Abstract Key functions of Ca 2+ signaling in rodent microglia include monitoring the brain state or the surrounding neuronal activity and sensing the danger or damage in their vicinity. Microglial Ca 2+ dyshomeostasis is a disease hallmark in many mouse models of neurological disorders but the Ca 2+ signal properties of human microglia remain unknown. Using a newly developed toolbox, we analyzed in situ Ca 2+ signaling of decades-old human cortical microglia. The data revealed marked compartmentalization of Ca 2+ signals, with signal properties differing across the compartments and resident morphotypes. The basal Ca 2+ levels were low in ramified and high in ameboid microglia. The fraction of cells with ongoing Ca 2+ signaling, the fraction and the amplitude of process Ca 2+ signals and the duration of somatic Ca 2+ signals decreased when moving from ramified via hypertrophic to ameboid microglia. In contrast, the size of active compartments, the fraction and amplitude of somatic Ca 2+ signals and the duration of process Ca 2+ signals increased along this pathway.