Non-destructive optical holographic imaging of microorganisms in situ off the Senegalese coast

A submersible digital holographic microscope (DHM) Holoflow@Sea was deployed during AWA fisheries surveys conducted in March 2013 and 2014 in the large upwelling ecosystem of the Canaries Current. The microscope collected about half a million of holograms of microorganisms and other particles suspended in the water column. Selected new results of reconstruction of phyto- and zooplankton species using improved algorithms with respect to previously published results are presented. Amplitude images are more detailed and, for some species, phase images provide useful additional information about morphology and composition. Extensive analysis confirms that the submersible DHM is suitable for in-situ imaging of organisms in the size range 2 μm-200 μm and species identification. When compared to standard procedures the microscope allows to rapidly monitor planktonic communities over a wide area. It contributes to a better understanding of the organization and functioning of the ecosystem and in particular the link between biogeochemistry cycles and small pelagic fish stock dynamics.