Fule for thought: If you know enough about the fish you will be counting, you might want to estimate the mass of the fish by imaging from two orthogonal positions (top and side camers), then apply statistical methods base on the distribution of volume of the (X percent are y cc, m percent are n cc, etc. and they have a packing factor of Z) fish to determine how many went through.
This might provide more accurate results than trying to actually count them.