Hi Jessica,

       Immunohistochemical staining with NeiN antibodies is the beat method to identify neuronal population at the present. For this purpose, both the mouse monoclonal (A60) and rabbit monoclonal are perfect. To identify cell origin of brain tumor, the rabbit antibody is better.   If you want to identify glutamatergic neurons, you can use EAAC1. Otherwise, you can use GABA for GABAergic neurons. For details, you can check this paper 

Front Neuroanat. 2016 May 13;10:54. doi: 10.3389/fnana.2016.00054. eCollection 2016.

        Good luck.

@Jessica: would you mind to inform us about which way / stain you had in mind: talking about cresyl violet (Nissl-stain) you might have intended also staining with a classical dye or classical histochemical approach but perhaps you are satisfied with Guoxiang Xiong's IHC - protocol....(the latter approach may be more elegant....(;-)) 

NeuN is wonderful but know it is not expressed in purkinge cells, and is very very low in some neurons of the hypothalamus (PVN, arcuate) .  Our paper gives how to stain with the mouse monoclonal antibodies (if in muse, you can buy a biotinylated version and we found that use of an antibiotin antibody gave beautiful results). our procedures and use of the mouse monoclonal on rat tissue is presented in the attached publications

Thank you for your responses! 

All have been very helpful! I think our lab have now decided we will have to try and use the Nissl stain, as the PVN and ARC cells are important populations for us.

Thanks again!

@Jessica:  

you might get some impression on other staining possibilities by Google ( or ScholarGoogle)-Search for e. g.:

" Staining of neurones in hypothalam* AND PVN AND ARC" (ca. 48,900 results) 

Histochemical Staining of neurones in hypothalam* AND PVN AND ARC (ca. 15,600 results) 

"Histochem*" Staining of neurones in hypothalam* AND PVN AND ARC (ca. 2400 results)

Also I would suggest to think about using CAGC or GCCA=gallocyanin chrome alum-stain (Google: | Chrome alum gallocyanin AND Staining of neurons in hypothalamus* AND PVN and ARC | = 339 results) .

CAGC (and more modern modifications) may stain neurosecretory material cf. e.g. Chromalaun - Gallocyanin staining according to BOCK ( 1966 ), modified after STOECKEL, PORTE, DELLMANN und GERTNER ( 1972 ).

Bock, R.: Ueber die Darstellbarkeit neurosekretorischer Substanz mit Chromalaun-Gallocyanin im supraoptico-hypophysaeren System beim Hund. Histochemie 6, 362–369 (1966). Google Scholar:http://scholar.google.com/scholar_lookup?title=%C3%9Cber%20die%20Darstellbarkeit%20neurosekretorischer%20Substanz%20mit%20Chromalaun-Gallocyanin%20im%20supraoptico-hypophys%C3%A4ren%20System%20beim%20Hund&author=R..%20Bock&journal=Histochemie&volume=6&pages=362-369&publication_year=1966

and: Stoeckel ME, Porte A, Dellmann HD, Gertner C. Stain Technol. 1972 Mar;47(2):81-5.

Selective staining of neurosecretory material in semithin epoxy sections by Gomori's aldehyde fuchsin, cf.  https://www.ncbi.nlm.nih.gov/pubmed/4113106

My best wishes, good luck and warm regards, WM 

Is there a particular reason why you are using 40um thickness for your section?

Dear Jessica,

If your concern for Nissl staining is the cresyl violet acetate, you might investigate thionin staining for Nissl substance.  I personally have always used cresyl violet acetate, but I have a friend that preferred thionin.

Since you are using 40 um frozen sections (collected into buffer and then dried onto slides?) I suggest defatting the sections before staining with cresyl violet acetate.  I have always gotten better staining that way with thick sections.  Some protocols written for frozen sections just have you start with an aqueous step before the stain, but I have only had that work for very thin sections.

Good Luck!

Jill