Hi Subhajit,

The specific protocol will vary somewhat depending on the species and age of rodent, what particular midbrain region you are interested in, and the downstream use of the dissected tissue will be. I have experience dissecting midbrain dopaminergic regions from E17 rat embryos and neonatal rats for primary culture, and in dissecting midbrain dopaminergic regions from adult rats for use in western blot. I can tell you how I have done that if you would like, but I don't have experience dissecting other midbrain regions or trying to dissect an entire intact midbrain from a rodent.

Thank you. I am looking for axes for dissection.

I've always used a coronal brain slicer with 1.0 mm slice intervals for dissecting SN/VTA from adult rats. If you want the entire midbrain, I'd suggest taking a test brain or two, cutting at each 1.0mm interval to determine where the cerebral aqueduct begins (which will be the rostral limit of the midbrain) and ends (4th ventricle/cerebellum marks the caudal limit of the midbrain), I would then dissect the cerebrum away from the midbrain to complete the dissection. Others may have a better approach.

good point; so you're doing serial sections. did you mount whole brain and cut ? Is it possible to know the very 1st section from your specimen; may you be free on test brain from rat. Also the very last section and the total number of slides should you have with the sections. Now if possible, tell me what is the number of slide that 1st show mid brain region; what is the number of slide which 1st show snpc

I dissected the whole brain, then immediately cut fresh on the brain slicer: http://www.kopfinstruments.com/Stereotaxic/906-10.html . It's a different piece of equipment from a microtome/vibratome/cryostat. You use it to block tissue for sectioning, or to cut reproducible slices for further dissection.

I wasn't doing serial sections for immunochemistry, I was taking thick (1mm) slices for further dissection, then homogenizing the dissected tissue for western blot.  The coordinates will vary somewhat depending on the size of the rats you are using (and which model of slicer you buy), which is why I suggested starting off by using some test brains to determine which sections you should take. If getting the whole midbrain very precisely matters to you, I might even opt for a 500-micron brain slicer. 

If you're going to cut slices to dissect for western blot or other biochemical assays, the very first section that you would want would be the very first one where you see the round cerebral aqueduct; the very last section would be the very last one where the cerebral aqueduct is still round. If you're making a large tissue block to serially-stain sections, you should cut rostrally at the point that produced the last section on your test brain where the third ventricle is present, and you should cut caudally at the point that produced the first section on your test brain where the fourth ventricle is present. Personally, I wouldn't trust any coordinates that I didn't first verify with my own instruments. There's too much variation in rodent brain size depending on how big you let your animals get. The nice thing is that once you have sliced one or two test brains, you know where to cut all future brains assuming that you use the same size/age of animal and the same slicer.

To determine the rostrocaudal extent of the SNpc, I would try staining my thick slices for TH (or even serial sections, if I was already going to do a serially-sectioned test brain) and compare to brain atlas to distinguish one dopaminergic region from another. I was personally doing fairly crude dissection and didn't bother distinguishing SN neurons from VTA neurons.

Hope this helps.

I don,t make such protocols

Please could you specify the goal of your study (immunohistochemistry, electrophysiology, molecular biology,...).