These arrived in my inbox from a collaborator recently:
Q: So… I [understand that I] need to stain the brain to estimate the volume or I will not see anything at all [in my CT scan], but I would like to know if there is any staining technique that could be used for both CT scanning and making slides,
A: So recently a paper was published saying that there’s no problem with doing microCT scanning followed by de-staining and then proceed as normal with histological staining. So stain away!
Multiscale imaging of the rat brain using an integrated diceCT and histology workflow | SpringerLink
Q: Also, is there any better (and healthier) way to fix the brain instead of formalin that may lead to the same results?
A: Do you mean like, safer and healthier for you? Not that I know of. 4% paraformaldehyde (PFA), which is 10% formalin without the stabilizing agent (usually methanol), is the standard. You should use freshly made-up PFA, not formalin.
There are other fixatives out there, but I believe they are all more dangerous, not less dangerous, than PFA. I’ve never looked into it very deeply, though, because PFA is just what everyone uses.
If you are more knowledgeable on these topics than I am and have any comments or corrections, please get in touch, I would love to hear from you!