I recommend to cut your sample in a cryostat. We usually sacrifice the animal and make a perfussion using Saline and cold paraformaldehyde 4%. The samples is postfixed for 2 hours at 4 degrees. Then, we put the sample in 15% sucrose in PBS overnight and then in 30% in PBS until it sinks. In the cryostat we usually cut at 8-30 um and we put the sections in gelatin coated slides. It is much better if you make longitudinal sections in order to visualize better the neuromuscular junctions.

For analyzing the neuromuscular juntions we run an IHC in order to label motor axons using beta-tubulin III (Biolegend) primary antibody and alpha-bungarotoxin conjugated to Alexa Fluor (Invitrogen) for motor end plates. For the secondary antibody we use the conjugated ones to Alexa Fluor from Invitrogen.