Fantastic, and thanks so much for the reference material! THis method may well work, esp if I can then incorporate a way to count pixels per layer into the script and then dump the output into a file (read in the current species mentioned, add any new species from this particular image, reoutput the old data with 0's in corresponding new species, then output a line of the new data).

Just gotta brush up on my Gimp-perl!

Although I may still use the cut-into-seperate-images method, as I'm thinking of spreading this script around to some other folk I know who do similar analyses, and they're not so gimp-savy, although they're all OSX users.

If only I could make this a photoshop plugin as well...