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Yes, you will be able to take the Canopy Tour without taking the cruiseship tour to Tabyana Beach. I believe there is a place a mile or so before you get to Tabyana where you can go to pay and start the tour. Check out songerling's message several posts down called "Our Roatan Experience- Canopy Tours and Snorkeling". I'm sure all of the taxi drivers know about the tour and where to go.
Hope this helps!