Co-registration of mouse cortical structures between in vivo and ex vivo images using tangential sectioning

Co-registration of neuronal structures between in vivo and ex vivo imaging is necessary to study structure-function correspondence in the mammalian brain. Here we describe a protocol based on tangential sectioning of the mouse brain. This protocol aligns in vivo two-photon calcium imaging volumes with ex vivo confocal imaging volumes and registers the same cortical structures in both volumes. This approach allows detailed analysis of the corresponding function and structure of these entities. For complete details on the use and execution of this protocol, please refer to Zhuang et al. (2021).