If landmarking three-dimensional data, try Slicer. If landmarking two-dimensional data, you could landmark in ImageJ. You’d import either the 2D or 3D landmark constellations into R and analyze in a package like geomorph.

If you’re ever in the area, the Cabela’s in Hamburg, Pennsylvania has a superb trout stream + pond and aquarium. I recall it being even better than the Dundee location.

They’re sclerotic ossicles! They are embedded in the soft tissues of the eyes and can be found in a number of unrelated fishes. People debate their function, but they are potentially useful in keeping the eyeball shape when swimming at high speeds. Deformed shape means lens will not be in focus.