Waxholm Space atlas of the rat brain: A 3D atlas supporting data analysis and integration

Abstract

<title>Abstract</title> Volumetric brain atlases are increasingly used to integrate and analyse diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present the new Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource. This full brain atlas features annotations of 222 structures, of which 112 are new and 57 revised compared to previous versions. It maps in detail the cerebral cortex, hippocampal region, striatopallidal areas, midbrain dopaminergic system, thalamic cell groups, the auditory system and main fibre tracts. We document the criteria underlying the new annotations and demonstrate how the atlas and related tools and workflows can be used by neuroscientists to support interpretation, integration, analysis, and dissemination of experimental rat brain data.