I have some rat brain tissue already horizontally sectioned that contain the spinal trigeminal nucleus, facial nucleus, and paratrigeminal nucleus. I am hoping to use anatomical landmarks to quantify various cell types in these regions, but all of the papers I am finding that examine these regions use coronal sections. 

Ideally, I would like to be able to differentiate subnuclei, but I would be fine with just having landmarks to differentiate the region borders. 

I have tried using various brain atlases to determine landmarks, but my sections are much more thin (40 microns) then those typically included in atlases.