Fig. 1: P2RY12⁺/CD206^-/CX3CR1-eGFP^high ramified microglia are the myeloid cell localized to capillaries.

a–c 3D volumetric reconstructions from a 20X confocal image of somatosensory cortex in CX3CR1-eGFP mice, where a is the composite image, b the CX3CR1-eGFP channel, and c the Iba1 channel (purple). d Scatter dot plot showing averaged values of the percentage of CX3CR1-eGFP⁺ cells that are also Iba1⁺. n = 12 values across 3 mice. e Scatter dot plot showing the raw data used to generate the graph in (d). These 12 values represent 1 brain slice, 4 slices per mouse, across 3 mice. f 3D volumetric reconstructions from a 63X confocal image showing a microglial cell next to a perivascular macrophage (PVM). White lines indicate a blood vessel track showing the perivascular location of these cells. 3D volumetric reconstructions from a 63X confocal image showing the CD206 channel (magenta) in (g), the P2RY12 channel (blue) in (h), the nuclear label (grey) in i, the composite in (j), and the eGFP channel in (k). The arrowhead denotes the CX3CR1-eGFP^high, P2RY12^positive, CD206^negative microglia. The arrow denotes the CX3CR1-eGFP^low, P2RY12^negative, CD206⁺ PVM. l Bar graph quantifying the mean CX3CR1-eGFP intensity of PVMs and microglia. n = 67 cells averaged across 3 mice. Two-tailed, paired t-test, p < 0.0027. m Bar graph quantifying the vascular coverage of eGFPhigh microglia along specific vessel types. Brown-Forsythe and Welch ANOVA tests with Dunnett’s T3 multiple comparison test. Multiplicity-adjusted p values include arteriole vs. venule, p > 0.9286; arteriole vs. capillary, p < 0.0194; venule vs. capillary, p < 0.0301. n = 43, 20× somatosensory cortex images/5 mice. n Bar graph quantifying vascular coverage of CD206+ cells along specific vessel types. Brown-Forsythe and Welch ANOVA  tests with Dunnett's T3 multiple comparison test. Multiplicity-adjusted p values include arteriole vs. venule, p <0.8215; arteriole vs. capillary, p < 0.3081; venule vs. capillary, p < 0.4267. n = 43, 20X somatosensory cortex images/5 mice. For m, n, area coverage was normalized to total area of each vessel type per image. o, p Pie charts depicting the percentage distribution of CX3CR1-eGFP⁺ microglia or CD206⁺ border-associated macrophages along arterioles, venules^, and capillaries- respectively. Data presented as mean ± s.e.m. LUTs have been adjusted in shown images. Source data are provided as a source data file.