Establishing Common Coordinate Framework for Quantitative Cell Census in Developing Mouse Brains

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Abstract Brain development is characterized by a diverse set of cell types that are born and connected into rapidly growing complex 3D structures across time. Quantitative understanding of cell type composition and distribution in different brain regions provides fundamental knowledge about the building blocks of the brain and serves as an essential baseline with which to assess changes that may occur in brain disorders. The importance of this information is reflected by the significant effort among the neuroscience community, including the creation of the BRAIN Initiative Cell Census Network, to improve our understanding of cell type compositions across different brain regions in the adult mouse brain. These efforts have been made possible and accelerated by technological advances in high-resolution 3D imaging coupled with computational analysis methods that can reveal cell type arrangement in the brain with unprecedented detail. For example, we developed a quantitative brain mapping method to uncover the spatial arrangement of GABAergic neuron subtypes in the adult mouse brain. For the adult mouse brain, the Allen Common Coordinate Framework (CCF) currently serves as the standard atlas resource with which to map and integrate results from different studies. The neuroscience community, on the other hand, does not have similar CCFs for the developing mouse brain. The lack of developmental CCFs significantly hinders progress on cell type mapping of the developing mouse brain by limiting the reproducibility and integration of data from different studies. To address this deficiency, we have assembled a highly synergistic, multi-institutional team with complementary skill sets to create developmental CCFs with associated ontology and true 3D anatomical labels while also demonstrating the application of our CCFs by generating quantitative mappings of GABAergic neurons in the developing mouse brain. Toward this end, we will first utilize MRI and light sheet fluorescent microscopy (LSFM) to develop high-resolution developmental CCFs at seven different developmental time points (E11.5, E13.5, E15.5, E18.5, P4, P14, and P56) with different cellular features, including total cell density, myelination, and neurovasculature. Second, we will create true 3D anatomical labels for the CCFs based on cellular and gene expression information, and build a comprehensive ontology that will allow anatomical region changes to be linked across development and maturation. Lastly, we will generate a cellular-resolution quantitative map of GABAergic neuronal subtypes using tissue clearing and LSFM imaging in developing mouse brains, which will serve as a substantial data resource to accelerate developmental neuroscience discovery. The successful completion of this project will enable a broad field of scientists to leverage modern brain mapping technologies more effectively in studying the developing mouse brain.