Putative synapse locations were obtained by Anish Simhal.
Around each synapse across each channel the sum of pixel intensities within an 11x11x11 cube are calculated to produce a feature vector. These feature vectors are combined into a data matrix. We replace the DAPI channels with their first principal component. The data matrix is then z-scored before running it through meda.
We did this for samples of size 1,000 and 10,000.