aMAP is a validated pipeline for registration and segmentation of high-resolution mouse brain data

Nat Commun. 2016 Jul 7:7:11879. doi: 10.1038/ncomms11879.


The validation of automated image registration and segmentation is crucial for accurate and reliable mapping of brain connectivity and function in three-dimensional (3D) data sets. While validation standards are necessarily high and routinely met in the clinical arena, they have to date been lacking for high-resolution microscopy data sets obtained from the rodent brain. Here we present a tool for optimized automated mouse atlas propagation (aMAP) based on clinical registration software (NiftyReg) for anatomical segmentation of high-resolution 3D fluorescence images of the adult mouse brain. We empirically evaluate aMAP as a method for registration and subsequent segmentation by validating it against the performance of expert human raters. This study therefore establishes a benchmark standard for mapping the molecular function and cellular connectivity of the rodent brain.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Atlases as Topic
  • Benchmarking
  • Brain / anatomy & histology*
  • Brain / diagnostic imaging
  • Brain / physiology
  • Connectome / methods*
  • Humans
  • Image Processing, Computer-Assisted / statistics & numerical data*
  • Imaging, Three-Dimensional / methods
  • Imaging, Three-Dimensional / statistics & numerical data*
  • Magnetic Resonance Imaging / methods
  • Magnetic Resonance Imaging / statistics & numerical data*
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Software