Immunohistochemistry, fluorescent microscopy, and image analysis are key tools for visualizing and analyzing specific proteins in a variety of tissues. Together these techniques are readily available in most laboratories and in an infinite number of variations. Herein, a working example is used relating to the aging human skeletal muscle being characterized by denervated muscle fibers that undergo atrophy and eventual death. As such, proteins normally restricted to embryonic development, muscle regeneration, and the myotendinous and neuromuscular junctions of the muscle fiber are observed in denervated muscle fibers. We describe a workflow from muscle biopsy sampling to lab bench and to image analysis. Our aim is—through a concrete example—to provide the reader with knowledge and insight into how to design an effective analysis workflow, which can then be utilized in specific research contexts.