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An Autonomous, in situ logging system for the collection of oceanographic data


The bulk of biological production on earth occurs in the World Ocean, where single celled plants, collectively known as phytoplankton, convert carbon dioxide into biomass through the process of photosynthesis. Oceanic production drives numerous large ecosystems upon which commercially important fisheries depend, as well as regulating the movement of carbon dioxide between the deep ocean and the atmosphere. Moreover, the ocean is the dominant heat reservior on earth (all of the heat in the atmosphere is contained within the top 10 meters of the ocean), thus making the ocean the primary regulator of global climate. Approximately half of the human population lives along coastlines, and the coastal ocean effects quality of life in numerous ways, for instance:

  • As a regulator of short and long term climate
  • As a source of food
  • As a place for the disposal of waste

  • Oceanographers study the physics, chemistry and biology of the World Ocean in an attempt to understand its structure and function. The earth is 70% ocean, and therefore to understand how the earth system works one must have a decent fundamental understanding of how the ocean works. One of the biggest problems facing Oceanographers today is the scarcity of the simplest data on the state of the ocean: temperature and salinity. Moreover, biological oceanographers require information on the abundance of plants and animals in the ocean, in order to determine such things as fisheries production and carbon fluxes. The sheer scale of the World Ocean makes such measurements very difficult to collect, not to mention extremely expensive. For instance, a research vessel costs on order of $10000 per day to operate and requires a great deal of specialized equipment (e.g. winches with conducting wires and slip rings). Several technologies have been developed to address this problem, for example sensor-equipped satellites and autonomous drifters. These technologies, however, are not without limitations: satellites can only make measurements of the top few centimeters of the ocean, and drifters by definition are passive and may not move into areas of interest.

    An Autonomous, Integrated Sensor Package for Environmental Sensing

    The Submersible Oceanographic aUtonomous Profiler (SOUP) is an integrated sensor package including a conductivity temperature depth sensor (CTD), an in situ fluorometer, and optical plankton counter (OPC), and a microprocessor-based logging system. Each component of the system is described below:


    Salinity, temperature and depth are measured with a SeaBird electonics model SBE19 CTD probe. The SBE19 measures temperature, salinity and depth at 2 Hz, with a resolution of 0.0001 C, 0.4 and 0.013 meters. Power is provided internally, from 9 "D" cells. Powered internally, the SBE19 is capable of collecting data for 60 hours.


    Phytoplankton contain chlorophyll a, and the concentration of chlorophyll a is a rough proxy for plant biomass. Chlorophyll reacts with light, which allows it to be measured: when light with a wavelength of 490 nanometers strikes a plant cell, the chlorophyll-a within the cell emits light at 695 nanometers, and the intensity of the light emitted is proportional to the amount of chlorophyll present. Fluorescence is measured at with WET Labs WETStar in situ fluorometer, and is logged through the CTD.


    Plankton is counted with a Focal Technologies optical plankton counter. The OPC consists of a sampling tunnel with two pressure casings mounted on either side. One casing contains a light emitting diode, while the other contains a light sensing photodiode. As the OPC is pulled through the water, plankton passes through the tunnel. The plankton passing through the light beam occlude it, and the amount of light occluded is proportional to size. Thus, the OPC both counts and sizes plankton as it is pulled through the water. In addition to counting plankton, the OPC incorporates a depth sensor (which may be used as a backup to the sensor on the CTD), a flow sensor (used for determining how much water has been sampled), and also makes measurements of light attenuance (a measurement of how "cloudy" the water is).

    Logger - electronics

    Logging the data from the above instruments is done with a very small 486-based microcomputer based on the DIMM processor (a.k.a "PC on a chip"), manufactured by JUMPtec AG of Deggendorf, Germany and sold as the matchbox PC by TIQIT Inc., of Menlo Park, California. The MPC incorporates the DIMM processor, an input/output module (serial ports and a network port through which data is collected and downloaded), a power supply, and two hard drives with a capacity of 16 and 340 megabytes. The matchbox PC is aptly named, having dimensions of 1 by 2 by 3 inches, and this allows it to be mounted in a very small pressure casing, which accompanies all of the instruments as they are deployed.

    Logger - pressure case

    The pressure casing for the SOUP system has been custom-made at UBC, and contains the MPC and a battery pack designed to permit ten hours of continuous operation. It is constructed of 1/2 inch thick anodized aluminum, is 5 inches in diameter and 18 inches long, and weighs approximately 10 kg. It has been designed to withstand pressures of 4500 psi (which corresponds to slightly over 3000 meters), and to date has been tested to 2900 psi (2000 m). Power and data connections to the instruments are with SUBCONN through-hull fittings rated to 10000 psi. The matchbox PC and battery pack are separated by an internal bulkhead and a through-hull fitting; this is to protect the matchbox PC in the event that the battery side floods (including the bulkhead complicated construction of the pressure case, but the $2000 cost of the matchbox PC makes this a worthwhile feature). Battery power is currently from disposable alkaline batteries, and a rechargable battery pack is in development.


    The matchbox PC is a fully functional 486 computer, and runs Windows 95. This allows the use of the native software supplied with each sensor, and greatly simplifies data collection. An integrated software package written for all of the sensors is currently in development in Visual Basic, and this will result in the data from all sensors being stored in a single file.

    Operation of the matchbox PC (i.e. starting and control of software) is done through an ethernet connection and a laptop computer, and a program called VNC (Virtual Network Computing; distributed free of charge by AT&T's Cabmridge labratories and is available at: VNC is a network management application that allows one computer to control another via an ethernet connection. When VNC is run on the laptop, a remote display of the Windows 95 environment of the matchbox PC is shown in a window on the laptop screen, and the matchbox PC may be operated as if it were directly connected to a keyboard, mouse and monitor. An ethernet connection requires only four cables (as opposed to 23 for a monitor, keyboard and mouse) which simplifies wiring a permits using a much less expensive 4 conductor through-hull fitting.


    SOUP is currently configured for profiling - the CTD, fluorometer, OPC and logger are mounted on a small aluminum frame pointed downwards - data is collected as the frame is lowered through the water at approximately 1 meter per second. It was designed and built for a study currently being conducted on the distribution of overwintering zooplankton in the Northeast Pacific (author's PhD thesis). It will be deployed monthly in the coming fall and winter at biological monitoring stations in the Strait of Georgia and open subarctic Pacific (a station approximately 1200 km due west of the tip of Vancouver Island). It is also being used in an ongoing BC Hydro study on the effect of the Port Moody Generating Station on the hydrography and biology of Port Moody Arm in Vancouver harbour.

    SOUP instrument package prior to deployment off the Fisheries and Oceans Canada research vessel John. P. Tully. In this configuration SOUP consists of just the logger and optical plankton counter, and is deployed to 700 meters.
    SOUP instrument on deck of the Fisheries and Oceans Canada research vessel Vector. In this configuration SOUP consists of the logger (on left), optical plankton counter (in centre of cage), CTD/flourometer (on right), and an underwater camera system(mounted outside the cage, on the left). The maximum depth of this configuration is 100 meters (the maximum depth rating for the camera system).
    SOUP in the small profiling frame on deck of the research vessel Vector. In this configuration SOUP consists of the CTD/flourometer (on right), optical plankton counter (in centre) and logger (on left, behind the OPC in this view). The maximum depth of this configuration is 600 meters. This configuration weights approximately 20lbs in water, and can be profiled by hand (as is done in Vancouver Harbour).

    There are numerous other applications for which SOUP is ideally suited. Because it is autonomous, it may be deployed from virtually any platform. For instance, in the deployments listed above, it will be deployed from a traditional oceanographic vessel (subarctic Pacific), a small fishing vessel and a gas powered winch (Strait of Georgia), and with a rope from a small motorboat or zodiac (Vancouver Harbour). As well, because it is operated through Windows 95, it simple to operate, with minimal training, by anyone familiar with the operation of a computer. This means that SOUP may be deployed on ships of opportunity without a scientist or technician present to operate it. Operation will be simplified further when the integrated logging software is completed, and will obviate the use of a laptop: it is planned to configure the software such that the logger will automatically create a new file when it is started, so that it can simply be turned on and put over the side, then turned off once it is retrieved. Furthermore, the sensors deployed can easily be changed, and also operated through their native software in the Windows 95 environment. Other sensors that are particularly of interest include transmissometers, nutrient analysers, tilt/roll sensors, and current meters. Basically, the uses for SOUP are limited by the imagination of the user, the sensors connected to it. Some particularly interesting applications include:

  • Rapid and spatially explicit surveys of phytoplankton and zooplankton biomass for oceanographic research and fisheries management
  • Mapping of harmful algal blooms
  • Mapping of the dispersal of pollutants (e.g. sewage outflows)
  • Environmental assessments (e.g. effect of mine tailings)

  • In short, SOUP is a fully functional PC that can be submerged to 3000 meters along with any instrument that normally logs data to a computer.