Microglia cover the whole brain parenchyma, where each microglia cell occupies a fixed position and, through its projections, surveils its own territory (Kierdorf and Prinz, 2017). Genetic (Bruttger et al., 2015) or pharmacologic (Elmore et al., 2014) partial ablation of adult microglia is followed by a recovery of their number and coverage of the brain parenchyma, supporting a fundamental role of microglial spatial organization in local surveillance (Nimmerjahn et al., 2005). Neurological disorders, particularly Alzheimer’s Disease (AD), associate with dysfunctional microglia, which cluster around amyloid-BETA (ABETA) plaques. Moreover, we reported that blood vessels, which depend on microglia to function correctly (Zhao et al., 2018), are dysfunctional around ABETA plaques (Alvarez-Vergara et al., 2021), showing vascular scars. Neither the normal tiling of microglia nor their clustering in AD has been studied as complex 3D structures. A proper characterization of microglia organization and their relation with the vasculature is key to understand the physiological role of microglia and the mechanisms underlying neurological diseases. To achieve this aim, we performed tissue clearing of brain sections from wild-type and AD mice models, used to obtain high spatial resolution images from big volumes. These images are suitable for quantifying microglia 3D organization, for which we have designed a computational model using the mathematical concept of 3D Voronoi tessellation that captures 3D organization of microglia in the form of a “tiling scale”. This approach will allow us to quantify the disorganization associated with neurodegeneration and, more importantly, to characterize the initial events of ABETA deposition.