I need coronal sections of the substania nigra and VTA for confocal fluorescent imaging. When cutting in the brain on the cryostat, what are some useful landmarks I can use (looking grossly) to know I have the right sections. The Paxinos atlas isn't very helpful.
Didi you try the Allen brain atlas?
http://atlas.brain-map.org/#atlas=1&plate=100960224&structure=549&x=5280&y=3744.0000697544647&zoom=-3&resolution=11.97&z=5
Hi Marina, 1. cut the cerebellum and the frontal part of the brain away and put this brain on the tissue table of your fozen microtome so that you can cut in the posterior-anterior direction. Helpfull landmartks for VTA are the Culliculi superiores and the development of the Hippocampus. Take a look to Paxinos Fig. 48, you will see no Hippocampus but Colliculi. Take a look to Paxinos Fig. 41 or 38. you will see the intermediaer hippocampus but no Colliculi anymore (Fig 38). This is exactly the region of VTA. This landmarks you will see while you are cutting. Before you start your IF make a Nissl-stain of a small amount of sections. This will help you to find the optimal sections for your immuno.
Good luck!
Thank you! These are transgenic rats that have green fluorescence in the SN/VTA, so no staining necessary.
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