Cell quantifications

To assess the density of cells, the number of Iba1⁺ CD206⁻ (microglia) or CD206⁺ cells (pvMΦ and mMΦ) were quantified on a fluorescence microscope (BZ-X810). Microglia and pvMΦ were normalized to the area of the region of interest and expressed as cells / mm². mMΦ were normalized to the length of the leptomeninges indicated by collagen IV immunofluorescence and finally expressed as cells/mm². At least three sections of a minimum of four mice were used for each analysis. For morphological change analysis, microglia images were captured using a confocal laser scanning microscope (LSM900, Carl Zeiss) and were analyzed using IMARIS software (Version 10.0, Oxford Instrument). To access morphological complexity, Sholl Analysis was performed using filament reconstruction mode in IMARIS. The intensity of microglial AXL was calculated as the summation of AXL fluorescence intensity within CD11b⁺ cells using IMARIS by creating a 3D surface rendering of individual microglia.