A, 3-D reconstruction of the ventral brainstem at the level of the pons viewed from ventral, showing the ventral surface of the pons (transparent grey surface), the boundaries of the pontine nuclei (dark blue solid surfaces), the descending fiber tracts ('peduncles'; light blue solid surfaces) together with a reference frame showing the boundaries of the coordinate system (same as in C). B, photograph of the rat bainstem seen from ventral. C - E show the reference frame and relative coordinates (0 - 100 %) for the pontine nuclei from 3 standard angles of view. The thin curved lines represent the boundaries of the pontine nuclei.
Application of the pontine nuclei internal coordinate system: A cuboid bounding box is oriented along the long axis of the brain stem at the level of the pons, and adjusting the boundaries to fit the (histologically defined) rostral, caudal, lateral, medial and ventral limits of the pontine nuclei. The ventral surface of the corticobulbar and corticospinal tracts is used as an intermediate landmark (for details, see Brevik et al., 2001). The origin of the relative coordinate system is defined as the intersection of the three planes formed by the medial and rostral sides of the bounding box, and the plane halfway between the ventral and dorsal planes. Relative coordinates, from 0 to 100%, are defined from rostral to caudal, medial to lateral, and from 'central' (the plane halfway from ventral to dorsal) to ventral (100%) and dorsal (-100%) within the pontine nuclei. Bar 500 µm., A, anterior; D, dorsal; M, medial; R, rostral.
Brevik A, Leergaard TB, Svanevik M, Bjaalie JG Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualisation, and comparison of spatial distribution data. Anat Embryol. 2001; 204:319-32 (Special issue: Computational neuroanatomy -- Tools for single neuron, system, and brain region analysis, ed. J.G. Bjaalie)