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Metadata Report for BODC Series Reference Number 928977

Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
SeaTech transmissometer  transmissometers
Sea-Bird SBE 13 Dissolved Oxygen Sensor  dissolved gas sensors
Sequoia Laser In-Situ Sediment Size Transmissometer  transmissometers; water temperature sensor; in-situ particle sizers
Sea-Bird SBE 911plus CTD  CTD; water temperature sensor; salinity sensor
LI-COR LI-192 PAR sensor  radiometers
Turner Designs SCUFA II Submersible Fluorometer  fluorometers
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Dr Alex Souza
Originating Organization Proudman Oceanographic Laboratory (now National Oceanography Centre, Liverpool)
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Oceans 2025
Oceans 2025 Theme 3
Oceans 2025 Theme 3 WP3.3
POL Dee Experiment

Data Identifiers

Originator's Identifier C001
BODC Series Reference 928977

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2008-02-12 11:06
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 0.026 decibars

Spatial Co-ordinates

Latitude 53.44783 N ( 53° 26.9' N )
Longitude 3.49350 W ( 3° 29.6' W )
Positional Uncertainty 0.05 to 0.1 n.miles
Minimum Sensor or Sampling Depth 1.22 m
Maximum Sensor or Sampling Depth 16.36 m
Minimum Sensor or Sampling Height 1.64 m
Maximum Sensor or Sampling Height 16.78 m
Sea Floor Depth 18.0 m
Sea Floor Depth Source -
Sensor or Sampling Distribution Variable common depth - All sensors are grouped effectively at the same depth, but this depth varies significantly during the series
Sensor or Sampling Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
Sea Floor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface


BODC CODERankUnitsTitle
ATTNMR011per metreAttenuation (red light wavelength) per unit length of the water body by 20 or 25cm path length transmissometer
DOXYPR011Micromoles per litreConcentration of oxygen {O2 CAS 7782-44-7} per unit volume of the water body [dissolved plus reactive particulate phase] by in-situ Beckmann probe
FVLTWS011VoltsRaw signal (voltage) of instrument output by linear-response chlorophyll fluorometer
IRRDUV011MicroEinsteins per square metre per secondDownwelling vector irradiance as photons of electromagnetic radiation (PAR wavelengths) in the water body by cosine-collector radiometer
NVLTLS011VoltsRaw signal (voltage) of instrument output by LISST scatterometer
OXYSBB011PercentSaturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by in-situ Beckmann probe and computation from concentration using Benson and Krause algorithm
POTMCV011Degrees CelsiusPotential temperature of the water body by computation using UNESCO 1983 algorithm
PRESPR011DecibarsPressure (spatial coordinate) exerted by the water body by profiling pressure sensor and correction to read zero at sea level
PSALCC011DimensionlessPractical salinity of the water body by CTD and computation using UNESCO 1983 algorithm and calibration against independent measurements
SIGTPR011Kilograms per cubic metreSigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm
TEMPCC011Degrees CelsiusTemperature of the water body by CTD and verification against independent measurements
TVLTZR011VoltsRaw signal (voltage) of instrument output by red light transmissometer

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

Problem Reports

Problem Report

Dissolved oxygen

All data from this channel should be used with caution as the values measured were unrealistic during this and several other cruises. Readings taken by the probe indicated that the sensor was constantly saturated. It is advised that the data should only be used for relative comparisons.

Data quality notes

LISST transmission and scattering

Users should be aware that the clear water values measured on different cruises are observed to increase and decrease at times, which is not consistent behaviour. In addition, the clear water scattering values are also sometimes less than and sometimes greater than those measured by the manufacturer at the time of last calibration (October 2006). This may be due to a problem with the instrument or the method in which the clear water values are measured.

Data Access Policy

Open Data supplied by Natural Environment Research Council (NERC)

You must always use the following attribution statement to acknowledge the source of the information: "Contains data supplied by Natural Environment Research Council."

Narrative Documents

Sea Bird Electronics SBE13 Dissolved Oxygen Sensor

The SBE 13 was designed as an auxiliary sensor for Sea Bird SBE 9plus, but can fitted in custom instrumentation applications. When used with the SBE 9 Underwater Unit, a flow-through plenum improves the data quality, as the pumping water over the sensor membrane reduces the errors caused by oxygen depletion during the periods of slow or intermittent flushing and also reduces exposure to biofouling.

The output voltage is proportional to membrane current (oxygen current) and to the sensor element's membrane temperature (oxygen temperature), which is used for internal temperature compensation.

Two versions of the SBE 13 are available: the SBE 13Y uses a YSI polarographic element with replaceable membranes to provide in situ measurements up to 2000 m depth and the SBE 13B uses a Beckman polarographic element to provide in situ measurements up to 10500 m depth, depending on the sensor casing. This sensor includes a replaceable sealed electrolyte membrane cartridge.

The SBE 13 instrument has been out of production since 2001 and has been superseded by the SBE 43.


Measurement range 0 to 15 mL L-1
Accuracy 0.1 mL L-1
Time response

2 s at 25°C

5 s at 0°C

Depth range

2000 m (SBE 13Y- housing in anodized aluminum)

6800 m (SBE 13B- housing in anodized aluminum)

105000 m (SBE 13B- housing in titanium)

Further details can be found in the manufacturer's specification sheet.

Prince Madog Cruise PD04_08 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911plus system (SN P23655-0620), with dissolved oxygen sensor. The CTD was fitted with a red (660 nm) beam transmissometer, a fluorometer, a Sequoia Scientific Laser In-Situ Scattering and Transmissometry (LISST) particle analyser and a LI-COR Underwater Quantum Sensor. The Sea-Bird sensors SBE 3,4 and 13 Beckmann were last calibrated by the manufacturer in January 2004. Also attached was a Sea-Bird SBE-35 Temperature Logger to supply an independent check of temperature. All instruments were attached to a Sea-Bird SBE 32 compact carousel. The table below lists more detailed information about the various sensors.

Sensor Model Serial Number Calibration Comments
Pressure transducer Paroscientific Digiquartz 42A-105 76076 21/01/2004 -
Conductivity sensor SBE 4 2543 14/01/2004 -
Temperature sensor SBE 3 P4100 21/01/2004 -
Dissolved oxygen SBE 13 Beckmann 130580 05/01/2004 -
Transmissometer 660 nm SeaTech T1000 T1021 03/03/1998 0.2 m path
Fluorometer Turner SCUFA II 262 - -
LISST 25 120 26/10/2006 Range: 1.25 to 250 µm
LI-COR LI 192SB 26 - -
Temperature Logger SBE-35 0041 29/05/2005 -

Change of sensors during cruise: None reported.

Sampling device

Rosette sampling system equipped with 5 l sampling bottles (manufactured by Ocean Test Equipment Inc.).

Sea-Bird Electronics SBE 911 and SBE 917 series CTD profilers

The SBE 911 and SBE 917 series of conductivity-temperature-depth (CTD) units are used to collect hydrographic profiles, including temperature, conductivity and pressure as standard. Each profiler consists of an underwater unit and deck unit or SEARAM. Auxiliary sensors, such as fluorometers, dissolved oxygen sensors and transmissometers, and carousel water samplers are commonly added to the underwater unit.

Underwater unit

The CTD underwater unit (SBE 9 or SBE 9 plus) comprises a protective cage (usually with a carousel water sampler), including a main pressure housing containing power supplies, acquisition electronics, telemetry circuitry, and a suite of modular sensors. The original SBE 9 incorporated Sea-Bird's standard modular SBE 3 temperature sensor and SBE 4 conductivity sensor, and a Paroscientific Digiquartz pressure sensor. The conductivity cell was connected to a pump-fed plastic tubing circuit that could include auxiliary sensors. Each SBE 9 unit was custom built to individual specification. The SBE 9 was replaced in 1997 by an off-the-shelf version, termed the SBE 9 plus, that incorporated the SBE 3 plus (or SBE 3P) temperature sensor, SBE 4C conductivity sensor and a Paroscientific Digiquartz pressure sensor. Sensors could be connected to a pump-fed plastic tubing circuit or stand-alone.

Temperature, conductivity and pressure sensors

The conductivity, temperature, and pressure sensors supplied with Sea-Bird CTD systems have outputs in the form of variable frequencies, which are measured using high-speed parallel counters. The resulting count totals are converted to numeric representations of the original frequencies, which bear a direct relationship to temperature, conductivity or pressure. Sampling frequencies for these sensors are typically set at 24 Hz.

The temperature sensing element is a glass-coated thermistor bead, pressure-protected inside a stainless steel tube, while the conductivity sensing element is a cylindrical, flow-through, borosilicate glass cell with three internal platinum electrodes. Thermistor resistance or conductivity cell resistance, respectively, is the controlling element in an optimized Wien Bridge oscillator circuit, which produces a frequency output that can be converted to a temperature or conductivity reading. These sensors are available with depth ratings of 6800 m (aluminium housing) or 10500 m (titanium housing). The Paroscientific Digiquartz pressure sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

Additional sensors

Optional sensors for dissolved oxygen, pH, light transmission, fluorescence and others do not require the very high levels of resolution needed in the primary CTD channels, nor do these sensors generally offer variable frequency outputs. Accordingly, signals from the auxiliary sensors are acquired using a conventional voltage-input multiplexed A/D converter (optional). Some Sea-Bird CTDs use a strain gauge pressure sensor (Senso-Metrics) in which case their pressure output data is in the same form as that from the auxiliary sensors as described above.

Deck unit or SEARAM

Each underwater unit is connected to a power supply and data logging system: the SBE 11 (or SBE 11 plus) deck unit allows real-time interfacing between the deck and the underwater unit via a conductive wire, while the submersible SBE 17 (or SBE 17 plus) SEARAM plugs directly into the underwater unit and data are downloaded on recovery of the CTD. The combination of SBE 9 and SBE 17 or SBE 11 are termed SBE 917 or SBE 911, respectively, while the combinations of SBE 9 plus and SBE 17 plus or SBE 11 plus are termed SBE 917 plus or SBE 911 plus.


Specifications for the SBE 9 plus underwater unit are listed below:

Parameter Range Initial accuracy Resolution at 24 Hz Response time
Temperature -5 to 35°C 0.001°C 0.0002°C 0.065 sec
Conductivity 0 to 7 S m-1 0.0003 S m-1 0.00004 S m-1 0.065 sec (pumped)
Pressure 0 to full scale (1400, 2000, 4200, 6800 or 10500 m) 0.015% of full scale 0.001% of full scale 0.015 sec

Further details can be found in the manufacturer's specification sheet.

Turner Designs Self-Contained Underwater Fluorescence Apparatus (SCUFA)

The Turner Designs SCUFA is a submersible fluorometer for chlorophyll and dye tracing operations that has been designed to operate in a wide range of concentrations, environmental conditions as well as operational modes (profiling or moored deployments). The instrument includes an integrated temperature probe and software which allow for automatic correction of fluorescence data from temperature effects. The superior ambient light rejection eliminates the effects of sunlight and allows the SCUFA to be used in surface waters without the need for external pumps or light shields.

Each instrument can be customised to meet user requirements. Users can choose one of the following channels: chlorophyll a, cyanobacteria (phycocyanin or phycoerythrin pigments), rhodamine WT, fluorescein and turbidity. Instrument options include turbidity, internal data logging and automatic temperature correction.

Three versions of the SCUFA are available: SCUFA I, II and III. SCUFA I and II are used for chlorophyll a applications, while SCUFA III is used for Rhodamine WT. Models II and III include a turbidity channel that is not present on model I. The SCUFA has been out of production since 2008.


Depth rating 600 m
Detector Photodiode
Temperature range -2 to 40°C
Maximum sampling rate

1Hz- digital

5 Hz- analog


12 bit- digital

1.2 mV- analog

Dynamic Range
Fluorescence 4 orders of magnitude
Turbidity 3 orders of magnitude

The table below presents the specifications for the different channels.

Specifications Chlorophyll Cyanobacteria Rhodamine WT/Fluorescein
Light source Blue

Orange- PC

Blue- PE

Excitation/Emission 460/685

595/670 (phycocyanin, PC)

528/573 (phycoerythrin, PE)

530/600 (rhodamine)

490/580 (fluorescein)

Minimum detection Limit
Fluorescence 0.02 µg L-1 150 cells mL-1 0.04 ppb
Turbidity 0.05 NTU 0.05 NTU 0.05 NTU

Further details can be found in the manufacturer's brochure.

LI-COR LI-192 Underwater Quantum Sensor

The LI-192 Underwater Quantum Sensor is used to measure photosynthetic photon flux density and is cosine corrected. The sensor is often referred to as LI-192SA or LI-192SB (the LI-192SB model was superseded by LI-192SA). One of the main differences is that the LI-192SA model includes a built-in voltage output for interfacing with NexSens iSIC and SDL data loggers.

Sensor specifications, current at January 2012, are given in the table below. More information can be found in the manufacturer's LI-192SA andLI-192SB specification sheets.

Sensor Specifications

(Specifications apply to both models unless otherwise stated)

Absolute Calibration ± 5 % in air traceable to NBS.
Sensitivity Typically 3 µA per 1000 µmol s-1 m-2 for LI-192SB and 4 µA per 1000 µmol s-1 m-2 for LI-192SA in water.
Linearity Maximum deviation of 1 % up to 10,000 µmol s-1 m-2.
Stability < ± 2 % change over a 1 year period.
Response Time 10 µs.
Temperature Dependence ± 0.15 % per °C maximum.
Cosine Correction Optimized for both underwater and atmospheric use.
Azimuth < ± 1 % error over 360 ° at 45 ° elevation.
Detector High stability silicon photovoltaic detector (blue enhanced).
Sensor Housing Corrosion resistant metal with acrylic diffuser for both saltwater and freshwater applications. Waterproof to withstand 800 psi (5500 kPa) (560 meters).

SeaTech Transmissometer


The transmissometer is designed to accurately measure the the amount of light transmitted by a modulated Light Emitting Diode (LED) through a fixed-length in-situ water column to a synchronous detector.


  • Water path length: 5 cm (for use in turbid waters) to 1 m (for use in clear ocean waters).
  • Beam diameter: 15 mm
  • Transmitted beam collimation: <3 milliradians
  • Receiver acceptance angle (in water): <18 milliradians
  • Light source wavelength: usually (but not exclusively) 660 nm (red light)


The instrument can be interfaced to Aanderaa RCM7 current meters. This is achieved by fitting the transmissometer in a slot cut into a customized RCM4-type vane.

A red LED (660 nm) is used for general applications looking at water column sediment load. However, green or blue LEDs can be fitted for specilised optics applications. The light source used is identified by the BODC parameter code.

Further details can be found in the manufacturer's Manual.

Sequoia Laser In-situ Sediment Size Transmissometer (LISST)

The Sequoia LISST measures particle size distribution of suspended sediments by laser diffraction. This technique allows particles of various compositions to be measured with a single device and, because the particle volume is roughly of the same order for all sizes, the required dynamic range of the sensors is reduced compared with single-particle counters.

The instrument includes optics for producing a collimated laser beam, a detector array, electronics for signal amplification and processing, a data storage and scheduling computer and a battery system. The primary measurement is the scattering of laser light at a number of angles, which is mathematically inverted to give a grain size distribution, and also scaled to obtain the volume scattering function. The size distribution is presented as concentration in each of 32 logarithmically-spaced grain-size class bins. Optical transmission, water depth and temperature are recorded as supporting measurements.

Several models are available and although the principals of operation are the same, their specifications vary slightly. The specifications for model LISST-100 are provided below.


Optical path length

5 cm (standard)

2.5 cm (optional)

Optical transmission 12 bit resolution
Particle size range

Type B: 1.25 to 250 micron diameter

Type C: 2.5 to 500 micron diameter

Resolution 32 size classes, log-spaced
VSF angle range 1.7 to 340 mrad
Maximum sample speed 4 size distributions per second (standard)
Temperature range -10 to 45 °C
Temperature resolution 0.01 °C
Pressure range 0 to 300 m
Pressure resolution 8 cm

Further details can be found in the manufacturer's manual.

Prince Madog Cruise PD04_08 CTD Processing

Sampling strategy

A total of 84 CTD casts were performed during the cruise throughout Liverpool Bay. Rosette bottles were fired throughout the water column on the upcast of most profiles. Data were measured at 24 Hz and averaged to 1 Hz by a PC running SEASAVE, Sea-Bird's data acquisition software. The raw Sea-Bird data, configuration and bottle files were supplied to BODC for further processing.

BODC post-processing and screening

  • Sea-Bird processing

    The raw CTD files were processed through the Sea-Bird SBE Data Processing software version 7.16. Binary (.HEX) files were converted to engineering units and ASCII format (.CNV) using the DATCNV program.

    Sea-Bird bottle files (.BTL), with information on pressure and other logged readings at the time of bottle firing, were also generated during the data conversion process.

    Sea-Bird software program ALIGNCTD was run to advance conductivity by 0 s and oxygen by 3 s (within the typical range given in the Sea-Bird manual). No adjustment was made to the temperature channel as the fast sensor response time renders this unnecessary, according to the Sea-Bird literature.

    To compensate for conductivity cell thermal mass effects, the data files were run through CELLTM, using alpha = 0.03, 1/beta = 7, typical values for this CTD model given in the Sea-Bird literature. After running WILD EDIT, FILTER was run on the pressure channel using the recommended time filter of 0.15 s. Next, a minimum CTD velocity of 0.0 m s-1 was used for LOOP EDIT in order to exclude scans where the CTD was travelling backwards due to ship's heave. Salinity, density (Sigma-theta kg m-3) and oxygen concentration (ml l-1) were then calculated and added to the output files using the DERIVE program. Finally, the first oxygen concentration channel and first salinity channel (both generated by DATCNV using data unadjusted by ALIGN CTD and CELL TM) were dropped using STRIP.

  • Reformatting

    The data were converted from ASCII format into BODC internal format (QXF) using BODC transfer function 357. The following table shows how the variables within the ASCII files were mapped to appropriate BODC parameter codes:

    Originator's Parameter Name Units Description BODC Parameter Code Units Comments
    Pressure, Digiquartz dbar CTD pressure PRESPR01 dbar -
    Oxygen, Beckman/YSI ml l-1 Dissolved oxygen concentration from Beckmann probe DOXYPR01 µmol l-1 Converted from ml l-1 to µmol l-1 by multiplying the original value by 44.66.
    Salinity - Practical salinity of the water body by CTD PSALCU01 - Generated by Sea-Bird software from CTD temperature and conductivity data
    Temperature [ITS-90] °C Temperature of water column by CTD TEMPCU01 °C -
    Voltage 2 Un-adjusted volts Voltage from CTD PAR Sensor LVLTLD01 Un-adjusted volts -
    Voltage 3 Un-adjusted volts Beam transmissometer voltage TVLTCR01 Un-adjusted volts -
    Voltage 4 Un-adjusted volts Voltage from CTD SCUFA Turner fluorometer FVLTWS01 Un-adjusted volts -
    Voltage 6 Un-adjusted volts LISST scatterometer voltage output NVLTLS01 Un-adjusted volts -
    Voltage 7 Un-adjusted volts LISST transmissometer voltage output TVLTZR01 Un-adjusted volts -
    - - Potential temperature POTMCV01 °C Generated by BODC using UNESCO Report 38 (1981) algorithm with parameters PSALCC01 and TEMPCC01
    - - Sigma-theta SIGTPR01 kg m-3 Generated by BODC using the Fofonoff and Millard (1982) algorithm
    - - PAR IRRDUV01 µE m-2 s-1 Generated by BODC from calibration of LVLTLD01
    - - Beam Attenuation ATTNMR01 m-1 Generated by BODC from calibration of TVLTCR01
    - - Salinity PSALCC01 - Generated by BODC from calibration of PSALCU01
    - - Temperature TEMPCC01 °C Generated by BODC from calibration of TEMPCU01
    - - Oxygen saturation OXYSBB01 % Generated by BODC during transfer using the Benson and Krause (1984) algorithm.
  • References

    Benson, B.B. and Krause, D., 1984. The concentration and isotopic fractionation of oxygen dissolved in freshwater and seawater in equilibrium with the atmosphere. Limnol. Oceanogr., 29(3), 620-632

    Fofonoff, N.P. and Millard, R.C., 1983. Algorithms for computations of fundamental properties of seawater. UNESCO Technical Papers in Marine Science No. 44, 53pp.

    UNESCO, 1981. Background papers and supporting data on the International Equation of State of Seawater 1980. UNESCO Technical Papers in Marine Science No. 38, 192pp

  • Banking

    Once quality control screening was complete, the CTD downcasts were banked. Finally, the data were binned against pressure at 0.5 dbar increments.

  • Screening

    Reformatted CTD data were transferred onto a graphics work station for visualisation using the in-house editor EDSERPLO. Downcasts and upcasts were differentiated and the limits manually flagged. No data values were edited or deleted. Flagging was achieved by modification of the associated quality control flag to 'M' for suspect values and 'N' for nulls.

Field Calibrations

  • Salinity

    41 independent salinity samples, obtained from the CTD rosette, were used to calibrate the CTD. 13 data points (casts C009, C013, C015, C017, C033, C035, C037, C045, C047, C063, C067, C077, C084) were identified as outliers and were removed from the analysis. The offset between CTD salinity and independent salinity samples was found, using regression analysis, to be significant at 95% confidence. A calibration equation was derived from the regression as follows, based on 28 observations: calibrated salinity = CTD salinity * 1.017915 - 0.630109. The residual range for the calibration is between -0.7686 and 0.0558 and the RMS error is 0.2175. The mean offset is -0.1549 and the standard deviation for this dataset is 0.2011.

  • Temperature

    88 independent temperature values were compared to pressure and CTD temperature. Eight data points were identified as outliers and were removed from the analysis. The offset between CTD temperature and SBE-35 temperature was found not to be significantly different from zero at 95% confidence. Therefore, there was no adjustment to the CTD temperature resulting from the application of manufacturer's coefficients during initial processing. The mean offset is -0.003134 and the standard deviation for this dataset is 0.007349.

  • Pressure

    There were no casts where the CTD pressure was logging in air. No adjustments were made to the values resulting from application of manufacturer's coefficients during the intial processing.

  • Beam attenuation

    Coefficients M and B were calculated, allowing calibration of the transmissometer with air readings taken during the cruise. M and B are calculated according to SBE Application Note No. 7:

    M = (Tw/W0)*(A0-Y0)/(A1-Y1)
    B= -M*Y1

    Where Tw is the percent transmission for pure water for the instrument (92.98%); W0 is the voltage output in pure water (4.649 volts); A0 is the manufacturer's air voltage (4.661 volts); Y0 is the manufacturer's blocked path voltage (0.000 volts); A1 is the cruise maximum air voltage (4.479 volts); Y1 is the current blocked path voltage (0.008 volts). For this cruise, M and B were calculated to be 20.8499 and -0.167, respectively.

    M and B are then inserted into the following equations (from SBE Application Note No. 7) to obtain calibrated beam attenuation:

    Light transmission [%] = (M * voltage output) + B
    Beam attenuation coefficient c = - (1/z) * ln (light transmission [decimal])

    M and B are the calibration coefficients, z is the transmissometer path length (0.2 m), light transmission[decimal] is light transmission [%] divided by 100, c = beam attenuation (m-1)

    Several casts (C007, C008, C037, C068) had logged voltages which were lower than the blocked path reading. The blocked path reading is normally expected to be lower than readings logged in the environment. There were two possible explanations: an incorrect blocked path reading or a problem with the transmissometer.

    Data from several previous cruises were examined to see if the behaviour of the transmissometer had changed over time. This was not found to be the case and it was felt that the transmissometer was functioning normally throughout this cruise. The blocked path reading for this cruise was 0.008 volts. For previous cruises, the lowest blocked path readings were consistently zero. As the transmissometer appeared to be behaving normally, the conclusion was that the supplied blocked path reading (0.008) was incorrect and it should be replaced by the blocked path reading used for previous cruises (0.000). This resulted in a new M and B value as follows: M = 20.8127, B = 0. These were the values used to obtain calibrated beam attenuation.

  • Dissolved oxygen

    The data are currently uncalibrated.

  • Fluorescence


  • LISST transmission and scattering

    The data are currently uncalibrated. However, the voltages can be calibrated to give optical transmission, beam attenuation, total volume concentration and Sauter mean diameter according to the following manufacturer's constants and calculations:

    Optical Transmission = b = (VT-VToff)/(VTO-VToff)

    Beam attenuation = -ln(b)/0.025 - units are metres-1, assumes 25 mm path

    Total volume concentration = TV = cal*[((VS-VSoff)/b)-(VSO-VSoff)] - units are µl l-1

    Sauter mean diameter = SMD = a*[TV/(-ln(b)] - units are µm

    Where cal = total volume concentration calibration constant = 160, a = Sauter mean diameter calibration constant = 0.09, VSO = clearwater scattering output = 0.150 V (see note below), VTO = clear water transmission output = 3.215 V (see note below), VSoff = scattering output offset = 0.10 V, VToff = transmission output offset = 0.10 V. Measured outputs are scattering = VS and transmission = VT.

    N.B. The clear water values quoted above are supplied by the manufacturer. Ideally these should be replaced by values determined by the LISST calibration cast, during which the instrument is placed in a tank of clean water. However, there is suspicion that these values may not be accurate. There are abnormally high values for some cruises, which the manufacturer suggests may be due to the calibration dip occurring in insufficiently clear water. Therefore, manufacturer's values have been quoted along with values measured by the instrument during previous cruises. Users are advised to use their own discretion in deciding which coefficients to apply.

    Date Cruise VT0 VS0
    2005-02-28 PD07_05 3.280 0.465
    2005-04-05 PD11_05 3.299 0.455
    2005-05-10 PD18_05 3.365 0.460
    2005-06-14 PD21_05 3.371 0.479
    2005-07-13 PD25_05 3.415 0.486
    2005-08-16 PD30_05 3.171 0.463
    2005-09-14 PD34_05 3.156 0.471
    2005-10-26 PD41_05 3.145 0.442
    2005-12-13 PD48_05 2.957 0.463
    2006-02-05 PD04_06/PD05_06 3.071 0.523
    2006-03-05 PD09_06 3.156 0.611
    2006-04-04 PD12_06 2.969 0.447
    2006-05-08 PD16_06 2.904 0.446
    2006-12-12 PD37_06 2.723 0.156
    2007-02-12 PD02_07 2.74 0.154
    2007-04-15 PD06_07 2.722 0.167
    2007-06-29 PD13_07 2.479 0.209
    2007-07-25 PD16_07 2.430 0.211
    2007-08-28 PD20_07 2.455 0.208
    2007-11-20 PD27_07 2.707 0.158
    2008-01-08 PD01_08 2.687 0.158
    - PD04_08 Not supplied Not supplied
  • PAR

    During instrument deployment, no effort was made to avoid data collection possibly being affected by ship shadowing. The LI-COR LI 192SB sensor number 26 was calibrated from raw voltages using the CEFAS supplied equation:

    PAR = 0.135278*exp(volts*3.4544)

Project Information

Oceans 2025 Theme 3, Work Package 3.3: Bottom Boundary Layer, Optics and Suspended Sediments Processes

This Work Package (WP) is a combination of Work Package 3.3 and 3.4 as proposed in the original Oceans 2025 proposal. It continues and expands the research undertaken in the Proudman Oceanographic Laboratory Dee Experiment project.

Sediment transport process models underpin scientific ability to predict the entrainment of sediments into the water column and the transport of sediments for forecasting seabed and coastal morphodynamic evolution. The difficulty in achieving accurate process models lies with the complex inter-dependence of sediment processes in the bottom boundary layer. Near the bed, the fundamentals of sediment transport are governed by interactions between the sediment transport triad; the bed, the hydrodynamics and the mobile sediments. These three components interrelate, being mutually interactive and interdependent.

POL aim to use a combination of high-frequency underwater acoustics and laser optical measurements to make co-located simultaneous measurements of the triad. These measurements provide an observational framework capable of assessing and advancing the latest sediment transport models available. These measurements will be made in a range of environments, with the objective of achieving significant advances in understanding and modelling capability in coastal sediment transport. POL will also address the dynamics of suspended sediment behaviour in the context of sediment supply to the coastal zone from estuaries, and of coastal water column optical properties. Ths will allow improvement of the modelling accuracy of coastal suspended sediment transport and enable development of a new description of sediment suspension and water opacity that will improve simulation of coastal primary productivity.

The specific objectives are:

  • Assess process-based models over different sediment types, cohesive to non-cohesive
  • Investigate intra-wave and turbulence processes over flat and rippled beds to improve process based sediment transport models; parameterisation of the process modelling output for input into large-scale area models
  • Advance the description and parameterisation of the impact benthic biota has on sediment transport processes (jointly with the Plymouth Marine Laboratory (PML))
  • Acquire new knowledge of the dynamics of sediment flocculation and its impact on suspended particulate material (SPM) in shelf seas and estuaries
  • Provide preliminary formulations for aggregation-disaggregation and test these formulations using shelf sea models of the Eastern Irish Sea
  • Develop understanding of the processes that affect the sediment fluxes between estuaries and the adjacent shelf sea.
  • Derive and apply formulations of the effects of SPM on optical attenuation and absorption and assess their potential impact on primary productivity using existing models


The study site chosen by POL for this research was the Dee Estuary, Liverpool Bay. POL performed fieldwork in the Hilbre Channel on the eastern side of the Estuary and the Welsh Channel on the western exit of the Estuary, with emphasis placed on two repeat stations, HC and WC. The fieldwork under Work Package 3.3 commenced in April 2007 and has been summarised below:

Cruise Dates Hilbre Channel Welsh Channel
PD06_07 2007-04-16 to 2007-04-19 18 hour CTD station
Mooring recovery
15 hour CTD station
Mooring recovery
PD04_08 2008-02-12 to 2008-02-15 25 hour CTD station
2 x mooring deployment
19 hour CTD station
1 x mooring deployment
PD02_09A 2009-02-02 to 2009-02-04 25 hour CTD station
1 x mooring deployment
22 hour CTD station
1 mooring deployment
PD06_09 2009-03-03 to 2009-03-05 25 hour CTD station
Mooring recovery
18 hour CTD station
Mooring recovery

More detailed information on this Work Package is available at pages 8 - 9 and 9-10 of the official Oceans 2025 Theme 3 document: Oceans 2025 Theme 3


Oceans 2025 Theme 3: Shelf and Coastal Processes

Over the next 20 years, UK local marine environments are predicted to experience ever-increasing rates of change - including increased temperature and seawater acidity, changing freshwater run-off, changes in sea level, and a likely increase in flooding events - causing great concern for those charged with their management and protection. The future quality, health and sustainability of UK marine waters require improved appreciation of the complex interactions that occur not only within the coastal and shelf environment, but also between the environment and human actions. This knowledge must primarily be provided by whole-system operational numerical models, able to provide reliable predictions of short and long-term system responses to change.

However, such tools are only viable if scientists understand the underlying processes they are attempting to model and can interpret the resulting data. Many fundamental processes in shelf edge, shelf, coastal and estuarine systems, particularly across key interfaces in the environment, are not fully understood.

Theme 3 addresses the following broad questions:

  • How do biological, physical and chemical processes interact within shelf, coastal and estuarine systems, particularly at key environmental interfaces (e.g. coastline, sediment-water interface, thermocline, fronts and the shelf edge)?
  • What are the consequences of these interactions on the functioning of the whole coastal system, including its sensitivity and/or resilience to change?
  • Ultimately, what changes should be expected to be seen in the UK coastal environment over the next 50 years and beyond and how might these changes be transmitted into the open ocean?

Within Oceans 2025, Theme 3 will develop the necessary understanding of interacting processes to enable the consequences of environmental and anthropogenic change on UK shelf seas, coasts and estuaries to be predicted. Theme 3 will also provide knowledge that can improve the forecasting capability of models being used for the operational management of human activities in the coastal marine environment. Theme 3 is therefore directly relevant to all three of NERC's current strategic priorities; Earth's Life-Support Systems, Climate Change, and Sustainable Economies

The official Oceans 2025 documentation for this Theme is available from the following link: Oceans 2025 Theme 3


Proudman Oceanographic Laboratory Dee Experiment


Sediment transport process models are a vital tool in allowing scientists to predict sediment transport and forecast seabed and coastal morphodynamic evolution. It is however, difficult to obtain accurate models due to the complex inter-dependence of sediment processes in the bottom boundary layer. This inter-dependence is governed by interactions between the sediment transport triad; the bed, the hydrodynamics and the mobile sediments.

Scientific Objectives

  • To use a varying suite of instruments to make co-located measurements of the sediment triad
  • To provide a framework to allow assessment and improvement of the latest sediment transport models
  • To address dynamics of suspended sediments in terms of supply of material to the coastal zone from estuaries
  • Development of a new description of suspended sediment and water opacity to improve simulation of coastal primary productivity


The study site chosen by POL for this research was the Dee Estuary, Liverpool Bay. POL performed fieldwork in the Hilbre Channel on the eastern side of the Estuary and the Welsh Channel on the western exit of the Estuary, with emphasis placed on two repeat stations, HC and WC. The fieldwork started in February 2005 and has been summarised below:

Cruise Dates Hilbre Channel Welsh Channel
PD03_05 2005-02-03 to 2005-02-04 25 hour CTD station
3 x mooring deployments
13 hour CTD station
1 mooring deployment
PD07_05 2005-03-03 to 2005-03-04 23 hour CTD station
Mooring recovery
19 hour CTD station
Mooring recovery
PD05_06 2006-02-08 to 2006-02-10 24 hour CTD station
2 x mooring deployment
22 hour CTD station
1 mooring deployment
PD09_06 2006-03-06 to 2006-03-09 23 hour CTD station
Mooring recovery
25 hour CTD station
Mooring recovery
PD04_07 2007-03-13 to 2007-03-16 25 hour CTD station
2 x mooring deployment
25 hour CTD station
1 mooring deployment


The Dee Experiment project was core funded by POL under Programme 2 (Shallow coastal seas) Theme 5 (Coastal and sediment processes) of POL's Science Programme 2001 - 2006. From March 2007 onwards, this core funding was replaced by funding from NERC's Oceans 2025 programme and the Dee Experiment research continued as part of Oceans 2025 Work Package 3.3.

Oceans 2025 - The NERC Marine Centres' Strategic Research Programme 2007-2012

Who funds the programme?

The Natural Environment Research Council (NERC) funds the Oceans 2025 programme, which was originally planned in the context of NERC's 2002-2007 strategy and later realigned to NERC's subsequent strategy (Next Generation Science for Planet Earth; NERC 2007).

Who is involved in the programme?

The Oceans 2025 programme was designed by and is to be implemented through seven leading UK marine centres. The marine centres work together in coordination and are also supported by cooperation and input from government bodies, universities and other partners. The seven marine centres are:

  • National Oceanography Centre, Southampton (NOCS)
  • Plymouth Marine Laboratory (PML)
  • Marine Biological Association (MBA)
  • Sir Alister Hardy Foundation for Marine Science (SAHFOS)
  • Proudman Oceanographic Laboratory (POL)
  • Scottish Association for Marine Science (SAMS)
  • Sea Mammal Research Unit (SMRU)

Oceans2025 provides funding to three national marine facilities, which provide services to the wider UK marine community, in addition to the Oceans 2025 community. These facilities are:

  • British Oceanographic Data Centre (BODC), hosted at POL
  • Permanent Service for Mean Sea Level (PSMSL), hosted at POL
  • Culture Collection of Algae and Protozoa (CCAP), hosted at SAMS

The NERC-run Strategic Ocean Funding Initiative (SOFI) provides additional support to the programme by funding additional research projects and studentships that closely complement the Oceans 2025 programme, primarily through universities.

What is the programme about?

Oceans 2025 sets out to address some key challenges that face the UK as a result of a changing marine environment. The research funded through the programme sets out to increase understanding of the size, nature and impacts of these changes, with the aim to:

  • improve knowledge of how the seas behave, not just now but in the future;
  • help assess what that might mean for the Earth system and for society;
  • assist in developing sustainable solutions for the management of marine resources for future generations;
  • enhance the research capabilities and facilities available for UK marine science.

In order to address these aims there are nine science themes supported by the Oceans 2025 programme:

  • Climate, circulation and sea level (Theme 1)
  • Marine biogeochemical cycles (Theme 2)
  • Shelf and coastal processes (Theme 3)
  • Biodiversity and ecosystem functioning (Theme 4)
  • Continental margins and deep ocean (Theme 5)
  • Sustainable marine resources (Theme 6)
  • Technology development (Theme 8)
  • Next generation ocean prediction (Theme 9)
  • Integration of sustained observations in the marine environment (Theme 10)

In the original programme proposal there was a theme on health and human impacts (Theme 7). The elements of this Theme have subsequently been included in Themes 3 and 9.

When is the programme active?

The programme started in April 2007 with funding for 5 years.

Brief summary of the programme fieldwork/data

Programme fieldwork and data collection are to be achieved through:

  • physical, biological and chemical parameters sampling throughout the North and South Atlantic during collaborative research cruises aboard NERC's research vessels RRS Discovery, RRS James Cook and RRS James Clark Ross;
  • the Continuous Plankton Recorder being deployed by SAHFOS in the North Atlantic and North Pacific on 'ships of opportunity';
  • physical parameters measured and relayed in near real-time by fixed moorings and ARGO floats;
  • coastal and shelf sea observatory data (Liverpool Bay Coastal Observatory (LBCO) and Western Channel Observatory (WCO)) using the RV Prince Madog and RV Quest.

The data is to be fed into models for validation and future projections. Greater detail can be found in the Theme documents.

Data Activity or Cruise Information


Cruise Name PD04/08
Departure Date 2008-02-12
Arrival Date 2008-02-15
Principal Scientist(s)Alejandro J Souza (Proudman Oceanographic Laboratory)
Ship RV Prince Madog

Complete Cruise Metadata Report is available here

Fixed Station Information

No Fixed Station Information held for the Series

BODC Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Flag Description
Blank Unqualified
< Below detection limit
> In excess of quoted value
A Taxonomic flag for affinis (aff.)
B Beginning of CTD Down/Up Cast
C Taxonomic flag for confer (cf.)
D Thermometric depth
E End of CTD Down/Up Cast
G Non-taxonomic biological characteristic uncertainty
H Extrapolated value
I Taxonomic flag for single species (sp.)
K Improbable value - unknown quality control source
L Improbable value - originator's quality control
M Improbable value - BODC quality control
N Null value
O Improbable value - user quality control
P Trace/calm
Q Indeterminate
R Replacement value
S Estimated value
T Interpolated value
U Uncalibrated
W Control value
X Excessive difference

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Flag Description
0 no quality control
1 good value
2 probably good value
3 probably bad value
4 bad value
5 changed value
6 value below detection
7 value in excess
8 interpolated value
9 missing value
A value phenomenon uncertain
B nominal value
Q value below limit of quantification