Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates

J Neurosci Methods. 2015 Jan 30:240:161-9. doi: 10.1016/j.jneumeth.2014.11.005. Epub 2014 Nov 18.


Background: Assignment of anatomical reference is a key step in integration of the rapidly expanding collection of rodent brain data. Landmark-based registration facilitates spatial anchoring of diverse types of data not suitable for automated methods operating on voxel-based image information.

New tool: Here we propose a standardized set of anatomical landmarks for registration of whole brain imaging datasets from the mouse and rat brain, and in particular for integration of experimental image data in Waxholm Space (WHS).

Results: Sixteen internal landmarks of the C57BL/6J mouse brain have been reliably identified: by different individuals, independent of their experience in anatomy; across different MRI contrasts (T1, T2, T2(*)) and other modalities (Nissl histology and block-face anatomy); in different specimens; in different slice acquisition angles; and in different image resolutions. We present a registration example between T1-weighted MRI and the mouse WHS template using these landmarks and reaching fairly high accuracy. Landmark positions identified in the mouse WHS template are shared through the Scalable Brain Atlas, accompanied by graphical and textual guidelines for locating each landmark. We identified 14 of the 16 landmarks in the WHS template for the Sprague Dawley rat.

Comparison with existing methods: This landmark set can withstand substantial differences in acquisition angle, imaging modality, and is less vulnerable to subjectivity.

Conclusions: This facilitates registration of multimodal 3D brain data to standard coordinate spaces for mouse and rat brain taking a step toward the creation of a common rodent reference system; raising data sharing to a qualitatively higher level.

Keywords: Anatomical landmarks; Brain MRI; Landmark-based registration; Mouse; Rat; Waxholm Space.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Atlases as Topic*
  • Brain / anatomy & histology*
  • Databases, Factual
  • Histological Techniques*
  • Image Processing, Computer-Assisted / methods*
  • Imaging, Three-Dimensional / methods
  • Magnetic Resonance Imaging / methods*
  • Male
  • Mice, Inbred C57BL
  • Rats, Sprague-Dawley