Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in Mouse Visual Cortex

• DOI: 10.1016/j.celrep.2020.107682
• Publication Date: 2020-05-26T20:34:46Z
• Authors: Jun Ho Song; Woochul Choi; You-Hyang Song; Jae-Hyun Kim; Daun Jeong; Seung-Hee Lee; Se-Bum Paik
• Keywords: Brain atlas; Lateral geniculate nucleus; Brain mapping

Recent breakthroughs in neuroanatomical tracing methods have helped unravel complicated neural connectivity whole-brain tissue at single-cell resolution. However, most cases, analysis of brain images remains dependent on highly subjective and sample-specific manual processing, preventing precise comparison across sample animals. In the present study, we introduce AMaSiNe, software for automated mapping single neurons standard mouse atlas with annotated regions. AMaSiNe automatically calibrates misaligned deformed slice samples to locate labeled neuronal positions from multiple into standardized 3D Allen Mouse Brain Reference Atlas. We exploit high fidelity reliability investigate topographic structures feedforward projections lateral geniculate nucleus primary visual area by reconstructing rabies-virus-injected slices space. Our results demonstrate that distinct organization can be precisely mapped using AMaSiNe.