Metadata Report for BODC Series Reference Number 860964
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Open Data supplied by Natural Environment Research Council (NERC)
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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 Challenger 128A CTD Data Documentation
Components of the CTD data set
The CTD data set for cruise CH128A consists of 88 vertical profiles. The data parameters are temperature, salinity, upwelling and downwelling irradiance, dissolved oxygen, chlorophyll and optical attenuance.
Data Acquisition and On-Board Processing
The CTD profiles were taken with an RVS Neil Brown Mk3B CTD incorporating a pressure sensor, conductivity cell, platinum resistance thermometer and a Beckmann dissolved oxygen sensor. Water was forced over the oxygen membrane by a SeaBird submersible pump. The CTD unit was mounted vertically in the centre of a protective cage approximately 1.5m square. Attached to the bars of the frame were a Chelsea Instruments Aquatracka fluorometer and a SeaTech red light (661 nm) transmissometer with a 25cm path length.
Above the frame was a General Oceanics rosette sampler fitted with twelve 10-litre Niskin water bottles. The bases of the bottles were 0.75 metres above the pressure head and their tops 1.55 metres above it. One bottle was fitted with a holder for twin digital reversing thermometers mounted 1.38 metres above the CTD temperature sensor.
Above the rosette was a PML 2pi PAR (photosynthetically available radiation) sensor pointing upwards to measure downwelling scalar irradiance. A second 2pi PAR sensor, pointing downwards, was fitted to the bottom of the cage to measure upwelling scalar irradiance. It should be noted that these sensors were vertically separated by 2 metres with the upwelling sensor 0.2 metres below the pressure head and the downwelling sensor 1.75 metres above it.
No account has been taken of rig geometry in the compilation of the CTD data set. However, all water bottle sampling depths have been corrected for rig geometry and represent the true position of the midpoint of the water bottle in the water column.
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.
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 (volts for PAR meters, fluorometer and transmissometer; ml/l for oxygen; mmho/cm 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, 1983) was calculated from the conductivity ratios (conductivity/42.914) and a time lagged temperature using the function described in UNESCO Report 37 (1981).
The data set was 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 (PXF) 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 multiplying the values by 44.66.
- Transmissometer voltages were corrected to the manufacturer's specified voltage by ratio using transmissometer air readings taken during the cruise.
- Transmissometer voltages were converted to percentage transmission by multiplying them by a factor of 20.
- The transmissometer data were converted to attenuance using the algorithm:-
|attenuance (m-1) = -4 loge (% transmission/100)|
Reformatted CTD data were transferred onto a high-speed graphics workstation. Using a custom in-house graphics editor, 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.
For this cruise, the RVS Neil Brown Mk 3B CTD system was equipped with a SeaBird pump, which sent water at a constant rate through the housing containing the existing Beckman oxygen electrode. Problems associated with the plumbing of the pump to the oxygen probe resulted in many profiles only recording good oxygen data on upcasts. To overcome this, the upcast data for oxygen, temperature and salinity channels were flagged to remove any spikes. The downcast oxygen values loaded into ORACLE were then replaced where necessary by upcast oxygen data using isopycnal (rather than pressure) matching to determine the replacement values to be used.
Once screened on the workstation, the CTD downcasts were loaded into a database under the ORACLE Relational Database Management System.
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 except for the calibration to express attenuance in terms of suspended matter concentration.
The pressure offset was determined by looking at the pressures recorded when the CTD was clearly logging in air (readily apparent from the conductivity channel). The following correction was calculated from 14 values:
|Pcorr = P - 0.16|
The CTD temperature was compared with readings from the digital reversing thermometers attached to the water bottles. Normal BODC practice is to use this comparison as a check to ensure against CTD malfunction rather than a calibration because the Neil Brown CTD thermometer is considered more accurate than the SIS digital reversing thermometers.
However, the CTD used on this cruise had not been accurately calibrated by RVS and the temperature data supplied to BODC were based on a nominal calibration. Consequently, the reversing thermometer data were used to recalibrate the CTD temperature data and the following correction has been applied:
|Tcorr = T - 0.032 (standard deviation 0.006)|
During screening an offset was noted in the salinity trace. This was attributed to the conductivity cell contamination. The following correction has been applied:
|CP57||0.041 PSU added between 158.0 db and 355.6 db|
Salinity was calibrated against water bottle samples measured on the Guildline 55358 AutoLab Salinometer during the cruise. Samples were collected in glass bottles filled to just below the neck and sealed with plastic stoppers. Batches of samples were left for at least 24 hours to reach thermal equilibrium in the lab containing the salinometer before analysis.
The correction determined for this cruise was:
|Scorr = S + 0.088 (standard deviation 0.003)|
Upwelling and Downwelling Irradiance
The PAR voltages were converted to W m-2 using the following equations determined in August 1995 supplied by RVS.
|Upwelling (#10):||PAR (W m-2) = exp (-4.98*volts + 6.565)/100.0|
|Downwelling (#12):||PAR (W m-2) = exp (-4.92*volts + 6.506)/100.0|
Note that these sensors have been empirically calibrated to obtain a conversion from W/m2 into µE/m2/s, which may be effected by multiplying the data given by 3.75.
Optical Attenuance and Suspended Matter
The air correction applied for this cruise was based on an air reading obtained during the cruise (4.736V). The manufacturer's voltage for the instrument used (SN079D) was 4.744V.
Large volume samples were taken for gravimetric analysis of the suspended particulate matter concentration. These were used to generate calibrations that expressed attenuance in terms of suspended particulate matter concentrations.
Robin McCandliss (University of Wales, Bangor) undertook this work, under the supervision of Sarah Jones. The optimal approach developed was to base the calibration on samples taken from near the seabed (i.e. those with the minimum content of fluorescent material). The data from all SES cruises where SPM samples were taken were pooled to derive the calibration equation:
|SPM (mg/l) = (2.368*Atten) - 0.801 (R2 = 79%)|
This calibration is valid for all SES cruises after and including cruise Charles Darwin CD93A. The clear water attenuance predicted by the equation is 0.336 per m, which agrees well with literature values.
No attempt has been made to replace attenuance by SPM concentration in the final data set. However, users may use the equation above to compute an estimated SPM channel from attenuance when required.
200ml of seawater collected at several depths on each cast were filtered and the papers frozen for acetone extraction and fluorometric analysis on land. A relatively small number of samples were taken on CH128B. Consequently, the data from both legs of CH128 were pooled for the calibration.
The extracted chlorophyll concentrations (range 0.1 to 2.94 mg m-3) were regressed against the corresponding fluorometer voltages, giving the following calibration which has been applied to the data:
|Chlorophyll (mg m-3) = exp (1.33 * volts - 2.75) (R2 = 56.7%, n = 176)|
Dissolved oxygen concentrations were determined by micro-Winkler titration of seawater samples taken from a range of depths on several CTD casts. These values were compared with oxygen readings derived from the oxygen sensor membrane current, oxygen sensor temperature, sea temperature and salinity values recorded by the CTD on the upcast. Hilary Wilson (University of Wales, Bangor), under the supervision of Dr. Paul Tett, carried out this work. The following equation was supplied to BODC and the coefficients A and B were applied to the data:
|[O2] = (A*C + B)* S' ml/l|
|where||A = 2.1507689 (casts CP1-CP80) or 3.39847069 (casts CP81-CP90)|
|C = oxygen sensor current (µA)|
|B = -0.1448435 (casts CP1-CP80) or -1.2152591 (casts CP81-CP90)|
|S'= oxygen saturation concentration (a function of water temperature and salinity).|
Finally, the data were converted to µM by multiplication by 44.66.
The calibration coefficients used for casts CP1-CP80 were derived using the pooled data from 4 of the profiles from which bottle oxygen samples were taken. The calibration for CP81-CP90 was based on data from cast CP81. Individual calibrations were derived for each of these profiles. These are included below for reference. However, please note that the whole cruise coefficients given above were applied to all profiles in the database.
Considerable manipulation of the oxygen data, such as the substitution of downcast data by isopycnal-matched upcast data, was required to produce the oxygen data channel in the final data set. This, combined with the uncertainties involved in the calibration of oxygen data, might mean that some users would wish to re-examine the oxygen processing. To facilitate this, BODC have systematically archived the raw data (including oxygen current and temperature) from both upcasts and downcasts. These data are available on request.
During the visual inspection of the oxygen data from this cruise it was noticed that there was a significant difference between the downcast and upcast data (sometimes 1-200 µM different at the surface). This difference was far greater than other SES cruises and was present, though it diminished in magnitude with depth, for the whole cast. Consequently, all the data in the final data set have been derived from the upcast rather than the odd 'patch' as in CH121B and CH126B. Looking at the data leaves a nagging doubt that the oxygen sensor was being very slow to equilibrate and there is no concrete evidence that it had reached equilibrium by the start of the upcast. Users are therefore recommended to use the CTD oxygen data from this cruise with a degree of caution.
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).
There is strong evidence that the oxygen sensor was exceptionally slow to equilibrate. Although the data presented in the final data set have been taken from the upcast, users are recommended to use the oxygen data from this cruise with caution.
Benson B.B. and Krause D. jnr. 1984. The concentration and isotopic fractionation of oxygen dissolved in fresh water and sea water 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.
Land Ocean Interaction Study (LOIS)
The Land Ocean Interaction Study (LOIS) was a Community Research Project of the Natural Environment Research Council (NERC). The broad aim of LOIS was to gain an understanding of, and an ability to predict, the nature of environmental change in the coastal zone around the UK through an integrated study from the river catchments through to the shelf break.
LOIS was a collaborative, multidisciplinary study undertaken by scientists from NERC research laboratories and Higher Education institutions. The LOIS project was managed from NERC's Plymouth Marine Laboratory.
The project ran for six years from April 1992 until April 1998 with a further modelling and synthesis phase beginning in April 1998 and ending in April 2000.
LOIS consisted of the following components:
- River-Atmosphere-Coast Study (RACS)
- RACS(A) - Atmospheric sub-component
- RACS(C) - Coasts sub-component
- RACS(R) - Rivers sub-component
- BIOTA - Terrestrial salt marsh study
- Land Ocean Evolution Perspective Study (LOEPS)
- Shelf-Edge Study (SES)
- North Sea Modelling Study (NORMS)
- Data Management (DATA)
Marine field data were collected between September 1993 and September 1997 as part of RACS(C) and SES. The RACS data were collected throughout this period from the estuaries and coastal waters of the UK North Sea coast from Great Yarmouth to the Tweed. The SES data were collected between March 1995 and September 1996 from the Hebridean slope. Both the RACS and SES data sets incorporate a broad spectrum of measurements collected using moored instruments and research vessel surveys.
|Principal Scientist(s)||John H Simpson (University of Wales, Bangor School of Ocean Sciences)|
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
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|
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|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|