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

- 16 anatomical landmarks reliably recognized in T1, T2, and T2* mouse brain MRI.
- All landmarks identified in Nissl histology and block-face images from the mouse brain.
- Most landmarks identified in MRI and histological images from the rat brain.
- Guidelines for locating each landmark presented in the Scalable Brain Atlas.
- Facilitates landmark-based registration to Waxholm Space and thus worldwide datasharing.

BackgroundAssignment 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 toolHere 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).ResultsSixteen 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 methodsThis landmark set can withstand substantial differences in acquisition angle, imaging modality, and is less vulnerable to subjectivity.ConclusionsThis 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.