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Metadata Report for BODC Series Reference Number 866093

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
SeaTech transmissometer  transmissometers
Chelsea Technologies Group Aquatracka fluorometer  fluorometers
SeaTech Light Back-Scattering Sensor  optical backscatter sensors
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Dr John Huthnance
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) OMEX II-II

Data Identifiers

Originator's Identifier CTD61
BODC Series Reference 866093

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 1997-06-17 02:07
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 2.0 decibars

Spatial Co-ordinates

Latitude 42.00200 N ( 42° 0.1' N )
Longitude 9.28817 W ( 9° 17.3' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor or Sampling Depth 0.99 m
Maximum Sensor or Sampling Depth 147.78 m
Minimum Sensor or Sampling Height -
Maximum Sensor or Sampling Height -
Sea Floor Depth -
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 -


BODC CODERankUnitsTitle
ATTNZR011per metreAttenuation (red light wavelength) per unit length of the water body by transmissometer
ATTNZR021per metreAttenuation (red light wavelength) per unit length of the water body by transmissometer (second sensor)
CPHLPR011Milligrams 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
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
FVLTAQ011VoltsRaw signal (voltage) of instrument output by in-situ Aquatracka chlorophyll fluorometer
NVLTST011VoltsRaw signal (voltage) of instrument output by SeaTech light backscatter nephelometer (LBSS)
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
POATCV011per metrePotential attenuance (unspecified wavelength) per unit length of the water body by transmissometer and computation using P-EXEC 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
PSALST011DimensionlessPractical salinity of the water body by CTD and computation using UNESCO 1983 algorithm
SIGTPR011Kilograms per cubic metreSigma-theta of the water body by CTD and computation from salinity and potential temperature using UNESCO algorithm
TEMPST011Degrees CelsiusTemperature of the water body by CTD or STD

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

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

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.

Aquatracka fluorometer

The Chelsea Instruments Aquatracka is a logarithmic response fluorometer. It uses a pulsed (5.5 Hz) xenon light source discharging between 320 and 800 nm through a blue filter with a peak transmission of 420 nm and a bandwidth at half maximum of 100 nm. A red filter with sharp cut off, 10% transmission at 664 nm and 678 nm, is used to pass chlorophyll-a fluorescence to the sample photodiode.

The instrument may be deployed either in a through-flow tank, on a CTD frame or moored with a data logging package.

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

Sea Tech Light Back-Scatter sensor

The instrument projects light into the sample volume using two modulated 880 nm Light Emitting Diodes. Light back-scattered from the suspended particles inthe water column is measured with a solar-blind silicon detector. A light stop between the light source and the light detector prevents the measurement of direct transmitted light so that only back-scattered light from suspended particles in water are measured.

The sensor has two ranges permitting the user to measure nearly all suspended particle concentrations found in open ocean or coastal waters. Range for the measurement of suspended particle concentration in water will be approximately 10 mg l-1 if High_Gain is selected. If Low-Gain is selected full scale will be a factor of 3.3 higher or approximately 33 mg l-1.


Range ~10 mg l-1 on High-Gain, ~33 mg l-1 on Low-Gain
Resolution 0.01% of full scale, ~ 1 µg l-1
Sensor Output 0-5 VDC
Time Constant <0.1 second
Power 9 to 28 VDC @ ~22 ma
Sensor Turn on Time ~1 second
Temperature Stability ~0.5%, 0-50 °C
Depth 6000 m
Size 3.2 cm Diameter, 14 cm length
Weight 0.26 kg in air, 0.13 kg in water
Material ABS Plastic housing filled with epoxy, clear epoxy optical windows

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

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.

RRS Charles Darwin 105B CTD Data Documentation

Instrumentation and Shipboard Procedures


The CTD profiles were taken with a Neil Brown Systems Mk IIIB CTD including a pressure sensor, a conductivity cell, a platinum resistance thermometer and a Beckmann dissolved oxygen sensor. The CTD unit was mounted vertically in the centre of a protective cage approximately 1.5m square.

The following instruments were also attached to the bars of the cage and logged as additional CTD channels:

  • Chelsea Instruments Aquatracka configured as a fluorometer.
  • SeaTech light backscatter sensor (LBSS nephelometer).
  • Two SeaTech 25-cm path-length red (661 nm) light transmissometers.
  • Two PML 2 PAR (photosynthetically available radiation) scalar irradiance sensors configured to measure downwelling and upwelling radiation.

Note that the downwelling light sensor was actually mounted on a pole placing it in line with the top of the water bottle rosette, 1.75 m above the pressure head. As a result, there was a vertical separation of some two metres between the upwelling and downwelling sensors. No geometrical correction of the light data has been attempted.

A General Oceanics 12-bottle tone-fire rosette pylon was fitted to the top of the CTD frame. 10-litre Niskin bottles were used throughout the cruise.

The first leg of this cruise was primarily a swath bathymetry survey of the OMEX II working area. Consequently, no CTD work was undertaken.

Data Acquisition

On each cast, the CTD was lowered continuously at 0.5 to 1.0 ms-1 to the closest comfortable proximity to the sea floor. The upcast was done in stages between the bottle firing depths. A tone fire system was installed to minimise the disruption caused to the data stream by the bottle-firing signal.

The data were logged by the RVS ABC data logging system. Output channels from the deck unit were logged at 32 Hz by a microprocessor interface (the Level A) which passed time-stamped averaged cycles at 1 Hz to a Sun workstation (the Level C) via a buffering system (the Level B).

On-Board Data Processing

The raw data comprised ADC counts. These were converted into engineering units ( Em-2s-2 for PAR meters, volts for fluorometer, LBSS and transmissometers; ml l-1 for oxygen; mmho cm-1 for conductivity; °C for temperature; decibars for pressure) by the application of laboratory determined calibrations. Salinity (Practical Salinity Units as defined in Fofonoff and Millard, 1982) was calculated using the standard UNESCO function from the conductivity ratio (conductivity/42.914) and a time lagged temperature.

The data set were submitted to BODC in this form on Quarter Inch Cartridge tapes in RVS internal format for post-cruise processing and data banking.

Post-Cruise Processing and Calibration at BODC


The data were converted into the BODC internal format to allow the use of in-house software tools, notably the workstation graphics editor. In addition to reformatting, the transfer program applied the following modifications to the data:

  • Dissolved oxygen was converted from ml/l to µM by multiplication by 44.66.
  • Transmissometer voltages were corrected to the manufacturer's specified voltage by ratio using transmissometer air readings taken during the cruise (see the calibration section for details). The voltages were then converted to percentage transmission by multiplying them by 20 and to attenuance using the algorithm:
attenuance (m-1) = -4 loge (% transmission/100)
  • The light meter calibration applied on the ship (based on incorrect coefficients) was removed, converting the data back to volts.


Reformatted CTD data were transferred onto a high-speed graphics workstation. Using custom in-house graphics editors, downcasts and upcasts were differentiated and the limits of the downcasts and upcasts were manually flagged.

Spikes on all the downcast channels were manually flagged. No data values were edited or deleted; flagging was achieved by modification of the associated quality control flag.

The pressure ranges over which the bottle samples had been collected were logged by manual interaction with the software. Usually, clusters of points recorded while the CTD was held stationary were used to determine this. These pressure ranges were subsequently used, in conjunction with a geometrical correction for the position of the water bottles with respect to the CTD pressure transducer, to determine the pressure range of data to be averaged for calibration values.

Once screened on the workstation, the CTD downcasts were loaded into a database under the ORACLE Relational Database Management System. These were later migrated to the National Oceanographic Database.


With the exception of pressure, calibrations were done by comparison of CTD data against measurements made on water bottle samples or from the reversing thermometers mounted on the water bottles as in the case of temperature. In general, values were averaged from the CTD downcasts but where visual inspection of the data showed significant hysteresis values were manually extracted from the CTD upcasts.

All calibrations described here have been applied to the data.


The pressure calibration was derived by averaging pressures logged in air from 78 of the 82 casts. The mean pressure in air was 1.41 db (SD 0.37 db) giving rise to the following pressure correction:

Corrected pressure (db) = Raw pressure - 1.41

CTD temperatures were compared with calibrated digital reversing thermometer data from all suitably equipped bottles fired at depths greater than 1000 m. Excellent agreement was obtained with no evidence of drift or sudden offsets at any stage during the cruise. Consequently, no adjustment has been made to the CTD temperature data.


The CTD salinity data were calibrated against 47 water bottle samples analysed on a Guildline Autosal bench salinometer. The following correction was obtained:

Corrected salinity = Raw salinity + 0.024 (SD 0.005)
Optical Attenuance

Two transmissometers were used in parallel during the cruise. Instrument SN80D functioned successfully throughout the cruise. The data from this instrument are stored in the database as parameter ATTNZR01. At the start of the cruise, SN79D was fitted as the second instrument, but it failed during cast CTD15. It was replaced in time for cast CTD21 by instrument SN116D.

The air correction data from laboratory measurements immediately prior to the cruise were as follows:

Instrument New Volts Cruise Volts Correction
116D 4.820 4.750 -0.058
80D 4.806 4.795 -0.009
79D 4.744 4.722 -0.019

However, information from the cruise gave a cruise value of 4.795 V for SN116D (giving an attenuance correction of -0.020 per m). This cruise value was applied in the BODC processing of the second attenuance channel.

However, when the data were examined, it could be clearly seen that whilst the data from SN80D and SN79D were both in excellent agreement and perfectly credible (minimum attenuance of 0.35 for SN80D and 0.36 for SN79D), there was a problem with the data from SN116D. The SN116D data were consistently higher than SN80D by roughly 0.04 per m, giving a minimum attenuance of 0.39 per m.

The obvious conclusion was that the air value for SN116D reported from the cruise was incorrect. This was supported by the fact that the air value for SN80D was identical to that reported for SN116D. Taking the laboratory air reading rather than the cruise value decreased the SN116D data by 0.038 per m, bringing them into line with SN80D. This was implemented as a post-load calibration.


The voltages logged by the ABC system from the SeaTech light backscatter sensor have been included in the database without the application of any further calibration.

Dissolved Oxygen

There were no oxygen water bottle data from this cruise. When this is the case it is normal BODC practice to delete the dissolved oxygen from the data set. However, during this cruise Charles Darwin rendezvoused with Belgica for an intercalibration CTD. The CTD casts were taken within 0.5 miles and at virtually the same time (Belgica was approximately 20 minutes after Darwin).

An oxygen calibration was attempted in which the Darwin CTD data (cast CTD91) were calibrated using bottle data from the Belgica cast. This gave rise to the following equation:

Corrected oxygen = Raw oxygen * 1.85 + 62.41 (N=11,R2=75%)

This calibration was then applied to the whole of the Darwin cruise. The limitations of this approach are obvious. For example, oxygen sensors are extremely prone to drift, which has not been monitored. The surface saturation values computed from the calibrated data varied during the cruise from 95% to 107%, which seems reasonable. However, it is recommended that the oxygen data be treated with caution.


The fluorometer was calibrated using extracted chlorophyll data assayed by HPLC. CTD voltages were regressed against the natural log of the sum of chlorophyll-a and diavinyl chlorophyll-a. The initial attempt produced a banana-shaped curve. Investigation showed that this was due to the very high noise levels in the fluorometer signal producing massive scatter for low chlorophyll concentrations. The problem was overcome by removing all points where the extracted chlorophyll value was <0.1µg/l. The result was the following calibration equation:

Chlorophyll (µg/l) = exp (voltage*1.6652 - 2.7584)  (N=254, R2=41.8%)
Upwelling and Downwelling Irradiance

The calibrations applied on the cruise used the wrong coefficients for upwelling irradiance (calibration for sensor 2 applied). These were removed and the following calibrations applied to the resulting voltages:

Downwelling irradiance ( Em-2s-1) = exp (-4.900*voltage + 7.237) * 0.0375
Sensor 1

Upwelling irradiance ( Em-2s-1) = exp (-4.970*voltage + 6.426) * 0.0375
Sensor 8

Note that the scaling factor (0.0375) is an empirically-derived term that converts the data from Wcm-2 to Em-2s-1. Consequently, the data may be converted to Wm-2 if required by dividing by 3.75.

Data Reduction

Once all screening and calibration procedures were completed, the data set was binned to 2 db (casts deeper than 100 db) or 1 db (casts shallower than 100 db). The binning algorithm excluded any data points flagged suspect and attempted linear interpolation over gaps up to 3 bins wide. If any gaps larger than this were encountered, the data in the gaps were set null.

Oxygen saturation has been computed using the algorithm of Benson and Krause (1984).


The oxygen calibration was based on bottle data from a single cast collected by another ship on an intercalibration station.


Benson B.B. and Krause D. jnr. 1984. The concentration and isotopic fractionation of oxygen dissolved in fresh water and seawater in equilibrium with the atmosphere. Limnol. Oceanogr. 29 pp.620-632.

Fofonoff N.P. and Millard Jr., R.C. 1982. Algorithms for Computation of Fundamental Properties of Seawater. UNESCO Technical Papers in Marine Science 44.

Project Information

Ocean Margin EXchange (OMEX) II - II


OMEX was a European multidisciplinary oceanographic research project that studied and quantified the exchange processes of carbon and associated elements between the continental shelf of western Europe and the open Atlantic Ocean. The project ran in two phases known as OMEX I (1993-1996) and OMEX II - II (1997-2000), with a bridging phase OMEX II - I (1996-1997). The project was supported by the European Union under the second and third phases of its MArine Science and Technology Programme (MAST) through contracts MAS2-CT93-0069 and MAS3-CT97-0076. It was led by Professor Roland Wollast from Université Libre de Bruxelles, Belgium and involved more than 100 scientists from 10 European countries.

Scientific Objectives

The aim of the Ocean Margin EXchange (OMEX) project was to gain a better understanding of the physical, chemical and biological processes occurring at the ocean margins in order to quantify fluxes of energy and matter (carbon, nutrients and other trace elements) across this boundary. The research culminated in the development of quantitative budgets for the areas studied using an approach based on both field measurements and modeling.

OMEX II - II (1997-2000)

The second phase of OMEX concentrated exclusively on the Iberian Margin, although RV Belgica did make some measurements on La Chapelle Bank whilst on passage to Zeebrugge. This is a narrow-shelf environment, which contrasts sharply with the broad shelf adjacent to the Goban Spur. This phase of the project was also strongly multidisciplinary in approach, covering physics, chemistry, biology and geology.

There were a total of 33 OMEX II - II research cruises, plus 23 CPR tows, most of which were instrumented. Some of these cruises took place before the official project start date of June 1997.

Data Availability

Field data collected during OMEX II - II have been published by BODC as a CD-ROM product, entitled:

  • OMEX II Project Data Set (three discs)

Further descriptions of this product and order forms may be found on the BODC web site.

The data are also held in BODC's databases and subsets may be obtained by request from BODC.

Data Activity or Cruise Information


Cruise Name CD105B
Departure Date 1997-06-10
Arrival Date 1997-06-23
Principal Scientist(s)John Huthnance (Proudman Oceanographic Laboratory)
Ship RRS Charles Darwin

Complete Cruise Metadata Report is available here

Fixed Station Information

Fixed Station Information

Station NameOMEX II-II Repeat Section T
CategoryOffshore route/traverse

OMEX II-II Repeat Section T

Section T was one of ten repeat sections sampled during the Ocean Margin EXchange (OMEX) II-II project between June 1997 and January 1998.

The CTD measurements collected at repeat section T, at the Iberian Margin, lie within a box bounded by co-ordinates 41° 59.6' N, 10° 0.8' W at the southwest corner and 42° 0.3' N, 08° 59.9' W at the northeast corner.

Cruises occupying section T

Cruise Start Date End Date
RRS Charles Darwin 105B 10/06/1997 22/06/1997
RV Belgica 9714C 21/06/1997 30/06/1997
RRS Charles Darwin 110A 23/12/1997 05/01/1998
RRS Charles Darwin 110B 06/01/1998 19/01/1998

Related Fixed Station activities are detailed in Appendix 1

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

Appendix 1: OMEX II-II Repeat Section T

Related series for this Fixed Station are presented in the table below. Further information can be found by following the appropriate links.

If you are interested in these series, please be aware we offer a multiple file download service. Should your credentials be insufficient for automatic download, the service also offers a referral to our Enquiries Officer who may be able to negotiate access.

Series IdentifierData CategoryStart date/timeStart positionCruise
865888CTD or STD cast1997-06-16 13:00:0042.00183 N, 10.00533 WRRS Charles Darwin CD105B
866265CTD or STD cast1997-06-16 14:04:0042.00267 N, 10.01367 WRRS Charles Darwin CD105B
866081CTD or STD cast1997-06-16 17:33:0041.99933 N, 9.83367 WRRS Charles Darwin CD105B
866277CTD or STD cast1997-06-16 20:10:0041.999 N, 9.674 WRRS Charles Darwin CD105B
866289CTD or STD cast1997-06-16 22:27:0041.99817 N, 9.54817 WRRS Charles Darwin CD105B
866290CTD or STD cast1997-06-17 03:45:0042.0 N, 9.44433 WRRS Charles Darwin CD105B
866308CTD or STD cast1997-06-17 05:43:0041.9995 N, 9.2285 WRRS Charles Darwin CD105B
866100CTD or STD cast1997-06-17 07:12:0042.00033 N, 9.0005 WRRS Charles Darwin CD105B
864547CTD or STD cast1997-06-21 11:12:0041.99583 N, 8.99933 WRV Belgica BG9714C
864559CTD or STD cast1997-06-21 12:53:0042.00033 N, 9.23517 WRV Belgica BG9714C
864154CTD or STD cast1997-06-21 15:24:0041.9965 N, 9.35683 WRV Belgica BG9714C
864560CTD or STD cast1997-06-21 17:39:0041.99817 N, 9.66633 WRV Belgica BG9714C
864572CTD or STD cast1997-06-21 20:49:0042.003 N, 10.01 WRV Belgica BG9714C
866984CTD or STD cast1997-12-28 20:52:0041.9945 N, 9.67233 WRRS Charles Darwin CD110A
866996CTD or STD cast1997-12-28 23:02:0042.00033 N, 9.55183 WRRS Charles Darwin CD110A
866751CTD or STD cast1997-12-29 01:03:0042.0025 N, 9.44533 WRRS Charles Darwin CD110A
867011CTD or STD cast1997-12-29 02:33:0042.00183 N, 9.38267 WRRS Charles Darwin CD110A
866855CTD or STD cast1997-12-29 04:40:0042.00217 N, 9.27917 WRRS Charles Darwin CD110A
867023CTD or STD cast1997-12-29 05:25:0042.00417 N, 9.22933 WRRS Charles Darwin CD110A
867035CTD or STD cast1997-12-29 07:41:0042.00017 N, 9.00167 WRRS Charles Darwin CD110A
867115CTD or STD cast1998-01-03 16:28:0042.00333 N, 9.44417 WRRS Charles Darwin CD110A
866879CTD or STD cast1998-01-03 18:51:0042.0025 N, 9.553 WRRS Charles Darwin CD110A
866695CTD or STD cast1998-01-03 21:15:0042.00033 N, 9.68167 WRRS Charles Darwin CD110A