Bacon's biliteral cipher was the main lead some time ago.

I tried some stuff with it, nothing interesting I found but that's because I'm missing something I'm sure.

This picture is nice and explain the concept very well

http://www.cabinetmagazine.org/issues/40/FriedmanNYPL2_FINAL.jpg

Maybe it's something similar to this but with more than just binary. I saw a cypher using a pig where 6 parts of the pig are either 1 or 0 (eye open/close, tail big/short, mouth open/close ....)