Lightsheet Resources

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.)