Protocol for immunofluorescence staining and large-scale analysis to quantify microglial cell morphology at single-cell resolution in mice

Here, we present a protocol for quantifying microglial cell morphology at the single-cell level in mice. We provide comprehensive details, starting from optimal mouse brain dissection to computational analyses of up to 350 microglial cells per brain slice. Analyzing the morphology of microglial cells is essential for understanding their functional and activation states in different conditions, including during disease development and progression, as well as for assessing the effect of therapeutic interventions. For complete details on the use and execution of this protocol, please refer to Lind-Holm Mogensen et al.¹ and Fixemer et al.².