Vertebrate blood is one thing that is opaque due to hemoglobin, and it cannot be made transparent. The same is true for the pigmented retina of the eyes. So transparent frogs and fishes still have opaque eyes and blood vessels.

Where pigments like the heme of the blood or the melanin of the skin or the visual pigments of the retina are absent, the opacity is due only to the variable refractive index, which causes light scattering, and in this case the tissue can be made transparent with methods like that described in the article which make the refractive index uniform (i.e. exactly like snow that transitions from opaque to transparent when melting).