Hi Haviva,

I am working with decalcified bone so my solutions may not work for you,
though I would send them along anyway.

I have some old bottles of India ink, old enough that it may be thicker
than new. We dab this on the back of the
specimen which shows up after processing like pepper.  Perhaps if you
score the bone the ink will stay on.  

On other specimens I have used suture material tied in a particular spot
to give me orientation.  In another case I marked the cassette just with
pencil.  Not to creative, but they worked for me.

Good luck,

Trisha