Metadata Report for BODC Series Reference Number 866394
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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.
3200 m (optional)
|-3 to 32°C||1 to 6.5 S cm-1|
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.
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.
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.
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.
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)|
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|
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.
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
Upwelling irradiance ( Em-2s-1) = exp (-4.970*voltage + 6.426) * 0.0375
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.
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.
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.
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.
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.
|Principal Scientist(s)||John Huthnance (Proudman Oceanographic Laboratory)|
|Ship||RRS Charles Darwin|
Complete Cruise Metadata Report is available here
Fixed Station Information
|Station Name||OMEX II-II Repeat Section R|
OMEX II-II Repeat Section R
Section R was one of ten repeat sections sampled during the Ocean Margin EXchange (OMEX) II-II project between June 1997 and September 1999.
The CTD measurements collected at repeat section R, at the Iberian Margin, lie within a box bounded by co-ordinates 42° 19.2' N, 10° 0.7' W at the southwest corner and 42° 20.8' N, 08° 59.8' W at the northeast corner.
Cruises occupying section R
|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|
|RV Belgica 9815C||27/06/1998||07/07/1998|
|RV Belgica 9919B||04/09/1999||11/09/1999|
|RV Belgica 9919C||14/09/1999||18/09/1999|
Related Fixed Station activities are detailed in Appendix 1
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|<||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.)|
|E||End of CTD Down/Up Cast|
|G||Non-taxonomic biological characteristic uncertainty|
|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|
|O||Improbable value - user quality control|
|0||no quality control|
|2||probably good value|
|3||probably bad value|
|6||value below detection|
|7||value in excess|
|A||value phenomenon uncertain|
|Q||value below limit of quantification|
Appendix 1: OMEX II-II Repeat Section R
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 Identifier||Data Category||Start date/time||Start position||Cruise|
|866369||CTD or STD cast||1997-06-17 22:41:00||42.33433 N, 9.626 W||RRS Charles Darwin CD105B|
|866136||CTD or STD cast||1997-06-18 01:33:00||42.34017 N, 9.49817 W||RRS Charles Darwin CD105B|
|866370||CTD or STD cast||1997-06-18 08:52:00||42.332 N, 9.00067 W||RRS Charles Darwin CD105B|
|866382||CTD or STD cast||1997-06-18 10:20:00||42.33233 N, 9.20017 W||RRS Charles Darwin CD105B|
|866148||CTD or STD cast||1997-06-18 11:31:00||42.33317 N, 9.28567 W||RRS Charles Darwin CD105B|
|866401||CTD or STD cast||1997-06-18 15:03:00||42.34433 N, 9.468 W||RRS Charles Darwin CD105B|
|866161||CTD or STD cast||1997-06-18 17:29:00||42.33567 N, 9.77833 W||RRS Charles Darwin CD105B|
|865944||CTD or STD cast||1997-06-19 11:50:00||42.3335 N, 10.0025 W||RRS Charles Darwin CD105B|
|864664||CTD or STD cast||1997-06-23 16:04:00||42.3325 N, 9.20117 W||RV Belgica BG9714C|
|864676||CTD or STD cast||1997-06-23 18:12:00||42.33133 N, 9.404 W||RV Belgica BG9714C|
|864210||CTD or STD cast||1997-06-23 20:23:00||42.33483 N, 9.70517 W||RV Belgica BG9714C|
|864688||CTD or STD cast||1997-06-23 23:25:00||42.33917 N, 10.01167 W||RV Belgica BG9714C|
|866947||CTD or STD cast||1997-12-27 07:32:00||42.3405 N, 9.277 W||RRS Charles Darwin CD110A|
|866867||CTD or STD cast||1997-12-30 16:06:00||42.33517 N, 8.99783 W||RRS Charles Darwin CD110A|
|864990||CTD or STD cast||1998-06-27 15:06:00||42.33167 N, 9.00267 W||RV Belgica BG9815C|
|865041||CTD or STD cast||1998-06-27 16:34:00||42.333 N, 9.20283 W||RV Belgica BG9815C|
|865053||CTD or STD cast||1998-06-27 19:59:00||42.336 N, 9.99617 W||RV Belgica BG9815C|
|880431||CTD or STD cast||1999-09-08 18:51:00||42.32717 N, 9.6245 W||RV Belgica BG9919B|
|880302||CTD or STD cast||1999-09-08 23:27:00||42.3325 N, 9.20517 W||RV Belgica BG9919B|
|880418||CTD or STD cast||1999-09-09 22:42:00||42.3305 N, 9.45933 W||RV Belgica BG9919B|
|880640||CTD or STD cast||1999-09-16 21:26:00||42.32983 N, 9.005 W||RV Belgica BG9919C|
|880652||CTD or STD cast||1999-09-17 14:00:00||42.3335 N, 9.77467 W||RV Belgica BG9919C|