Fig. 5: The content and creation of the WHS atlas of the Sprague Dawley rat brain version 4.

a, The basic elements of the WHS rat brain atlas. The atlas consists of volumetric reference data acquired by MRI (a1), a coordinate system with its origin based on internal landmarks (a2), an annotation set of 222 brain regions (a3) and a hierarchically organized terminology (a4). b, The three-step workflow for creating the atlas annotation set. First, the reference data (b1) is used for boundary interpretation and initial annotations. Second, the reference data and supplementary information, such as expert-drawn 2D annotations (b1′) and histological data³⁹ (b1″), are used for evaluation and adjustment. Third, the brain region annotations are validated. The annotations are always defined directly in the reference dataset, while different types of supplementary information, spatially registered to the MRI reference dataset, were used depending on the needs for defining a given brain region annotation. In most cases, the annotations were based on a mix of information (orange and red arrows). Note that the cyto- and myeloarchitecture sections (b1′) are not perfectly matching the reference data (b1 and b1′) since they are from a different brain. aci, anterior commissure, intrabulbar part; aca, anterior commissure, anterior limb; acp, anterior commissure posterior limb; T2*, T2*-weighted (gradient echo) image; DTI, diffusion tensor image; DWI, diffusion weighted image; LPMC, lateral posterior thalamic nucleus, mediocaudal part; LPLC, lateral posterior thalamic nucleus, laterocaudal part; DLG, dorsal lateral geniculate nucleus; Sg, medial geniculate body, suprageniculate nucleus; MGD, medial geniculate body, dorsal division; Po, posterior thalamic nucleus; MGM, medial geniculate body, medial division; MGV, medial geniculate body, ventral division; VLG, ventrolateral geniculate nucleus. Scale bar 500 µm.