Cx3cr1-iCre mice are generated using gene editing technology to replace the coding sequence (CDS) region of the endogenous mouse Cx3cr1 gene with an improved Cre recombinase (iCre) expression element. This results in an expression pattern of Cre recombinase that is similar to that of the endogenous gene. When these mice are crossed with mice containing a loxP site-flanked sequence, Cre recombinase-mediated recombination leads to deletion of the flanked sequence in brain microglia and macrophages in other parts of the offspring mice.