His process:

Tomita first removes the scales and skin of fish that have been preserved in formaldehyde, he leaves the organism to soak in a mixture of blue stain, ethyl alcohol, and glacial acetic acid before utilizing the enzyme trypsin to break down protein and muscles, stopping the reaction as soon as they become transparent but before they lose their form. The bones are then stained by soaking the fish in a combination of potassium hydroxide and red dye, before the specimen is preserved in glycerin.

The pieces themselves are sold at Tokyu Hands department store in japan.

More information at www.shinsekai-th.com | Thanks to Wired & Designboom for the tips