Synapse density analysis was performed on three-month-old hiPSC neurons cocultured with wildtype human astrocytes (Sciencell) on acid-etched glass. Manual counts of synaptic density were done in three steps using NIH ImageJ. First, the colocalization plugin was used to identify colocalization of VGLUT1 and PSD95. Second, the particle analysis function was used to restrict size 50-infinity. Third, dendrites were traced using the NeuronJ plugin. The mask generated by particle analysis was overlayed on the trace generated by NeuronJ and synapses were manually counted.
