An active texture-based digital atlas enables automated mapping of structures and markers across brains

Nat Methods. 2019 Apr;16(4):341-350. doi: 10.1038/s41592-019-0328-8. Epub 2019 Mar 11.


Brain atlases enable the mapping of labeled cells and projections from different brains onto a standard coordinate system. We address two issues in the construction and use of atlases. First, expert neuroanatomists ascertain the fine-scale pattern of brain tissue, the 'texture' formed by cellular organization, to define cytoarchitectural borders. We automate the processes of localizing landmark structures and alignment of brains to a reference atlas using machine learning and training data derived from expert annotations. Second, we construct an atlas that is active; that is, augmented with each use. We show that the alignment of new brains to a reference atlas can continuously refine the coordinate system and associated variance. We apply this approach to the adult murine brainstem and achieve a precise alignment of projections in cytoarchitecturally ill-defined regions across brains from different animals.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Brain / anatomy & histology
  • Brain / diagnostic imaging*
  • Brain Mapping / methods*
  • Brain Stem / diagnostic imaging
  • Computational Biology / methods*
  • Image Processing, Computer-Assisted / methods*
  • Machine Learning
  • Magnetic Resonance Imaging
  • Male
  • Mice
  • Mice, Inbred C57BL
  • Motor Neurons
  • Neuroanatomy
  • Neurons
  • Probability
  • Spinal Cord / diagnostic imaging