Microglial removal by a second CSFR1 inhibitor, PLX5622, shows similar effects on excitatory circuit connectivity, compared with the PLX3397 treatment. A–C, Example cortical images of IBA1 staining of microglia in control cortex, PLX5622-treated cortex, and the cortex repopulated with microglia 1 week after stopping PLX5622 treatment. D–F, The averaged photostimulation-evoked EPSC input maps of visual cortex in control mice in D, PLX5622 treatment mice in E, and repopulated cortex in F. G, Photostimulation-evoked EPSC inputs of recorded layer 5 excitatory neurons differ significantly between control (n = 14 cells from 4 mice) and 3-week-long PLX5622-treated groups (n = 13 cells from 4 mice) (p = 0.027; Mann–Whitney U test). Also, the enhanced cortical connectivity of layer 5 excitatory cells (n = 5 cells from 4 mice) is reversed with microglia repopulation at a week after stopping PLX5622 treatment, as the total inputs of these cells did not differ from control cells in adult cortex (p = 0.559). Data are plotted as mean ± SEM. **p < 0.05. In addition to all-layers inputs, cortical layer specific inputs are also plotted.