do this at initialization, not in later updates)