Glass Bottle The process of diaphonization has also been known as "clearing and staining." The animals are rendered transparent (the "clearing") by bathing in a soup of trypsin, a digestive enzyme that slowly breaks down their flesh. They also soak in several batches of bone, muscle, or cartilage dyes (the "staining"), with alizarin red and alcian blue the most commonly used. The result is a visually striking display of anatomy