The CSF1R inhibitor PLX5622, but not PLX73086, crosses the blood–spinal cord barrier to deplete virtually all microglia. a–c Representative confocal images of CD11b and P2ry12 immunostainings showing the almost complete elimination of microglia in the spinal cord of naïve (uninjured) C57BL/6 mice after treatment with the CSF1R inhibitor PLX5622 compared to those fed PLX73086 or the control diet. Mice were killed after 21 days of treatment. d–h Quantification of microglia in the spinal cord of uninjured C57BL/6 mice treated with PLX5622, PLX73086 or the control diet (d), as well as at the lesion epicenter in Cx3cr1creER::R26-TdT mice killed at 1 (e), 7 (f), and 14 (g) days post-injury (dpi) (n = 4–5 mice per group/time point). i Quantification of the proportional area of spinal cord tissue permeable to FITC-conjugated lectin injected intravenously prior to tissue fixation. j Quantification of Ly6G+ neutrophils at the lesion epicenter at day 1 post-SCI in mice treated with either PLX5622, PLX73086, or the control chow (n = 4–5 per group). k Quantification of the number of granulo-myelomonocytic cells at the lesion epicenter at 7 and 14 dpi in Cx3cr1creER::R26-TdT::LysM-eGFP mice treated with either PLX5622, PLX73086, or the control diet (n = 4–5 mice per group/time point). For all injured mice, treatment was initiated 3 weeks before SCI and continued until sacrifice. Data are expressed as mean ± SEM. **p < 0.01, ***p < 0.001, ****p < 0.0001, PLX5622 or 1 dpi compared to the control group; and &&p < 0.01, &&&&p < 0.0001, PLX5622 compared with the PLX73086 group. Statistical analysis was performed using a one-way (d–g, i, j) or two-way (k) ANOVA followed by a Bonferroni’s post hoc test. Scale bar: (a–c, in c) 200 µm