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Metadata Report for BODC Series Reference Number 1072364

Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
Neil Brown MK3 CTD  CTD; water temperature sensor; salinity sensor; dissolved gas sensors
Unknown chlorophyll fluorometer  fluorometers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Tony Bale
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Online delivery of data Download available - Ocean Data View (ODV) format
Project(s) Atlantic Meridional Transect (AMT)

Data Identifiers

Originator's Identifier 281CTD1
BODC Series Reference 1072364

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 1996-10-07 11:03
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 1.0 decibars

Spatial Co-ordinates

Latitude 6.48250 S ( 6° 29.0' S )
Longitude 29.27083 W ( 29° 16.2' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 1.49 m
Maximum Sensor or Sampling Depth 202.27 m
Minimum Sensor or Sampling Height 5128.92 m
Maximum Sensor or Sampling Height 5329.71 m
Sea Floor Depth 5331.2 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
CPHLPS011Milligrams per cubic metreConcentration of chlorophyll-a {chl-a CAS 479-61-8} per unit volume of the water body [particulate >unknown phase] by in-situ chlorophyll fluorometer and calibration against sample data
FVLTZZ011VoltsRaw signal (voltage) of instrument output by in-situ chlorophyll fluorometer
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
TEMPCU011Degrees CelsiusTemperature of the water body by CTD and NO verification against independent measurements

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

No Problem Report Found in the Database

RSS James Clark Ross Cruise AMT3 CTD Data Quality Document

Fluorescence voltage (FVLTZZ01)

Many of the fluorescence voltages were above the maximum limit for this parameter. These values were flagged as suspect. There are no fluorescence profiles for casts 268CTD1, 268CTD2, 269CTD1, 269CTD2, 270CTD1, 270CTD2, 271CTD1, 271CTD2, 272CTD1 and 272CTD2.

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

James Clark Ross Cruise AMT3 CTD Instrumentation


Neil Brown Mark IIIB (Instrument Systems, Inc.) CTD
Rosette fitted with 12 10-litre General Oceanics water bottles.
PML fluorometer (not used for all casts).

Neil Brown MK3 CTD

The Neil Brown MK3 conductivity-temperature-depth (CTD) profiler consists of an integral unit containing pressure, temperature and conductivity sensors with an optional dissolved oxygen sensor in a pressure-hardened casing. The most widely used variant in the 1980s and 1990s was the MK3B. An upgrade to this, the MK3C, was developed to meet the requirements of the WOCE project.

The MK3C includes a low hysteresis, titanium strain gauge pressure transducer. The transducer temperature is measured separately, allowing correction for the effects of temperature on pressure measurements. The MK3C conductivity cell features a free flow, internal field design that eliminates ducted pumping and is not affected by external metallic objects such as guard cages and external sensors.

Additional optional sensors include pH and a pressure-temperature fluorometer. The instrument is no longer in production, but is supported (repair and calibration) by General Oceanics.


These specification apply to the MK3C version.

Pressure Temperature Conductivity

6500 m

3200 m (optional)

-3 to 32°C 1 to 6.5 S cm-1

0.0015% FS

0.03% FS < 1 msec


0.003°C < 30 msec

0.0001 S cm-1

0.0003 S cm-1 < 30 msec

Further details can be found in the specification sheet.

James Clark Ross Cruise AMT3 CTD Processing

Originator's Processing

The CTD profiles were processed onboard using RVS software.

BODC data processing

  • Reformatting

    The data files were sent to BODC in RVS internal format. All available channels were listed into ASCII format using RVS software. Non-null channels were then converted to PXF, a BODC internal format. The data were processed from 1Hz averaged down- and upcast data. Sigma-theta was calculated and output from the raw data during the conversion to PXF format.


    Originator's Parameter Originator's Units Description BODC code BODC Units Comments
    press decibars Pressure PRESPR01 decibars -
    temp °C Temperature TEMPCU01 °C -
    salin - Salinity PSALCU01 - -
    fluor V Fluorometer voltage FVLTZZ01 V For 39 casts (of 49). Unknown type
    - - Salinity - calibrated PSALCC01 - Calibrated against bottle salinity data
    - - Calibrated fluorometer CPHLPS01 mg m-3 FVLTZZ01 calibrated against bottle extracted chl-a data
    - - Potential temperature POTMCV01 °C Computed using UNESCO POTEMP function
    - - Sigma-theta SIGTPR01 kg m-3 Computed using UNESCO SVAN function
  • Screening

    The PXF data were compared with the original data files to ensure that no errors had been introduced during the conversion process. The data channels were then screened on a graphics workstation using in-house visualisation software. This allows multiple channels to be viewed simultaneously. The start and end-points of the downcast were marked. The pressure ranges over which bottles were fired were also marked. The bottle firing events were identified by disturbances in CTD parameters on the upcast profiles. All spurious and null data were flagged with appropriate BODC quality control flags.

    The following notes were made during screening of AMT3 data.

    272CTD1 had a limited downcast, and 273CTD2 had no downcast, so the upcasts for these were used for further processing.
    268CTD1 to 272CTD2 had no fluorescence profiles.
    274CTD1 and 274CTD had very high fluorescence values.
    298CTD1, 298CTD2 and 299CTD1 had noisy fluorescence signal but only the very large values were flagged as suspect.

    Temperature and salinity profiles appeared to be of good quality.

  • Loading into the BODC database

    After the data had been screened and quality controlled, the data were loaded into the BODC database under the Oracle RDBMS.

    The data from 49 casts were loaded into the data tables.


Calibration of the temperature and salinity calibrations had been made during the cruise by scientific personnel, but no corrections had been applied to the data. The results of the calibration exercise are published in the AMT3 cruise report, p.34, section 4.4.1, 'Salinity and Temperature Calibrations':

  • Pressure

    The pressure sensor had a mean reading of 1.5 decibar while the CTD was logging in air - this was identified during BODC processing. A pressure correction was, therefore, applied to the data when they were listed from the BODC database.

    PRESPR01(corr) = PRESPR01(raw) - 1.5 decibar (BODC calibration 1586).

  • Temperature

    CTD values = reversing thermometer values - 0.0119 °C ( = 0.0294).

    Due to the high standard deviation in the calibration data set, no correction has been applied to the final data set.
  • Salinity

    CTD values = Salinometer values + 0.0033 ( = 0.0082).

    This salinity calibration was applied to the data at BODC.

    PSALCC01 = PSALCU01 - 0.0033 (BODC calibration 1587)

  • Fluorometer

    The fluorometer attached to the CTD frame was a PML fluorometer. It is not known at BODC whether this was a linear or log-response instrument.

    The CTD fluorescence values were compared with fluorometric chlorophyll-a measurements made on CTD bottles. This relationship showed a linear form, and a regression was carried out. The resulting equation has been applied to the fluorescence data to create a calibrated chlorophyll-a channel.

    CPHLPS01 = 0.0253 * FVLTZZ01 + 0.0387 (BODC calibration 2923, R2 = 0.828, N = 122).

    This calibration overestimated values slightly at low concentrations.

Project Information

The Atlantic Meridional Transect (AMT) - Phase 1 (1995-2000)

Who was involved in the project?

The Atlantic Meridional Transect (AMT) programme was designed by and implemented as a collaboration between Plymouth Marine Laboratory (PML) and Southampton Oceanography Centre (SOC). The programme was hosted by Plymouth Marine Laboratory and involved additional researchers from UK and international universities throughout its duration.

What was the project about?

When AMT began in 1995 the programme provided a platform for international scientific collaboration, including the calibration and validation of SeaWiFs measurements and products. The programme provided an exceptional opportunity for nationally and internationally driven collaborative research and provided a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, the data collected by the AMT consortium informed on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.

The scientific aims were to assess:

  • mesoscale to basin scale phytoplankton processes
  • the functional interpretation of bio-optical signatures
  • the seasonal, regional and latitudinal variations in mesozooplankton dynamics

When was the project active?

The first phase of the AMT programme ran from 1995 to 2000 and consisted of a total of 12 cruises. A second phase of funding allowed the project to continue for the period 2002 to 2006 with a further 6 cruises.

Brief summary of the project fieldwork/data

The AMT programme undertook biological, chemical and physical oceanographic research during the annual return passage of the RRS James Clark Ross between the UK and the Falkland Islands or the RRS Discovery between the UK and Cape Town, a distance of up to 13,500 km. This transect crossed a range of ecosystems from sub-polar to tropical and from euphotic shelf seas and upwelling systems to oligotrophic mid-ocean gyres. The transect route was covered north-south in September/October and south-north in April/May of each year.

The measurements of hydrographic and bio-optical properties, plankton community structure and primary production completed on the first 12 transects (1995-2000) represent the most coherent set of repeated biogeochemical observations over ocean basin scales. This unique dataset has led to several important discoveries concerning the identification of oceanic provinces, validation of ocean colour algorithms, distributions of picoplankton, identifying new regional sinks of pCO2 and variability in rates of primary production and respiration.

Who funded the project?

The programme was funded by the Natural Environment Research Council (NERC) and further support was received from the National Aeronautics and Space Administration (NASA) with equipment and funding from the Sea-viewing Wild Field-of-view Sensor (SeaWiFS) project.

Data Activity or Cruise Information


Cruise Name JR19960916 (AMT3, JR15)
Departure Date 1996-09-16
Arrival Date 1996-10-25
Principal Scientist(s)Tony Bale (Plymouth Marine Laboratory)
Ship RRS James Clark Ross

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
Q value below limit of quantification