Multimodal 3D mouse brain atlas framework with skull-derived coordinate system

Abstract Magnetic resonance imaging and light-sheet microscopy enable non-disruptive 3-dimensional imaging of mouse brains. A combination of complementary information from these modalities is essential for studying disease progression, developing effective therapies, and translating findings into clinical procedures. Although both technologies rely on atlas mapping for quantitative analysis, integration of data from these modalities has been challenging due to morphological differences between brain samples. In this study, we have developed a multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen’s Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The coordinate system allows users to precisely translate spatial positions from ex vivo modalities to locations in a living mouse brain. Consequently, the atlas resource, which is accessible via NeuroPedia, will allow the combination of results obtained from in vivo and ex vivo mouse brain measurements and accurate navigation in the brain during stereotaxic interventions.