I have done some loss of function experiments in primary hippocample neurons. The neurons were transduced with a lentivirus having a GFP reporter. The neurons were further stained with postsynaptic (PSD95- Alexa 546) and presynaptic (Synapsin1- Alexa 633) proteins. We are trying to quantify synapse density in transduced neurons, considering one synapse as the colocalisation of Red, far-red and Green channel. I have tried it in Fiji (another version of ImageJ) but I am getting stuck in particle analysing step. Can anyone suggest of other ways to do it?