There is no such thing as best procedure for free-floating immunohistochemistry that will work for every tissue, much less a variety of antigens.

In order for someone to assist you in a meaningful way, you have to provide details.  

I am trying to get the signal in the brain using Millipore Anti-Insulin Receptor Antibody (for beta subunit). Secondary antibody I am usping is Alexa Fluor. I played a little bit with athe protocol and SDS permeabilization seems to work but I was hoping to hear how others get the signal. 

Does anybody use SDS permeabilization? 

Thanks,

Jan