Automated 3-D mapping of single neurons in the standard brain atlas using single brain slices

Recent breakthroughs in neuroanatomical tracing methods have helped unravel complicated neural connectivity in whole brain tissue at a single cellular resolution. However, analysis of brain images remains dependent on highly subjective manual processing. In the present study, we introduce AMaSiNe, a novel software for automated mapping of single neurons in the standard mouse brain atlas. The AMaSiNe automatically calibrates alignment angles of each brain slice to match the Allen Reference Atlas (ARA), locates labeled neurons from multiple brain samples in a common brain space, and achieves a standardized 3D-rendered brain. Due to the high fidelity and reliability of AMaSiNe, the retinotopic structures of neural projections to the primary visual cortex (VISp) were determined from single and dual injections of the rabies virus onto different visual areas. Our results demonstrate that distinct retinotopic organization of bottom-up and top-down projections could be precisely mapped using AMaSiNe.