Enhanced and unified anatomical labeling for a common mouse brain atlas

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 and
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, here we adopt the FP labels
into the CCF to merge two 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.