FIJI Syn_Bot Macro

This macro was developed by Cagla Eroglu's Lab at Duke University to count the number of colocalized synaptic puncta in fluorescence microscopy images. The macro and related experimental methods are thoroughly described in our BioRxiv paper. Briefly, neuronal synapses contain specific proteins in the presynaptic terminal that differ from those found in the postsynaptic terminal. At a neuronal synapse these terminals are ~50nm apart and thus immunohistochemical staining of a protein from each compartment will give a colocalized signal due to the resolution limits of traditional fluorescence microscopy. The primary components of analyzing these sorts of images include: reduction of noise thresholding of each image channel counting of puncta in each channel calculating which puncta colocalize with puncta in the other channel