Hi Arya,

you could try PSD95 (post synaptic density) antibody.

If you need to count pre-synaptic terminals, SV2 might be a good marker for you. It is ubiquitously expressed in synaptic vesicles and there is a good monoclonal antibody that recognizes all three isoforms available through the Developmental Studies Hybridoma Bank (DSHB), so its pretty cheap. A caution here is that SV2 also may be found in other secretory vesicles and you can certainly see it by IHC in cell bodies where it is synthesized.

   Synaptotagmin can also be used to label presynaptic terminals. There are mul;tiple synaptotagmin isoforms, but synaptotagmin 1 and 2 account for most synapses in the CNS. I think that Synaptic Systems sells an anti-synaptotagmin antibody that recognizes both Synaptotagmin1 and Synaptotagmin2.

   Synaptophysin is often used for labeling presynaptic terminals because it is widely expressed, but depending on what the goals of your project are and the brain regions you are exploring, you might have isoform selectivity issues with the antibody as synaptophysin has two distinct isoforms. 

   If you are looking to count specific populations of synapses, vesicular neurotransmitter transporters can be a very useful tool for identifying specific types of pre-synaptic terminals.

   PSD-95 may not be ideal because it is not expressed ubiquitously in post-synaptic densities (it is typically associated with glutamatergic synapses). I don't know of any specific postsynaptic marker that is ubiquitous.

The best method to analyze the spine density is the golgi staining method or the Use of GFP transgenic mice.

Synaptophysin would label the presynaptic areas. But what about the post-synaptic areas? You can use MAP2 antibody for doing that. If you perform a dual staining with synaptophysin and MAP2 then you can count the areas where they superimpose in the cells. Hope it helps.

MAP-2 can be a great marker for dendrites, as it labels the dendritic microtubule cytoskeleton, and can be extremely useful. However, MAP-2 is not a specific marker of post-synaptic terminals and if the goal is to count synapses, it is not an ideal marker. If my recollection is correct, microtubules are typically absent from post-synaptic spines, which would lead to an undercounting of synapses.

MAP2 will help locating the cells and if there are synaptophysin labelings, the superimposed areas will indicate where the synapses are, like a guiding map. Otherwise it becomes difficult to designate whether the staining is coming from blood cells or some debris. There are so many antibodies out there in the market these days and with the help of all the journals in the field of neuroscience it is not that difficult to find a good one. Only thing is that we have to dedicate some time to do that search.