[Histonet] Marking of mouse brain tissue


I am sectioning Para formaldehyde fixed, sucrose cryoprotected mouse brain
tissue on the microtome to then perform free floating tyrosine hydroxylase
IHC with a cresyl violet counterstain to count CV+/TH- neurons in the SNpc
region.  Before sectioning I need to mark the tissue so I can load them all
onto slides in the same orientation.  I have tried puncturing the tissue
with various sizes of needle and have found it difficult to get a hole large
enough to be visible to the eye yet small enough to avoid the SNpc and avoid
the sections breaking apart during the staining process.  Is there a dye I
could puncture with that wouldn't spread to the rest of the tissue or
interfere with my IHC?  Any other suggestions?

Many thanks in advance.

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