Tissue macrophages in the central nervous system (CNS), including parenchymal microglia and non-parenchymal meningeal, perivascular and choroid-plexus macrophages, are important for the development and homeostasis of the healthy CNS. Also, there is a growing body of evidence that microglia plays a key role in neurological and psychiatric disorders. The aim of our study was to understand the spatial arrangement of these cells in the CNS and its change after peripheral inflammation, by using a genetic tool that can label Iba1-positive CNS macrophages (Nakayama et al., Nat Commun, 2018). Tissue clearing and 3D-imaging technique (CUBIC) clarified an activation of microglia in the spinal cord and brain region after peripheral inflammation.