The most reliable is direct morphometry by using EM. Worth the effort.

George

Thanks George, We want to analyze the effect of drugs so I guess EM would cost a lot for our case, is it better to use IF using pre- and post synaptic markers? Is it better to do count the spines as well?

It be simple, you could screen with synaptophysin to start.

Or PSD-95 as postsynaptic marker

Or FM1-43 to label actived synapse after high potassium bath.

As suggested previously also, EM based morphometry would be the most accurate way of counting synapses, however, it may not be very cost effective.

ICC/IF is a less expensive/less time consuming approach and you should be able to repeat the staining a couple of times to check the reproducible of your results. As far as the various synaptic markers are concerned, at Novus, we suggest the following markers for pre-synaptic, post-synaptic and synaptic vesicles analysis:

1.       Synapsin I Antibody [NB300-104] pre-synaptic marker http://www.novusbio.com/Synapsin-I-Antibody_NB300-104.html

2.       Synaptophysin Antibody [NB300-653] pre-synaptic marker http://www.novusbio.com/Synaptophysin-Antibody_NB300-653.html

3.       PSD-95 Antibody (6G6-1C9) [NB300-556] post-Synaptic Marker http://www.novusbio.com/PSD-95-Antibody-6G6-1C9_NB300-556.html

4.       VAMP2 Antibody [NBP2-24599] Synaptic Vesicles Marker http://www.novusbio.com/VAMP-2-Antibody_NBP2-24599.html