Quantification of the density and morphology of dendritic spines and synaptic protein distribution using Thy1-YFP transgenic mice

Synaptopathy, which encompasses morphological deficits and any abnormal protein distribution of synapses, is a critical feature of many neurological diseases. We here provide a protocol using mice stably expressing a Thy1-YFP transgene to assess synaptic features in vivo. We describe steps for recording the entire morphology of projection neurons using confocal microscopy based on YFP signals. We detail assessment of the density and size of dendritic spines and the distributions of synaptic proteins using ImageJ and statistical analysis using Prism. For complete details on the use and execution of this protocol, please refer to Shih et al. (2020).1