Metadata Report for BODC Series Reference Number 647216
No Problem Report Found in the Database
Open Data supplied by Natural Environment Research Council (NERC)
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DI267- Optical Plankton Counter (OPC)
The OPC was deployed as part of the Auto-sampling and Recording Instrumented Environmental Sampler (ARIES) package.
Onboard data processing
No cruise specific information relating to on-board data processing has been supplied to BODC. The format of the supplied data files suggest standard Marine Laboratory Aberdeen (MLA) processing.
BODC data processing
A total of 47 processed OPC data files were supplied to BODC.
The parameters in the OPC data files were mapped to BODC parameter codes and transferred to BODC QXF format.
The following OPC parameters were transferred: date/time (mean value over sample period), Sample Number, Sample Volume, latitude (mean), longitude (mean), echo sounding (mean), sample depth (start),sample depth (end), mean sample depth, OPC concentration in each size class. Parameters not transferred are date/time (start/end), latitude (start/end), longitude (start/end) and echo sounding (start/end).The exact source for the navigation was unknown but is assumed to be GPS derived and the echo sounding (bathymetry) was assumed to be uncorrected depth.
The following transformations were applied during transfer:
- Sample volume was converted from m3 to litres.
- OPC counts were converted to counts/litre using the corresponding sample volume
During transfer negative depth (start and/or end) values were set to null and flagged accordingly, or else the transfer failed. Cycles in the original data where the sample volume=0.0000 are not transferred. It was assumed that no water was sampled over the period and even if counts were evident it was not possible to calculate a concentration/unit volume without estimation. All the remaining associated information (navigation and bathymetry) is available separately in the underway data set.
The data were visually inspected using the BODC in house software Xerplo.
Particle concentration spectra data were visually inspected for obvious out lying individual data values. When encountered these were flagged as suspect.
Time/Positional checks: visually checked by comparing the OPC data with the baseline 'master' underway navigation data. Latitude and Longitude time series were identical between OPC and underway confirming that there were no discrepancies in time or position.
The bathymetric data transferred from the originators files is uncorrected bathymetric depth. Corrected bathymetric depth is available in the underway data set. The time series have a similar profile but the uncorrected data are offset by approximately +20 - 25 m.
Elevated concentrations, particularly in the smaller size classes were evident in the near surface data. This was assumed to be contamination by air bubbles and was commonly associated with deployment and recovery of ARIES. Due to the volume of potentially suspect data, flagging of individual points was not attempted.
An artifact of the transformation from raw data to ESD is that there are parts of the size spectrum with identical values. This is most noticeable in the first 8 size classes but is also evident elsewhere. The degree of replication is dependent on the algorithm used. The transformation algorithm was not supplied with the data and interested parties should contact the data originator.
FRS- Focal Technology Optical Plankton Counter (OPC)
The following is summary of the standard operating protocol for the Optical Plankton Counter (OPC) employed at Marine Laboratories Aberdeen (MLA). These are described in full by Heath (2001).
The OPC is manufactured by Focal Technology (Canada). The basic principle of the OPC is that particles passing through the sampling tunnel interrupt a collimated light beam. Each particle produces a pulse with a size which is related to the equivalent spherical diameter (ESD) of the particle. The pulse height is digitized, and the resulting value is referred to as the digital size. Thus, each particle is registered as a bytes of data with a value related to the particle ESD. Focal Technology supply a non-linear calibration equation to convert digital size to ESD (microns).
The standard OPC is designed to transmit data by frequency shift key (FSK) up a conducting cable to a support vessel. A data logger intercepts the serial data stream prior to the FSK converter and integrates in real time over user defined time and size bins. The logger also receives analogue inputs from a flow meter and a pressure sensor, digitizes these data and incorporates them into the record associated with each time integral.The logger is programmed by serial communications from a PC. The logged data are stored in lithium backed-up memory, and down loaded over a serial link to a PC for processing.
In a typical MLA setup incoming particle size information (bytes) would be accumulated into 128 bins of equal width in terms of digital size, over 30 sec time intervals. The logger does not exploit the full dynamic size range of the OPC. This is because a) the ESD calibration is highly non-linear over the upper half of the digital size range, and b) particle in the upper half of the range are very rarely encountered and such organisms are probably very able to avoid the sampling tunnel. The upper limit of the largest size bin is therefore equivalent to a particle diameter of 5500 µm. An additional bin catches all particles larger than this limit.
The system can be used in two ways:
- lowered deployment with the ship stationary (DIP)
- towed deployment (TOW)
The software for communicating with the logger puts a flag in the down loaded file to indicate which type of deployment has taken place. If the deployment was a DIP then the user is prompted to supply the latitude, longitude and echo sounding at the deployment location. If the deployment was a TOW, position and echo sounding data are logged independently on a separate PC from that used to communicate with the OPC logger. These data are referred to as navigation data and are merged with the OPC data in subsequent processing. The clock in the OPC logger is manually synchronized with that in the source of navigation data before deployment,logging of navigation data commences before initiation of logging of OPC data, and termination of logging of navigation data occurs after the OPC logger is powered down on recovery. Thus, the navigation data file is of longer duration than the OPC logger file, and be time-synchronized. A typical logging interval for navigation data would be 60s
The logger has been used to record data over a range of time intervals from 1 or 2 seconds for lowered profiles in shallow water, to 60 sec in long deep tows. There is a trade off between time interval and number of bins with respect to the capacity of the memory in the logger; 128 bins and a 1s interval equates to approximately 25 minutes endurance.
Processing software is used to decode the raw data file produced by the logger. The software assigns a latitude, longitude and echo sounding to the start, end and mid time of each sample of data. In the case of DIP deployments the same position is assumed for all samples. In the case of TOW deployments positions and echo soundings are interpolated at OPC times from the logged navigation data file.For a towed deployment the navigation data are first checked to ensure they are clean- especially with respect to erroneous echo soundings. A graphical editing programme is used to help manually clean up a the navigation data file. The edited data are written out to a new file which can be used in the data processing.
Using calibration data (pressure sensor, free flow meter and pumped flow meter) supplied by a logger configuration file:
- Pressure, counts and flow data are converted from high and low bytes to digitized variables by: variable = (256 * high byte) + low byte
- Digitized pressure is converted to metres of seawater by a calibration equation of the form: Depth (m) = A + B*variable
- Digitized flow rate is in units of impeller rev s-1, and is converted to speed through the water by: Speed (ms-1) = variable /flowcal, where flowcal has the units of revolutions m-1
The sample volume is calculated. The processing software checks the flow meter data and if it is acceptable then it is used. If not, then the volume is calculated using the distance towed over the ground in the sample interval with some correction for wire veer/recovery speed. There is an option to completely override the flow meter data it is KNOWN to be malfunctioning. In this instance all the calculations are made using distance towed. Flow meter data are utilised wherever possible.
The logged particle count data are in bins of equal width with respect to digital size. There are options to re-bin on a scale of ESD,volume, logESD or logVolume. The MLA typically realign the counts across a new set of user defined bins of equal ESD width, ususally 136 classes of 40 µm bin width, with 100 µm ESD for the lower limit.
The result of the processing is a .DAT file with a fixed structure independent of deployment type.
M.R. Heath (2001). Programmable data logger for the Focal Technology Optical Plankton Counter (OPC): Principles of operation and software manual. FRS Marine laboratory internal document.
Marine Productivity programme (MarProd)
The Marine Productivity programme (MarProd) was a Thematic Programme of the Natural Environment Research Council. It was funded for a period of five years starting in 2000. Its main goal was "to develop coupled modelling and observation systems for the pelagic ecosystem, with emphasis on physical factors affecting zooplankton dynamics" with the following specific objectives:
To identify the dominant spatial and temporal scales of physical parameters and zooplankton population dynamics, by observation, modelling and retrospective analysis
To parameterise the critical processes governing zooplankton dynamics by observations and experiments
To construct and validate spatially explicit models of zooplankton and their food and predators, capable of resolving short term changes in population structure
To provide data for model validation by developing and applying new interdisciplinary techniques to a wide spectrum of biological and physical parameters
To develop a database and information system for historic and new data and models.
The programme was composed of two phases: Phase 1 projects (2000-2002) focused on the use of historical datasets and existing biological models, complemented by laboratory experiments and remote-sensing analyses to gain a better understanding of the dynamics of zooplankton populations in shelf seas. The main, field-based Phase 2 of the programme (2001-2005) focused on the open ocean. The fieldwork phase took place between November 2001 and December 2002 and consisted of four surveys in the northern North Atlantic in early winter 2001 and 2002, and in spring and summer 2002.
MarProd was a major UK contribution to the international Global Ocean Ecosystem Dynamics project (GLOBEC).
|John T Allen (Southampton Oceanography Centre), Steven J Hay (Fisheries Research Services Aberdeen Marine Laboratory)
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
|Below detection limit
|In excess of quoted value
|Taxonomic flag for affinis (aff.)
|Beginning of CTD Down/Up Cast
|Taxonomic flag for confer (cf.)
|End of CTD Down/Up Cast
|Non-taxonomic biological characteristic uncertainty
|Taxonomic flag for single species (sp.)
|Improbable value - unknown quality control source
|Improbable value - originator's quality control
|Improbable value - BODC quality control
|Improbable value - user quality control
|no quality control
|probably good value
|probably bad value
|value below detection
|value in excess
|value phenomenon uncertain
|value below limit of quantification