Dear Arjun,

c-fos and Arc, as well as c-fos promoter are good choices for studying neuronal activation. Also it might be worth looking into activity-depended promoters. 

A good article on the latter can be found here : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005930/

More information on c-fos can be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4801051/

There are more specific ones depending on which brain area you are looking at, for example a good marker for amydgala neurons is Zif268.

Best of luck to your research, i hope the above information comes useful.

I largely agree with theofanis. I would consider c-fos, fosB, arc; the caveat is that the threshold for c-fos induction is variable across neuronal subtypes (too many studies only focus on hippocampus): e.g., it is difficult to induce in motoneurons and in some inhibitory interneurons. In addition, it depends on the type of activity one wants to explore: for pathological excitation (e.g., epilepsy), atf3 would work well. NPAS4 and MEF4 are also interesting alternatives. At non-transcriptional level, S6 phosphorylation has been shown (cell paper) to be a marker of activity.

Thank you both. I will check the suggestions that you made. I am wondering if we have something else other than c-FOS to mark neurons in cortex

Traditional IEG (c-Fos, Arc, Egr1/Zif268) are great markers of neuronal activity. However, they are also regulated by neuromodulators via cAMP, neurotrophins and other paracrine factors and their kinetics are relatively slow. Mike Greenberg's lab showed that Npas4 has a much more pure response to activity-dependent signaling via Ca2+ (Lin et al., Nature. 2008). Activity Signaling sells a well validated recombinant Npas4 Ab that I generated (www.npas4.com) for marking recent neuronal activity across the brain. It works well in IHC, ICC, Western, ChIP-Seq and iDISCO-mediated whole-brain imaging.