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

Cell Rep. 2020 May 26;31(8):107682. doi: 10.1016/j.celrep.2020.107682.


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.

Keywords: Allen Mouse Brain Reference Atlas; automated brain mapping; brain image registration; brain slice calibration; mouse brain slice; retrograde tracing; single-neuron mapping; standard 3D brain atlas; topographic projection; visual cortex.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Brain / anatomy & histology*
  • Brain / diagnostic imaging*
  • Brain Mapping / methods*
  • Imaging, Three-Dimensional
  • Mice
  • Neurons / metabolism*