Background information
Reference Articles
- Clearing for Deep Tissue Imaging
- Systematic Evaluation of Chemically Distinct Tissue Optical Clearing Techniques in Murine Lymph Nodes
- EZ Clear for simple, rapid, and robust mouse whole organ clearing
- Large-scale tissue clearing (PACT): Technical evaluation and new perspectives in immunofluorescence, histology, and ultrastructure
- Passive Clearing and 3D Lightsheet Imaging of the Intact and Injured Spinal Cord in Mice
- Practical Considerations for Quantitative Light Sheet Fluorescence Microscopy
- Tutorial: practical considerations for tissue clearing and imaging
- Tissue Clearing
- SeeDB: A Simple and Morphology-preserving Optical Clearing Agent for Neuronal Circuit Reconstruction
Industry Resources
Please note the refractive index when researching these products.
- abcam - Tissue clearing made easy
- BioLegend - Ce3D Tissue Clearing
- Miltenyi Biotec - MACS Imaging Solution
Clearing Methods
| Method | Author | RI | Components | LS Z.1 | Commnent |
|---|---|---|---|---|---|
| Scale A,B,U | Miyawaki, Riken, JP | 1.38 | Glycerol, Urea, Triton | + | Alternative to BABB, less quenching, for myelinated tissue |
| CLARITY | Chung and Deisseroth, Stanford, USA | ~1.45 | SDS PAGE and electrophoretic clearing | ++ | Very good results when it works, high failure rate (> 50 %) |
| CUBIC | Susaka et al, Riken, JP | 1.47- 1.49 | Optimized Scale | ++ | Published in Cell, April 2014 |
| FocusClear | CelExplorer Labs | ~1.45 | Commercial medium | ++ | |
| RapiClear | CelExplorer Labs | 1.47 – 1.55 | Based on FocusClear, more flexible in RI, cheaper | + | Comes in variants 1.47 – 1.49 – 1.52 - 155 |
| TDE | Hell et al, various labs tried | Tunable | 97% 2,2’-Thiodiethanol in water | + | TDE as mounting medium for different clearing (e.g. DMSO) , difficulties in reproducibility |
| LUMOS | Efimova et al, Moscow | 1.45 - 1.47 | Not Known | ++ | Good results, some scattering left Compatible with immunostainings, in situs and lipophilic tracer dyes |
| Glycerol/H2O (80/20) | Generic | 1.45 | Simple mix of Glycerol and Water | + | Easy to reproduce, cheap |
| PACT, RIMS | Bin Yang et al. | 1.45 | Perfusion assisted clearing, | + | Lab of Viviane Gradinaru |
(Kindly provided from T. Pratt, Zeiss.)
Clearing Methods – Organic Solvent Based
The below Clearing Methods – are Organic Solvent Based and are not directly compatible with Lightsheet Z.1 as they are likely to deteriorate the optics.The samples can be enclosed in Glass (Simax R.I 1.472) and therefore used in a lightsheet.
See the associated White paper for expanding Clearing Solutions for those Simax methods when using these organic solvents.
| Method | Author | RI | Components | Comment |
|---|---|---|---|---|
| SeeDB | Ke et al, JP | 1.47- 1.49 | Sucrose / Fructose saturated | Very high viscosity sugar solutions, hard to get homogeneous medium, buoyancy of specimen, bubbles. |
| ClearT, ClearT2 | Kuwajima et al, 2013 | ~1.45 | formamide/ polyethylene glycol | Formamide is highly corrosive, will damage dipping objectives |
| BABB | Spalteholz 1914 | 1.53-1.57 | Benzyl alcohol - Benzyl Benzoate | Aka Murray’s Clear, LSFM: Dodt, Stelzer, Giese |
| Spalteholz | Spalteholz 1914 | 1.54 | Commercial medium | |
| 3DISCO | Erturk et al | 1.56 | developed starting from BABB; THF, DBE, DCM | Fast and cheap clearing, fast fluorescent quenching |
(Kindly provided from T. Pratt, Zeiss.)