Table 5.
Decolorization reagents for different pigments
| Pigments | Chemicals/cocktails | Limitations | Clearing methods or cocktails |
|---|---|---|---|
| Heme | Hydrogen peroxide | Quenching of protein fluorescence | iDISCO, iDISCO+ |
| Sodium hydroxide (NaOH) | pH shifting at higher concentration of erythrocytes | – | |
| Ammonium solution | Potential pH shifting like NaOH | PEGASOS | |
| Acid acetone | Significant loss of GFP signal | – | |
| Quadrol | – | CUBIC, PEGASOS, vDISCO, Bone CLARITY | |
| THEED | Significant loss of GFP signal, but the signal is still detectable | Deep-Clear | |
| N-butyldiethanolamine | – | CUBIC-L | |
| N-methyldiethanolamine (in combination with CHAPS) | – | SHANEL | |
| 1,3-BAC | – | CUBIC-HL | |
| 1-methylimidazole | – | CUBIC-P | |
| MXDA | – | MACS | |
| SDS | Request for gel embedding | CLARITY and its derivatives | |
| Melanin | Hydrogen peroxide | Quenching of protein fluorescence | EyeCi, FlyClear, Deep-Clear |
| Lipofuscin | Copper(II) sulfate (CuSO4) | Quenching of protein fluorescence | – |
| Sudan Black | Turning black of tissues | PACT | |
| Ommochromes & pterins | THEED | Significant loss of GFP signal, but the signal is still detectable | FlyClear, Deep-Clear |
| Maillard reaction | Thioglycerol | – | SeeDB, Ce3D, hFRUIT, SWITCH |
| Sodium sulfite | – | SWITCH | |
| Chlorophyll | Chloral hydrate | Quenching of protein fluorescence | – |
| Triton X-100 | Insufficient chlorophyll removal | Scale-like | |
| SDC | – | ClearSee | |
| SDS | Request for gel embedding | PEA-CLARITY | |
| Ethanol (in combination with acetic acid) | Quenching of protein fluorescence | TOMEI-I |