Atlas Annotation

Over the years the Allen Brain institute has constantly improved and updated their brain region annotation atlases. Unfortunately the old annotation atlases are not always aligned with the new ones. For example, the CCFv2 annotations and the Nissl volume are not compatible with the CCFv3 annotation and the corresponding average brain volume. This package proposes a number of methods for deforming the Nissl volume and the CCFv2 annotations in order to re-align them to CCFv3.

Contents

• Installation
  • Python Version and Environment
  • Install “Atlas Annotation”
• Data
  • Remote Storage Access
  • Get the Data
• Examples
  • Registration
  • Image Manipulation
  • Utilities
  • Concrete examples
• Notebooks, Widgets, and Experiments

API Reference

• atlannot package
  • Subpackages
  • Submodules
  • Module contents