Document Type


Publication Title

Link Foundation Ocean Engineering and Instrumentation Fellowship Reports


Coastal marine ecosystems such as coral reefs, kelp forests, sea grass beds and mangroves have significant societal value. As economic resources they support tourism, fisheries and storm protection while ecologically they host high biological diversity and productivity. Many basic biological, chemical, and physical processes taking place in these marine ecosystems occur at ‘micro-­‐scales’ less than a millimeter in size. Examples of significant micro-­‐scale activities include: coral bleaching of their single-­‐ celled symbiotic algae, larval settlement and attachment, competition between sessile organisms along thin interfaces, and fluxes of particles to and from the seafloor. It is also important to consider that these shallow ocean environments are complex and dynamic. The physical environment is in continuous flux with variations in conditions such as pH, temperature, and fluid motion. Simultaneously, organisms interact with each other in non-­‐linear ways across a wide range of scales. It is therefore difficult or impossible to fully replicate these natural systems in the lab. A distinct need thus exists to make in situ observations under natural conditions. Such observations are of interest to scientist across diverse disciplines such as physiology, ecology, biomechanics, and marine geology. Previous calls for technology to perform such micro-­‐scale imaging in the ocean include that of V. Smetacek who asked “Could such an instrument (an in situ computerized telemicroscope) do for microbial ecology what Galileo’s telescope did for astronomy?”(Nature, 2002). My work seeks to address existing observational deficiencies by developing and applying underwater microscopic imaging techniques for studying benthic ocean environments at scales of less than a millimeter. Specifically, I have designed and built the Benthic Underwater Microscope (BUM), this is the first system to perform non-­‐invasive imaging of seafloor environments in situ at nearly micrometer resolution. Funding from the Link Fellowship provided the means to complete the development and validation of the BUM. Additionally, I prepared a manuscript describing the BUM that is currently in submission for scientific publication. During my funding from the Link Foundation I also began work to further enhance the BUM’s capabilities by incorporating micro-­‐Particle Image Velocimetry (μPIV). This is flow visualization technique for measuring micro-­‐scale fluid velocity fields, which are important to mass exchange and a variety of biological and geochemical processes.


Jules Jaffe

Publication Date



Year received Link Fellowship: 2014-2015



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