Table 1.
Successful applications of the passive CLARITY protocol for tissue clearing and three-dimensional imaging
| Tissue/organ | Species | Hydrogel perfusion/embedding | Clearing solution | Clearing time | RI* homogenization | References |
|---|---|---|---|---|---|---|
| Skeletal muscle (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 42 days (adult) | 80% glycerol | (27) |
| Brain (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 21 days (adult) | FocusClear/85-87% glycerol | (20) |
| Brain (section) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 7 days (adult) | PBST | (28) |
| Brain (whole)/lung (whole)/testis (whole)/kidney (whole)/intestine (whole)/spleen (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 30 days (adult) | FocusClear/80% glycerol | (29) |
| Brain (whole)/spinal cord (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 28-42 days (adult brain)/14-28 days (adult spinal cord) | TDE | (30) |
| Brain (whole)/spinal cord (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=7.5) | 36 days (adult brain)/21 days (adult spinal cord) | FocusClear | (31) |
| Brain (section)/spinal cord (section) | Mouse/rat | +/+ | 8% SDS in boric acid (pH=7.5) | 4 days (adult mouse)/6 days (adult rat) | 80% Glycerol/65% TDE | (32) |
| Brain (whole) | Rat | +/+ | 4% SDS in boric acid (pH=8.5) | 28-56 days (adult) | RapiClear | (33) |
| Brain (section) | Rat | +/+ | 4% SDS in boric acid (pH=8.5) | 6 days (age P0) to 20 days (age P24) | TDE | (34) |
| Brain (section) | Human | −/+ | 4% SDS in boric acid (pH=8.5) | 14 days (adult) | ScaleA2 solution | (35) |
| Brain (whole) | Mouse/rat /human (section) | +/+ | 4% SDS in boric acid (pH=8.5) | 21 days (adult mouse)/60 days (adult rat)/5-10 days (adult human) | 87% glycerol/ScaleA2 solution | (36) |
| Cerebellum (whole) | Mouse/human (section) | −/+ | 4% SDS in boric acid (pH=8.5) | 7 days (adult mouse)/>28 days (human adult) | RIMS+PBS+Tween-20 | (37) |
| Spinal cord (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=7.5) | 14 days (adult) | CUBIC clearing solution | (38) |
| Whole body | Zebrafish | -/+ | 8% SDS in boric acid (pH=8.5) | 5-7 days (adult) | RIMS | (39) |
| Fetus (whole)/brain (whole)/lung (whole)/heart (whole)/kidney (whole)/muscle† (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 3-10 days (fetus)/10 days (other tissues) | RIMS | (40) |
| Liver (section) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 30 days (adult) | RIMS | (41) |
| Retina | Rat | −/+ | 4% SDS | 5 days | RIMS | (42) |
| Lung (whole) | Mouse | −/+ | 8% SDS in boric acid (pH=8.5) | ND | RIMS | (39) |
| Intestine (section) | Mouse/human | +/+ | 4% SDS in boric acid (pH=8.5) | 12-14 days (adult) | 80% glycerol | (43) |
| Ovary (whole) | Mouse | +/+ | 4% SDS in boric acid (pH=8.5) | 35 days (adult) | FocusClear | (44, 45) |
| Testis (whole) | Zebrafish | −/+ | 8% SDS in boric acid (pH=8.5) | 13 days (adult) | RIMS | (46) |
| Stem-cell-derived cortical cultures | Mouse | ND | ND | ND | ND | (47) |
RI; Refractive index, SDS; Sodium dodecyl sulfate, TDE; 2,20-thiodiethanol, RIMS; Refractive index matching solution, PBS; Phosphate-buffered saline, ND; No data, PBST; Phosphate-buffered saline+Triton X-100, and †; The passive CLARITY was performed on muscle until the clearing stage and without immunolabelling and imaging.