ZEISS Z.1 - Solvent Tissue Clearing Technique Imaging Guide


The ZEISS Z.1 is a light sheet microscope that is prevalent at imaging cores and uses an immersion objective (Clr Plan - NeoFluar 20x/1.0 nd = 1.45 +/- 0.03) to image cleared tissues. However, the Z.1 was not designed to be directly compatible with solvent-based clearing techniques like Visikol HISTO, iDISCO, 3DISCO, BABB or uDISCO as these technique could damage the immersion objective. Therefore, tissues cleared with these techniques must be imaged in a sealed container. 

Preparing your tissue for imaging

To prepare your solvent cleared tissue for imaging, the sample needs to be mounted in a sealed container and directions for how to do this are provided by Zeiss here

Matching you refractive index

Zeiss suggests reducing the high RI (1.50 to 1.56) of solvent based techniques by using a series of ethanol/DBE treatments after tissue clearing. However, this will likely cause your nuclear stains to come out of your tissue. Additionally, this adds one more variable to your optimization/imaging work and we suggest instead to first image your tissue at their original RI. If you then need to reduce the RI of the tissue to improve image quality we would suggest then using the ethanol/DBE treatments. However, this might cause your tissue to become more opaque.