Thanks for the reply, I managed to find what i was looking for here:
[url]TH3 and glcolz option in Oven_Homogeneity.C (posted by tpochep) a function is defined for making empty bins transparent 
Thanks for the reply, I managed to find what i was looking for here:
[url]TH3 and glcolz option in Oven_Homogeneity.C (posted by tpochep) a function is defined for making empty bins transparent