Establishing neuroanatomical correspondences across mouse and marmoset brain structures

Abstract

Interest in the common marmoset is growing due to evolutionarily proximity to humans compared to laboratory mice, necessitating a comparison of mouse and marmoset brain architectures, including connectivity and cell type distributions. Creating an actionable comparative platform is challenging since these brains have distinct spatial organizations and expert neuroanatomists disagree. We propose a general theoretical framework to relate named atlas compartments across taxa and use it to establish a detailed correspondence between marmoset and mice brains. Contrary to conventional wisdom that brain structures may be easier to relate at higher levels of the atlas hierarchy, we find that finer parcellations at the leaf levels offer greater reconcilability despite naming discrepancies. Utilizing existing atlases and associated literature, we created a list of leaf-level structures for both species and establish five types of correspondence between them. One-to-one relations were found between 43% of the structures in mouse and 47% in marmoset, whereas 25% of mouse and 10% of marmoset structures were not relatable. The remaining structures show a set of more complex mappings which we quantify. Implementing this correspondence with volumetric atlases of the two species, we make available a computational tool for querying and visualizing relationships between the corresponding brains. Our findings provide a foundation for computational comparative analyses of mesoscale connectivity and cell type distributions in the laboratory mouse and the common marmoset.

Fig. 1.

A. A sagittal view of the Allen mouse reference brain with CCF3 segmentation. B. High-level branches of the Allen atlas hierarchy. C. A sagittal view of the Brain/MINDS marmoset reference brain with refined segmentation. D. High-level branches of the marmoset brain atlas hierarchy. Color coded nodes in the trees: red: cerebrum/telencephalon; blue: interbrain/diencephalon; yellow: brain stem; green: pons; purple: midbrain; magenta: medulla oblongata; brown: cerebellum.

Fig. 2.

A. The Allen atlas hierarchy superimposed on marmoset leaf-level regions (red). B. The RIKEN atlas hierarchy superimposed on mouse leaf-level regions (red).

Fig. 3.

A. Fractional volume of some leaf-level cortical structures in the mouse (not filled bars) and marmoset (filled bars) cortices. Arrows point to retrosplenial, temporal and parietal association cortices. B. Sample cortical regions’ fractional volume in cortex in mouse and marmoset (left), in mouse reference brain and Allen atlas hierarchy (middle), in marmoset reference brain and RIKEN atlas hierarchy (right). For a full list of abbreviations and brain regions in both species, refer to Supplementary Table 1.

Fig. 4.

A. Hierarchical trees of Allen (top) and RIKEN (bottom) brain atlases taken from the Brain Architecture Portal (http://brainarchitecture.org). B-D. Sample outputs of the visualization tool for motor cortical areas. B. 3D views of the mouse reference brain (left, 100 μm isotropic) and marmoset reference brain (right, voxel size 240×240×224 μm³) with the primary and secondary motor areas labeled in blue and orange, respectively. Note that only 3 out of the 8 leaf-level structures in the marmoset brain are shown in the titles. C. Sample coronal sections through motor cortices (color labeled) in mouse (left) and marmoset (right). D. Primary (blue) and secondary (orange) motor cortex areas in the mouse (left) and marmoset (right) atlas hierarchies.