Fig. 1: Microglia regulate basal cerebral blood flow and neurovascular coupling.

a Schematics for longitudinal comparison of CBF reactivity in the same mouse: the baseline, the microglia-depletion state after PLX3397 chows, and microglia-repopulation after returning to normal chows. b Immunohistochemistry images showing IBA1⁺ cells co-stained with DAPI in baseline, PLX and repopulation conditions. Bar = 400 μm. Higher magnification images are shown below. Bar = 150 μm. c Quantification of IBA1⁺ cells in (b). Each dot indicates an individual mouse. n = 5 mice for each condition. Data are presented as mean ± s.e.m. Source data are provided as a Source Data file. d Laser speckle contrast imaging was used to measure the CBF responses to whisker stimulation across an intact skull (Created in BioRender. Lab, K. (2025) https://BioRender.com/r39k612). e Left, Representative images of mouse CBF changes pre-, during and post-whisker stimulation. Bar = 4 mm. Red square boxes (enlarged on Right), denote the region for CBF quantification in whisker stimulation. Bar = 1 mm. f Representative real-time CBF responses to 5 Hz whisker stimulation (marked by the bar; 30 s). g–i Comparison of the basal CBF (g), whisker stimulation-induced CBF changes (h) and CBF plateau (i) at the baseline, PLX-treated, and repopulation states. Each dot indicates an individual mouse. n = 8 mice for each condition. Data are presented as mean ± s.e.m. p-values were determined by one-way ANOVA for paired samples with Tukey post hoc test. Source data are provided as a Source Data file. j Representative real-time CBF responses to 8% CO₂ hypercapnia stimulation (marked by the bar; 5 min). k Comparison of the hypercapnia-induced CBF changes at the baseline, PLX-treated, and repopulation states. Each dot indicates an individual mouse. n = 8 mice for each condition. Data are presented as mean ± s.e.m. p-values were determined by one-way ANOVA for paired samples with Tukey post hoc test. Source data are provided as a Source Data file. l Scheme of CBF evaluations at the baseline (1st CBF) and tamoxifen-induced acute microglia ablation (2nd CBF) in Cx3cr1-CreERT2;R26R-DTA mice. m, n CBF changes to whisker stimulation (m) and hypercapnia (n) at the baseline and after tamoxifen (TAM)-induced acute microglia ablation in the same mouse. Each line tracks the changes in CBF response in the same mouse. Each dot indicates an individual mouse. n = 5 mice for each condition. p-values were determined by paired t-test two sided. Source data are provided as a Source Data file. o Representative micrographs showing different responses to whisker stimulation in the pial artery (white lines, dilation) and the pial vein (blue lines, no visible dilation) above the contralateral barrel cortex. Bar = 30 μm. p Comparison of whisker stimulation-induced dilation of a pial artery in the mice under control chow or PLX3397 chow. Each dot indicates an individual mouse. n = 10 mice for control group. n = 9 mice for PLX group. p-values were determined by unpaired t-test two sided. Data are presented as mean ± s.e.m. Source data are provided as a Source Data file. q Representative micrographs showing dilation of the penetrating artery in the barrel cortex after whisker stimulation. Bar = 10 μm. r Comparison of whisker stimulation-induced dilation of penetrating artery in barrel cortex in the mice under control chow or PLX3397 chow. Each dot indicates an individual mouse. n = 5 mice for each group. p-values were determined by unpaired t test two sided. Data are presented as mean ± s.e.m. Source data are provided as a Source Data file. s Schematics for the generation of transgenic mice expressing microglia-specific Gq-DREADD and Gi-DREADD for compound 21-mediated chemogenetic manipulation (Created in BioRender. Lab, K. (2025) https://BioRender.com/y79i174). t Representative micrographs showing CBF baseline and compound 21 (C21)-induced CBF change in microglia-specific Gq-DREADD expression mice. Bar = 5 mm. u Real-time CBF responses after intraperitoneal injection of C21 (arrow) in mice of the labeled genotype. v Summary of microglia Gq or Gi activation-induced CBF changes in different conditions. Each dot indicates an individual mouse. n = 7 mice for Gq⁺Cre⁺C21⁺ group; n = 6 mice for Gi⁺Cre⁺C21⁺ group; n = 6 mice for Gq⁺Cre⁻C21⁺ group; n = 5 mice for Gq⁺Cre⁻C21⁺ group. Data are presented as mean ± s.e.m. Source data are provided as a Source Data file. w Comparison of the CBF changes to whisker stimulation in microglia-Gq mice and WT littermates with or without the C21 injection. Each dot indicates an individual mouse. n = 7 mice for Gq⁺C21⁻ group; n = 7 mice for Gq⁺C21⁺ group; n = 6 mice for Gq⁻C21⁻ group; n = 6 mice for Gq⁻C21⁺ group. ***p < 0.0001 as determined by paired t-test two sided. Source data are provided as a Source Data file.