Anatomical identification is the first step, you will find the suprachiasmatic rostral from the arcuate and above the optic chiasma, after the chiasma has entered the brain you will find the retrochiasmatic area and caudal to that the ARC will appear. You can consult Paxinos Brain Atlas in order to be able to cut and collect your sections properly. For immunohistochemical labelling there are several neurotransmitters that are present in both nuclei such as GABA and Glutamate, but there are also several that are not, Arginine-Vasopressin (AVP) and Vasointestinal Peptide (VIP) are SCN peptides, while Alpha-Melanocyte Stimulating Hormone (a-MSH), Cocaine Amphetamine Regulated Transcript (CART), Neuropeptide Y and Agouti Related Protein (AgRP) are present in the Arcuate and not in the SCN. I hope you find this information helpful. Good luck!!
Anatomical identification is the first step, you will find the suprachiasmatic rostral from the arcuate and above the optic chiasma, after the chiasma has entered the brain you will find the retrochiasmatic area and caudal to that the ARC will appear. You can consult Paxinos Brain Atlas in order to be able to cut and collect your sections properly. For immunohistochemical labelling there are several neurotransmitters that are present in both nuclei such as GABA and Glutamate, but there are also several that are not, Arginine-Vasopressin (AVP) and Vasointestinal Peptide (VIP) are SCN peptides, while Alpha-Melanocyte Stimulating Hormone (a-MSH), Cocaine Amphetamine Regulated Transcript (CART), Neuropeptide Y and Agouti Related Protein (AgRP) are present in the Arcuate and not in the SCN. I hope you find this information helpful. Good luck!!