I have flash frozen brains in the past using isopentane with dry ice in it but I found that some of them cracked. What is the optimal time to leave the brain in the isopentane such that it is frozen solid but the cells are still viable?
Er....what?
If all you're using these brains for is western blotting, cell viability is irrelevant: all you care about is protein.
You'll be crushing the tissue under liquid nitrogen and then dissolving some tissue powder in some sort of lysis buffer (RIPA or SDS or similar).
You don't even need to use isopentane: you could just drop the brains straight into liquid N2, or place them on dry ice. The time taken to freeze solid is far shorter than the half-life of virtually every protein you might be interested in.
The only time isopentane is really necessary is for rapid freezing: to preserve cellular architecture for histology (liquid n2 alone freezes too slowly, due to leidenfrost effect).
If you want cell viability (!?) then you shouldn't be freezing them like this at all, you should be isolating and amplifying the cells of interest in culture, then freezing them as for normal cultured cells.
Agreed, you can just snap freeze with liquid nitrogen and then keep them at -80 until you analyze. Then you will have to homogenize the tissue anyway. Not sure what you mean by 'cracked'. Cell viability won't be an issue for western blot, as also mentioned above, proteins will be fine. If you, however, want to do histology and keep your tissue as protected as possible, then use TissueTek to freeze your samples. Just place them in a tube filled with tissuetek and use dry ice-isopentane slurry. You will see tissuetek turning white showing its frozen and then you can keep the samples on dry ice for a bit and move to -80.
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