The protocol was created to calculate the percentage of synapses that contains clusters of a peptide. It first defines synapses by isolating the colocalization between a presynaptic and a postsynaptic marker. Then, clusters of the peptide (3rd channel) are defined using thresholder and ROI watershed plugin. The protocol then calculate the percentage of synapses that contains clusters of the peptide.
Users must defines the parameters in each plugins according to their images (level of the threshold, spot detector, colocalization studio…).