The recent past has seen major advances in our understanding of the complexity of the macrophage landscape of the brain. Specifically, bulk and single-cell transcriptomics and advanced cytometry have defined distinct brain macrophage populations in the parenchyma and border locations, such as the perivascular niches, the meninges and choroid plexus. Likewise, using the mouse as a model system we have come to appreciate that brain macrophages activate distinct response modules when triggered in pathology, including pro-inflammatory and dampening signatures. Interference with these modules bears potential for future therapies. However, rationale approaches towards this goal will require a better definition of the in vivo impact of these response modules with respect to their imbedding in the neuronal and glia network, as well as emerging task division within the brain macrophage compartment in physiology and pathophysiology. We recently established novel binary transgenic models based of ‘split Cre’ fragments that allow dissecting functions of brain macrophage subpopulations. Here, we propose to use these newly developed tools to investigate contributions of various brain macrophages to CNS physiology and pathophysiology.