Yes there are alternative ways to roughly identify anatomical locations without additional staining.

Here are two approaches that help you

1: Learn to identify key anatomical landmarks in the mouse brain. The brain atlases can be helpful resources. By comparing your sections to the atlas, you can get a rough idea of the anatomical location.

2: Another way is to use a bright-field microscope with a low magnification objective to get an overview of the entire brain slice. This may help you identify gross anatomical features.

Hi Nicholas,

I find that the hippocampus is particularly useful when trying to orientate during cryosectioning. When performing coronal sectioning, it starts from the top of the brain (rostral hippocampus) and eventually settles along the sides (caudal hippocampus) . The substantia nigra will be located at the ventral midbrain when you can start seeing the caudal hippocampus.

This tool from the Allen Institute may be useful:

https://connectivity.brain-map.org/3d-viewer?v=1

All the best!

Hi Nicholas Brennan

I would recommend you to use a atlas either Allen Mouse Brain Atlas or Franklin-Paxinos Atlas. While cutting observe each section with naked eye and look for an highlighted area in each part of the brain. With practice in a few whole brain sections, you'll be able to cut every region of the brain.

Best of luck,

Thanks,