Because the mouse brain is so delicate, I would recommend flash freeze OCT.

Here's an excellent protocol that we use frequently. 

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556166/

Hope this helps!

I am also ise brain tissue and i also used the OCT, it is very good with brain tissue.

Breifly: after the fixation of the brain the 4%PFA for 24-36 hrs, wash in 1xPBS 3 times 10 min each,  Place the tissue to 15 and 30 % sacrose in 4°C overnight, or until it has sunk , then put the tissue in OCT for 1hr then the tisue are Placed and embedded with OCT using the Liquid nitrogen. preseve the tissue afterwards in -20 or -80

Dear  Shih-Liang Lee and Manal Tawfik Hussein Mohamed ,

thank you for your  suggestions. The attached link is very informative and I will try accordingly. Thanks.

I prefer OCT embedding for most IHC applications.  Whether the brain should be fixed or frozen unfixed depends on your antigen.  If fixing, you might be able to get away with immersion fixation for embryonic and early post-natal brain - less than P10 - but when we are being very careful - we fix by perfusion.  . 

After fixation, you will need to cryoprotect in graded sucrose - 10, 20 and 30% is what we use and then embed in OCT.  Sometimes to improve cutting we infiltrate the tissue with OCT/30% sucrose - for a few hours before embedding in OCT and freezing. Relatively detailed methods can be found in the following paper - 

Radner et al Developmental Neurobiology - 73:209-229 2013.  

DOI 10.1002/dneu.22057 

It depends on the thicknes of your sections you like to investigate. If you need thin sections, about 3-6µm I recommand paraffin embedding. If you work with thicker sections (20-40 µm) you can use free floating frozen sections. Here you have to perfuse your animal with 4% PFA in PBS pH 7.4, store ithe brain over night in the same fixativ,kryoprotect it in 30%sucrose (or you can use a gradiant  10%, 20%,30% sucrose) until it is sunken on the ground of the vial. Prepare your sections, store them in PBS until you will do your immuno reaction, but not longer then 2-3 weeks.

If you like to do your immuno later you shoud store your sections in a solution of 30%sucrose and glycerol equal parts and freez them at -20°C.  You can store your sections in this way for years.

Good luck!

Dear William J Brunken and Ute Neubacher , 

Thank you so much to both of you. Your suggestions have cleared my doubt and i have build a confidence. I will be doing the embedding according to your advice. Thanks a ton.

How about frozen sections - better results, Professor Paul Manger from the University of the Witwatersrand does a lot of this work, why not contact him, he is very approachable. He also has many publications describing this technique.