I would take a look at "Tracking the Small with the Smallest - Using Nanotechnology in Tracking Zooplankton" by Lard et al. 2010. They have been using fluorescent quantum dots to track zooplankton. Really cool stuff. Hope this helps.
Danny Grunbaum at the University of Washington had a 3D video setup and did some really neat modeling/observational work with plankton. His web page is at http://faculty.washington.edu/random/.