A schematic of the CLARITY process on a molecular level. Biomolecules within the tissue are covalently linked to acrylamide monomers via reaction with formaldehyde. The acrylamide is thermally polymerized to form a hydrogel network crosslinked by the attached biomolecules and a small chemical crosslinker. An electric field is applied to actively transport SDS micelles through the tissue where they collect and remove the unattached lipids, leaving only the crosslinked biomolecules inside a swollen hydrogel matrix.