Is there any protocol with free-floating frozen slices? I have never done IHC in skeletal muscle so I would like to confirm if there is any secret during the frozen or in another step.
Depending on your targets, over fixation is a big issue with IHC in muscles. Be sure to use a strong detergent (such as .2% TritonX) to allow for penetration of antibodies. I'd recommend extracting the muscles and staining free floating if possible. Check out the attached paper for similar methods I have used with success! A short fixation time is used on extracted muscles.