Enhanced and unified anatomical labeling for a common mouse brain atlas

Uree Chon,Daniel J Vanselow,Keith C Cheng,Yongsoo Kim

doi:10.1038/s41467-019-13057-w

Abstract

Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.

Highlights

Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context
We present highly segmented open source anatomical labels on the Allen common coordinate framework (CCF), which are accessible via our website
Our labels are largely based on FP labels with cortico-striatal projection based detailed segmentations in the dorsal striatum and further segmentations based on fluorescent transgenic markers

Summary

Introduction

Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. The two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. Our digital map data is freely available for viewing and downloading from our web-based atlas implementation at http://kimlab.io/brain-map/atlas/

Methods

Results

Conclusion