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Updated: Dec 20, 2025
Large-scale Three-dimensional Imaging of Cellular Organization in the Mouse Neocortex
Published on: September 5, 2018
Precise Mapping of Single Neurons by Calibrated 3D Reconstruction of Brain Slices Reveals Topographic Projection in
Jun Ho Song1, Woochul Choi2, You-Hyang Song3
1Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea; Information and Electronics Research Institute, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.
Abstract:
Recent breakthroughs in neuroanatomical tracing methods have helped unravel complicated neural connectivity in whole-brain tissue at single-cell resolution. However, in 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 of single neurons in the standard mouse brain atlas with annotated regions. AMaSiNe automatically calibrates misaligned and deformed slice samples to locate labeled neuronal positions from multiple brain samples into the standardized 3D Allen Mouse Brain Reference Atlas. We exploit the high fidelity and reliability of AMaSiNe to investigate the topographic structures of feedforward projections from the lateral geniculate nucleus to the primary visual area by reconstructing rabies-virus-injected brain slices in 3D space. Our results demonstrate that distinct organization of neural projections can be precisely mapped using AMaSiNe.
