To better characterize the patterns of activation of peri-infarct microglia in photothrombotic stroke and the consequences of minocycline treatment, we measured two aspects of Iba1 immunolabeling: (i) the “circularity” of labeled cells, which is increased as a result of the morphological changes associated with activation; (ii) the percentage of total area occupied by Iba1 immunolabeling (subsequently described as “area fraction”), which in the peri-infarct tissue predominantly detects alterations in microglial numbers arising from the balance between cell migration, death, and proliferation. Here, AIF1 is linked to stroke disorder.