Hi Christopher Jones

Any of your thionine-based Nissl staining work well for hypothalamus histochem. Are you using a mouse model? ( C57BL/6J mouse )? Then Nissl staining techniques should also work fine. If you want to further isolate the nuclei then look at literature by Miklόs Palkovits which is a wealth of information.

If you are wanting to develop nuclei markers of disease progression or growth then you might want to look into something like isotopic in situ hybridization and make use of a compound marker- some researchers use cholera toxin B.