Laser microscopy acquisition and analysis of premotor synapses in the murine spinal cord

Loss of synapses on spinal motor neurons is a major feature of several neurodegenerative diseases; however, analyzing these premotor synapses is challenging because of their small size and high density. This protocol describes confocal and Stimulated Emission Depletion (STED) imaging of murine spinal premotor synapses and their segment-specific quantification by confocal microscopy. We detail the preparation of spinal cord segments, followed by image acquisition and analysis. This protocol enables in-depth analysis of pathological changes in spinal premotor synapses during neurodegeneration. For complete details on the use and execution of this protocol, please refer to Buettner et al. (2021).