Methods for determining the effect of a Clostridial neurotoxin on muscle are disclosed. In particular, methods for determining a potency and/or diffusion of a neurotoxin based on a nuclear index and/or an amount of muscle atrophy are disclosed. The methods may be used to distinguish two different Clostridial neurotoxins. In certain embodiments, the neurotoxins are obtained from Clostridium botulinum.