Stem cells have an intrinsic ability to produce daughter cells. As the organism ages, gut function declines, the stem cells become abnormal, and the cell surfaces in the gut do not regenerate efficiently. There is evidence of inflammation associated with injury accumulating in the gut. In vivo optical imaging and femtosecond laser ablation has enabled detailed studies of cellular dynamics in the gut of rodents. These imaging techniques revealed stem cells in the intestine reorganize to restore homeostasis after perturbation by laser ablation of a few cells at the base of the stem cell crypt. In this work we investigated the correlation between the damage in the crypts and the number of macrophages that penetrate the crypt epithelium and are inside the crypt as a result of an induced injury. Damage in the crypt was positively correlated with the area of macrophage processes invading into the crypt supporting the hypothesis.