Metadata Report for BODC Series Reference Number 1113365

Metadata Summary

Data Description

Data Category CTD or STD cast
Instrument Type
Sea-Bird SBE 43 Dissolved Oxygen Sensor  dissolved gas sensors
Chelsea Technologies Group 2-pi PAR irradiance sensor  radiometers
Sea-Bird SBE 911plus CTD  CTD; water temperature sensor; salinity sensor
WETLabs C-Star transmissometer  transmissometers
Paroscientific 410K Pressure Transducer  water temperature sensor; water pressure sensors
Sea-Bird SBE 3plus (SBE 3P) temperature sensor  water temperature sensor
Sea-Bird SBE 4C conductivity sensor  salinity sensor
Chelsea Technologies Group Aquatracka III fluorometer  fluorometers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Rob Thomas
Originating Organization British Oceanographic Data Centre, Liverpool
Processing Status banked
Project(s) -

Data Identifiers

Originator's Identifier CTD041
BODC Series Reference 1113365

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2012-11-01 13:59
End Time (yyyy-mm-dd hh:mm) 2012-11-01 14:52
Nominal Cycle Interval 1.0 decibars

Spatial Co-ordinates

Latitude 2.92922 S ( 2° 55.8' S )
Longitude 24.98371 W ( 24° 59.0' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor Depth 4.97 m
Maximum Sensor Depth 501.61 m
Minimum Sensor Height 4826.39 m
Maximum Sensor Height 5323.03 m
Sea Floor Depth 5328.0 m
Sensor Distribution Variable common depth - All sensors are grouped effectively at the same depth, but this depth varies significantly during the series
Sensor 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 CODE Rank Units Short Title Title
ACYCAA01 1 Dimensionless Record_No Sequence number
ATTNDR01 1 per metre Attn_Red_25cm Attenuation (red light wavelength) per unit length of the water body by 25cm path length red light transmissometer
CPHLPS01 1 Milligrams per cubic metre chl-a_water_ISfluor_sampcal Concentration 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
DOXYSC01 1 Micromoles per litre WC_dissO2_calib Concentration of oxygen {O2 CAS 7782-44-7} per unit volume of the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data
DWIRPP01 1 Watts per square metre DWIrr_2-piPAR Downwelling 2-pi scalar irradiance as energy (PAR wavelengths) in the water body by 2-pi scalar radiometer
OXYSSC01 1 Percent BK_SBE43 Saturation of oxygen {O2 CAS 7782-44-7} in the water body [dissolved plus reactive particulate phase] by Sea-Bird SBE 43 sensor and calibration against sample data and computation from concentration using Benson and Krause algorithm
POPTDR01 1 Percent Trans_Red_25cm Transmittance (red light wavelength) per 25cm of the water body by 25cm path length red light transmissometer
POTMCV01 1 Degrees Celsius WC_Potemp Potential temperature of the water body by computation using UNESCO 1983 algorithm
PRESPR01 1 Decibars Pres_Z Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level
PSALCC01 1 Dimensionless P_sal_CTD_calib Practical salinity of the water body by CTD and computation using UNESCO 1983 algorithm and calibration against independent measurements
SIGTPR01 1 Kilograms per cubic metre SigTheta Sigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm
TEMPST01 1 Degrees Celsius WC_temp_CTD Temperature of the water body by CTD or STD
UWIRPP01 1 Watts per square metre ScalarUwirPAR Upwelling 2-pi scalar irradiance as energy (PAR wavelengths) in the water body by 2-pi scalar radiometer

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

James Cook Cruise JC079 AMT22 CTD Data Quality Document

Temperature, salinity, potential temperature and sigma-theta: Entrainment features were visible in a number of casts, both in the frame mounted (primary) and vane mounted (secondary channels). These features were apparent throughout the thermocline/pycnocline and continued down to approximately 200 dbar. The level of entrainment can be indicated by a variation between data points of 0.2 °C in the temperature, of 0.02-0.03 in the salinity and 0.1 kg m-3 in sigma-theta. The vane mounted sensors should theoretically be of better quality than the frame mounted sensors as they are held outside the water mass being carried down within the CTD frame structure, however there was a lot of spiking with spurious data that was not present on the primary channels. Therefore the primary temperature, salinity and density were retained for banking in the NODB, while secondary channels were discarded.

Chlorophyll: In circumstances where data were collected at pressures > 200 dbar, negative concentrations were frequently visible. These were flagged as anomalous. These resulted from the chlorophyll calibration being optimised for the euphotic zone, in particular the fluorescence/chlorophyll maximum.

Dissolved oxygen concentration and oxygen saturation: Cast 63 showed a step in the values and these were flagged suspect in the profile below this point. Overall profiles appear good.

Attenuance and transmissance: As with some of the other channels there were a few spikes that were flagged suspect. Cast 65 (down and up casts) appeared noisy in the surface. Overall the profiles appear of good quality.

Down and up-welling PAR irradiance: Optics casts were taken pre-dawn and at solar noon. Therefore, for almost half the casts, the PAR values are negligible as they were recorded in the dark.

Data Access Policy

Public domain data

These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.

The recommended acknowledgment is

"This study uses data from the data source/organisation/programme, provided by the British Oceanographic Data Centre and funded by the funding body."

Narrative Documents

Sea-Bird Dissolved Oxygen Sensor SBE 43 and SBE 43F

The SBE 43 is a dissolved oxygen sensor designed for marine applications. It incorporates a high-performance Clark polarographic membrane with a pump that continuously plumbs water through it, preventing algal growth and the development of anoxic conditions when the sensor is taking measurements.

Two configurations are available: SBE 43 produces a voltage output and can be incorporated with any Sea-Bird CTD that accepts input from a 0-5 volt auxiliary sensor, while the SBE 43F produces a frequency output and can be integrated with an SBE 52-MP (Moored Profiler CTD) or used for OEM applications. The specifications below are common to both.


Housing Plastic or titanium

0.5 mil- fast response, typical for profile applications

1 mil- slower response, typical for moored applications

Depth rating

600 m (plastic) or 7000 m (titanium)

10500 m titanium housing available on request

Measurement range 120% of surface saturation
Initial accuracy 2% of saturation
Typical stability 0.5% per 1000 h

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

RRS James Cook Cruise JC079 AMT22 CTD Instrumentation

The CTD unit was a Sea-Bird Electronics 911 plus system, with dissolved oxygen sensor. The CTD was fitted with an altimeter, up and downwelling PAR sensors, two BB-RTD sensors (one red light and one green light), transmissometer and a fluorometer as auxilliary sensors. All instruments were attached to a 24 position stainless steel Sea-Bird SBE 32 carousel. The table below lists more detailed information about the various sensors.

Sensor Model Serial Number Calibration Date Comments
Sea-Bird deck unit 11 plus n/a - -
Sea-Bird underwater unit 9 plus 0943 - -
Pressure transducer Paroscientific 410K-134 Digiquartz temperature compensated pressure sensor 110557 2012-05-29 -
Conductivity sensor 1 SBE 4C 2571 2012-08-21 -
Conductivity sensor 2 SBE 4C 3054 2012-08-31 -
Temperature sensor 1 SBE 3P 2919 2012-09-11 -
Temperature sensor 2 SBE 3P 4151 2012-09-13 -
Dissolved oxygen SBE 43 0363 2012-01-26 Voltage 0 for casts 1-58.
Dissolved oxygen SBE 43 2055 2012-06-27 Voltage 0 for casts 59-74.
Scattering meter WetLabs BBRTD - red light (700 nm wavelength) BBRTD-849 2011-03-19 Voltage 1 for casts 1-15 and 17-58.
Voltage 2 for cast 16.
Voltage 3 for casts 59-74.
Scattering meter WetLabs BBRTD - green light (532 nm wavelength) BBRTD-949 2012-03-08 Voltage 2 for casts 1-15 and 17-58.
Voltage 1 for cast 16.
Altimeter - 112522 - Voltage 3 for casts 1 to 58.
Transmissometer WetLabs C-star - 0.25 m path red light CST-1426DR 2011-06-22 Voltage 4
Fluorometer Chelsea AQUA tracka MkIII 088195 2012-08-21 Voltage 5
PAR sensor - upwelling irradiance Chelsea 2-pi PAR sensor 05 2011-06-14 Voltage 6
PAR sensor - downwelling irradiance Chelsea 2-pi PAR sensor 01 2011-06-14 Voltage 7

Change of sensors during cruise: The SBE43 oxygen sensor was changed from cast 59 until the end of the cruise. The backscatter sensors were switched for cast 16 and then swiched back for cast 17. The altimeter on voltage 3 was removed from cast 59 and the backscatter sensor moved from voltage 1 to voltage 3 for the rest of the cruise.

Sampling device

Rosette sampling system equipped with 24 x 20 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 .

Chelsea Technologies Group Aquatracka MKIII fluorometer

The Chelsea Technologies Group Aquatracka MKIII is a logarithmic response fluorometer. Filters are available to enable the instrument to measure chlorophyll, rhodamine, fluorescein and turbidity.

It uses a pulsed (5.5 Hz) xenon light source discharging along two signal paths to eliminate variations in the flashlamp intensity. The reference path measures the intensity of the light source whilst the signal path measures the intensity of the light emitted from the specimen under test. The reference signal and the emitted light signals are then applied to a ratiometric circuit. In this circuit, the ratio of returned signal to reference signal is computed and scaled logarithmically to achieve a wide dynamic range. The logarithmic conversion accuracy is maintained at better than one percent of the reading over the full output range of the instrument.

Two variants of the instrument are available, both manufactured in titanium, capable of operating in depths from shallow water down to 2000 m and 6000 m respectively. The optical characteristics of the instrument in its different detection modes are visible below:

Excitation Chlorophyll a Rhodamine Fluorescein Turbidity
Wavelength (nm) 430 500 485 440 *
Bandwidth (nm) 105 70 22 80 *
Emission Chlorophyll a Rhodamine Fluorescein Turbidity
Wavelength (nm) 685 590 530 440 *
Bandwidth (nm) 30 45 30 80 *

* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.

The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l -1 to 100 µg l -1 . The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).

The instrument accuracy is ± 0.02 µg l -1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).

Further details are available from the Aquatracka MKIII specification sheet .

Chelsea Technologies Photosynthetically Active Radiation (PAR) Irradiance Sensor

This sensor was originally designed to assist the study of marine photosynthesis. With the use of logarithmic amplication, the sensor covers a range of 6 orders of magnitude, which avoids setting up the sensor range for the expected signal level for different ambient conditions.

The sensor consists of a hollow PTFE 2-pi collector supported by a clear acetal dome diverting light to a filter and photodiode from which a cosine response is obtained. The sensor can be used in moorings, profiling or deployed in towed vehicles and can measure both upwelling and downwelling light.


Operation depth 1000 m
Range 2000 to 0.002 µE m -2 s -1
Angular Detection Range ± 130° from normal incidence
Relative Spectral Sensitivity

flat to ± 3% from 450 to 700 nm

down 8% of 400 nm and 36% at 350 nm

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

Paroscientific Absolute Pressure Transducers Series 3000 and 4000

Paroscientific Series 3000 and 4000 pressure transducers use a Digiquartz pressure sensor to provide high accuracy and precision data. The sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.

The 3000 series of transducers includes one model, the 31K-101, whereas the 4000 series includes several models, listed in the table below. All transducers exhibit repeatability of better than ±0.01% full pressure scale, hysteresis of better than ±0.02% full scale and acceleration sensitivity of ±0.008% full scale /g (three axis average). Pressure resolution is better than 0.0001% and accuracy is typically 0.01% over a broad range of temperatures.

Differences between the models lie in their pressure and operating temperature ranges, as detailed below:

Model Max. pressure (psia) Max. pressure (MPa) Temperature range (°C)
31K-101 1000 6.9 -54 to 107
42K-101 2000 13.8 0 to 125
43K-101 3000 20.7 0 to 125
46K-101 6000 41.4 0 to 125
410K-101 10000 68.9 0 to 125
415K-101 15000 103 0 to 50
420K-101 20000 138 0 to 50
430K-101 30000 207 0 to 50
440K-101 40000 276 0 to 50

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

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.


Pathlength 10 or 25 cm
Wavelength 370, 470, 530 or 660 nm

~ 20 nm for wavelengths of 470, 530 and 660 nm

~ 10 to 12 nm for a wavelength of 370 nm

Temperature error 0.02 % full scale °C -1
Temperature range 0 to 30°C
Rated depth

600 m (plastic housing)

6000 m (aluminum housing)

Further details are available in the manufacturer's specification sheet or user guide .

RRS James Cook Cruise JC079 AMT22 CTD Processing

Sampling strategy

All casts were conventional profiling casts with water sampling. A stainless steel (SS) CTD system was used. The frame was normally deployed pre-dawn and at solar noon each day.

A total of 73 out of 74 CTD casts were completed for water bottle sampling during the cruise. Cast 01 was cancelled due to a termination problem at the bottom of the downcast before any bottles could be fired. There was a problem during cast 65 where communication was lost for part of the downcast.

BODC Cruise processing

CTD casts were recorded using the Sea-Bird data collection software Seasave-Win32. The software outputs were then processed following the BODC recommended guidelines using SBE Data Processing-Win32 v7.20g; the processing routines are named after each stage in brackets < >. The software applied the calibrations as appropriate through the instrument configuration file to the data in engineering units output by the CTD hardware.

An ascii file (CNV) containing the 24 Hz data for up and down casts was generated from the binary Sea-Bird files for each cast <DatCnv>. Files were created for each cast containing the mean values of all the variables at the bottle firing events <Bottle Summary>. Using the CNV files processing routines were applied to remove pressure spikes <WildEdit>, the oxygen sensor was then shifted relative to the pressure by 2 seconds, to compensate for the lag in the sensor response time <AlignCTD> and the effect of thermal 'inertia' on the conductivity cells was removed <CellTM>. The surface soak was identified for each cast, removed and LoopEdit run. Salinity and oxygen concentration were re-derived and density (sigma-theta) were derived <Derive> after the corrections for sensor lag and thermal 'inertia' had been applied. The CTD files produced from Sea-Bird processing were converted from 24 Hz ascii files into 2 Hz ascii files of the complete cast (down and upcasts) with all channels for archive at BODC and also to 1 dbar downcast files for calibration and visualisation onboard <BinAverage>. The initial salinity and oxygen channels produced at the DatCnv stage, along with the conductivity, voltage and altimeter channels were removed from the 1 dbar downcast files <Strip>.

The Sea-Bird 1 dbar downcast files were converted from the Sea-Bird CNV format to the tab delimited ODV format using the mapping described below:

Parameter Name in Sea-Bird CNV Units Parameter Name in ODV file Units Comments
prDM: Pressure, Digiquartz dbar Pressure dbar -
t090C: Temperature ITS-90, °C Temperature_1 ITS-90, °C -
t190C: Temperature, 2 ITS-90, °C Temperature_2 ITS-90, °C -
flC: Fluorescence, Chelsea Aqua 3 Chl Con µg l -l Fluorometer_notional_calibration mg m -3 Units equivalent. No conversion applied.
par: PAR/Irradiance, Biospherical/Licor W m -2 PAR_up W m -2 -
par1: PAR/Irradiance, Biospherical/Licor, 2 W m -2 PAR_down W m -2 -
turbWETbb0: Turbidity, WET Labs ECO BB m -1 sr -1 Backscatter@700nm m -1 sr -1 Provisional calibration applied during the cruise. Final calibration to be applied post cruise and data supplied as a separate series.
turbWETbb1: Turbidity, WET Labs ECO BB, 2 m -1 sr -1 Backscatter@532nm m -1 sr -1 Provisional calibration applied during the cruise. Final calibration to be applied post cruise and data supplied as a separate series.
xmiss: Beam Transmission, Chelsea/Seatech/WET Labs CStar % Beam transmission % -
bat: Beam Attenuation, Chelsea/Seatech/WET Labs CStar m -1 Beam attenuance m -1 -
sal00: Salinity, Practical PSU Salinity_1_SBEcal PSU -
sal11: Salinity, Practical, 2 PSU Salinity_2_SBEcal PSU -
sbeox0ML/L: Oxygen, SBE 43 ml l -1 Oxy conc ml/l ml l -1 -
sbeox0Mg/L: Oxygen, SBE 43 mg l -1 Oxy conc mg/l mg l -1 -
sigma-é00: Density kg m -3 Density(sigma-theta)_1 kg m -3 -
sigma-é11: Density, 2 kg m -3 Density(sigma-theta)_2 kg m -3 -

Calibrated salinity, oxygen and fluorometer channels were then added to the profiles using calibration equations derived from the bottle file data compared against discrete samples collected from the CTD water bottles on each cast.

Field Calibrations

BODC post-processing and screening


The profiles were banked to the National Oceanographic Database (NODB) following BODC procedures.

Project Information

No Project Information held for the Series

Data Activity or Cruise Information


Cruise Name JC079 (AMT22)
Departure Date 2012-10-10
Arrival Date 2012-11-24
Principal Scientist(s)Glen A Tarran (Plymouth Marine Laboratory)
Ship RRS James Cook

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