I have been passively clearing both whole mouse brains and 2 mm brain slices.
In both cases the tissue happened to swell massively, and shrank a bit after being incubated in glycerol, but never really went back to its original size.
Has this happened to anybody or perhaps I am doing something wrong?
its normal for samples to swell in Clearing solution. I never used glycerol only FocusClear.
For me the samples return to their original size.
As far as I know FocusClear gives better results in comparison to glycerol. The hydrogel likes more the FocusClear and returns to normal size.
I also would mention that if the samples really swell massively, it could be due to another problem.
How long do you cleared the tissue? Very very long clearing could maybe compromise the hydrogel structure and also maybe hydrogel monomer composition could have and effect. But if you followed the standard hydrogel recipe and cleared your slices for 2-3 weeks everything should be fine.