A quantitative cholinergic and catecholaminergic 3D Atlas of the developing mouse brain

The complex organization of brain regions during development requires a three-dimensional approach to facilitate the visualization and quantification of dynamic changes taking place throughout this important period. Using the tissue clearing method combined with immunohistochemistry, three-dimensional (3D) lightsheet microscopy and a multiresolution registration technique, we provide the first 3D atlases of the main cholinergic (CH) and catecholaminergic (CA) systems in the mouse brain from embryonic day 12 (E12) to post-natal day 8 (P8). We report that in several brain structures, there is a logarithmic scale increase of choline acetyltransferase and tyrosine hydroxylase positive neurons from E18 to P8. In addition, a detailed voxel-wise analysis revealed abrupt modifications in the developmental trajectory of many brain structures during the transition from E18 to P0. Our atlases will not only facilitate developmental studies aimed at quantitatively determining the fate of CH or CA neurons in utero but also be used as an anatomical reference to quantify other neuronal populations present in the annotated regions. In the future, these maps will be a reliable tool to study developmental malformations associated with neurological and psychiatric disorders.