PlanktoMetrix – a computerized system to support microscope counts and measurements of plankton

Abstract We developed a computerized image-analysis system, PlanktoMetrix, the first system to conduct all steps of conventional microscope-based phytoplankton and zooplankton analyses (counting, measuring sizes, entering data, computations, storage in database) simultaneously using real-time digital imaging. The microscope field that displays the sample is continuously scanned by a digital camera and screened on a computer monitor, on which cell counts and measurements of linear dimensions are made by mouse clicks. When the microscope tasks are completed, computations of species abundances, estimates of biovolume per individual, species biomass per unit volume, and total assemblage biomass concentration are made automatically and stored into a database. All raw and computed data are exportable to common spreadsheet platforms. PlanktoMetrix offers the production of high-quality data in less time, with lower user fatigue and fewer typing errors; therefore, more time can be devoted to data analysis rather than generation. Furthermore, PlanktoMetrix allows collecting organism size data regularly, thus offering plankton ecologists a tool for following seasonal, ontogenetic, and other well-documented but generally ignored changes in plankton size and morphology. An example of PlanktoMetrix-generated cell size time series shows that the dinoflagellate Peridiniopsis elpatiewskyi undergoes a distinct annual cycle with larger cells in winter and smaller cells in summer. PlanktoMetrix is distributed free to interested users and will likely be available in the future as an open-source platform.