Fig 2: Repopulated microglia and brain-engrafted macrophages are not activated and phagocyte less synaptic compartments. a Experimental design for in vivo synaptosome phagocytosis assays. Injection of pre-stained synaptosomes was timed to be the same as previous experiments. Three days later, on day 36 after WBRT, ipsilateral hemispheres were harvested and used for engulfment measurement using FACS or Immunofluorescent staining. b FACS analysis result showing levels of microglia that engulfed pre-stained PSD-95 signals. c Representative images showing engulfment of pre-stained synaptosomes by microglia near injection site. White arrows point at microglia that have engulfed pre-stained synaptosomes. scale bar = 20 µm. d Dot plot to show quantification result of synaptosome engulfment by immunofluorescent staining. e–g Dot plots showing cell surface C5aR, and intracellular CD68 and CD107a protein levels in microglia and BEMs. Statistical analyses were performed using two-way ANOVA with Tukey’s multiple comparisons test. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001. N = 5–6