I am currently performing passive tissue clearing on an entire rat brain. It has been 2 and a half weeks, and the brain has swollen quite a bit, as was to be expected. The cortex has been cleared, yet subcortical areas remain opaque. I know that I have to be patient and wait for the passive clearing to penetrate deeper areas. However the gel has started to flake off in areas, and when I take the brain out of solution it is losing its rigidity and becoming more jelly like.
Should I keep clearing in order for the subcortical areas to become cleared? Or should I stop where I am now to avoid excessive tissue damage to the cleared parts of the brain?