Metadata Report for BODC Series Reference Number 1169241

• Metadata Summary

• Problem Reports

• Data Access Policy

• Narrative Documents

• Project Information

• Data Activity or Cruise Information

• Fixed Station Information

• BODC Quality Flags

• SeaDataNet Quality Flags

Metadata Summary

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

D376 CTD Instrumentation

CTD unit and auxiliary sensors

The CTD system used on cruise D376 was the Sea-Bird 911plus . This was mounted on a stainless steel rosette frame, equipped with 24 10-litre Ocean Test Equipment water bottles (fixed to a Sea-Bird 24-position Carousel (serial number 32-0518)). Data were recorded using a Sea-Bird 11plusdeck unit (serial number 11P-34173-0676).

The package was fitted with the following scientific sensors:

The pressure sensor was situated approximately 30 cm below the base of the water bottles, 75 cm below the centre of the water bottles.

The discrete salinity samples collected from water bottles on the CTD were analysed in the ship's constant temperature laboratory using a Guildline Autosal model 8400 salinometer (serial number 60839). Dissolved oxygen concentrations from further water samples were determined using a Winkler titration technique.

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

Specifications for the SBE 9 plus underwater unit are listed below:

Further details can be found in the manufacturer's 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.

Chelsea Technologies Group ALPHAtracka and ALPHAtracka II transmissometers

The Chelsea Technologies Group ALPHAtracka (the Mark I) and its successor, the ALPHAtracka II (the Mark II), are both accurate (< 0.3 % fullscale) transmissometers that measure the beam attenuation coefficient at 660 nm. Green (565 nm), yellow (590 nm) and blue (470 nm) wavelength variants are available on special order.

The instrument consists of a Transmitter/Reference Assembly and a Detector Assembly aligned and spaced apart by an open support frame. The housing and frame are both manufactured in titanium and are pressure rated to 6000 m depth.

The Transmitter/Reference housing is sealed by an end cap. Inside the housing an LED light source emits a collimated beam through a sealed window. The Detector housing is also sealed by an end cap. A signal photodiode is placed behind a sealed window to receive the collimated beam from the Transmitter.

The primary difference between the ALPHAtracka and ALPHAtracka II is that the Alphatracka II is implemented with surface-mount technology; this has enabled a much smaller diameter pressure housing to be used while retaining exactly the same optical train as in the Mark I. Data from the Mark II version are thus fully compatible with that already obtained with the Mark I. The performance of the Mark II is further enhanced by two electronic developments from Chelsea Technologies Group - firstly, all items are locked in a signal nulling loop of near infinite gain and, secondly, the signal output linearity is inherently defined by digital circuitry only.

Among other advantages noted above, these features ensure that the optical intensity of the Mark II, indicated by the output voltage, is accurately represented by a straight line interpolation between a reading near full-scale under known conditions and a zero reading when blanked off.

For optimum measurements in a wide range of environmental conditions, the Mark I and Mark II are available in 5 cm, 10 cm and 25 cm path length versions. Output is default factory set to 2.5 volts but can be adjusted to 5 volts on request.

Further details about the Mark II instrument are available from the Chelsea Technologies Group ALPHAtrackaII specification sheet.

D376 CTD Originator Processing

Sampling Strategy

A total of 61 CTD casts were performed during the cruise, which sailed between Swansea (U.K.) and Southampton (U.K.) via the Celtic Sea shelf edge. Upon deployment, the CTD package was typically 'soaked' at a depth of ten metres to allow the pumps to flush through. The package was then brought back to the surface prior to commencing the downcast. Casts 46-59 were performed in quick succession, with no water bottles attached to the CTD frame. Between these casts the CTD package was returned briefly to deck whilst the ship re-positioned.

For D376, primary salinity and temperature refer to the data set generated by the sensors within the CTD package, whilst secondary salinity and temperature were obtained from the sensors mounted on the CTD vane.

Comparison between primary and secondary temperature and conductivity sensors were good, with the only exception being the temperature sensors on the first cast. The secondary sensor (mounted on the vane) was replaced upon CTD recovery, after which there was good agreement. It is possible that this sensor had been damaged due to its exposed position.

Data Processing

Following the completion of each CTD cast the data were saved to the deck unit PC and transferred over the network to a Unix data disk. Post-processing was performed using Sea-Bird Data Processing software version 7.21f and also using Matlab R2012a.

Raw data files were converted from engineering units to binary .cnv files using the DATCNV program. Individual Sea-Bird bottle data files (.ros), containing information on pressure and other readings logged at the time of bottle firing, were also generated during the data conversion process. The WILDEDIT program was run to remove any large spikes in the data, before ALIGNCTD advanced the primary temperature sensor on each cast by three seconds to address an apparent lag between temperature and conductivity sensors. Similarly, oxygen was advanced relative to pressure by four seconds thus ensuring dissolved oxygen concentrations were made with values measured from the same parcel of water. CELLTM was run, according to Sea-Bird's recommendations, to remove conductivity cell thermal mass effects from the measured conductivity. Subsequently, FILTER applied a low-pass filter value of 0.2 to smooth the rapidly changing pressure data. This was followed by the calculation of twin salinities, twin densities and depth using the DERIVE program. The final two steps were TRANSLATE, which output ASCII .cnv files for each cast and BOTTLESUM, which generated ASCII bottle files (.btl) from the existing .ros files.

Despiking of the 24 Hz data stream (pressure, oxygen, temperature and salinity) was achieved by visualisation of the data in Matlab. If a spike occurred in pressure, primary temperature or primary salinity, the whole corresponding scan was deleted. If the spike was present in oxygen, the value was set to NaN and all remaining channels left unedited. Spikes in secondary temperature or salinity resulted in NaNs being assigned to the secondary temperature, conductivity, salinity and density values, but the associated primary sensor output was not altered.

Following despiking of the data the Sea-Bird module BINAVERAGE averaged the 24 Hz data into 2 db bins, using the downcast data only.

Calibrations

Salinity

167 discrete salinity samples from the fired water bottles were analysed and compared with concurrent salinity measurements derived from the CTD sensors. Both were in good agreement. The following calibration equations were established and applied to the CTD salinity data for the cruise:

y = 0.997x + 0.1074 , R² = 0.9999 (primary salinity)

y = 1.001x - 0.0367 , R² = 0.9999 (secondary salinity)

Dissolved oxygen

149 discrete oxygen samples from the fired water bottles were analysed and compared with the measurements made with the CTD oxygen sensor. Some of these samples did not compare favourably. If the difference was greater than 0.5 mg/l, they were removed from the calibration data set. These outliers were largely associated with three single casts. The following calibration equation was established and applied to the CTD oxygen data for the cruise:

y = 1.0093x + 0.1348 , R² = 0.9714

Fluorescence

Bottle chlorophyll-a values were compared with corresponding chlorophyll-a measurements derived from the CTD fluorometer. Regression equations describing the relationship were generated for each cast. Any samples shallower than 50 metres between 7am and 9pm were excluded from this exercise, due to the quenching effect daylight can have on fluorescence readings. A whole cruise relationship between CTD and bottle was subsequently established:

CTD_chl = 0.982 * BOT_chl - 0.042

The data originator opted not to apply this calibration to the CTD fluorometer sensor data. Users wishing to do so can utilise the following equation:

CTD_calib = 1.018 * CTD_chl + 0.043

Data archival

The data originator produced several versions of the CTD data set for D376:

• 24 Hz non-despiked, non-calibrated CTD data

• 24 Hz despiked, non-calibrated CTD data

• 24 Hz despiked, calibrated (oxygen and salinity) CTD data

• 2 db despiked, non-calibrated CTD data

• 2 db despiked, calibrated (oxygen and primary salinity) WOCE-formatted CTD files

All of these versions are archived at BODC, but the WOCE-formatted versions alone have been ingested into the BODC relational database. This version is the default format used to service data requests.

Note:

In order to generate the WOCE-formatted version of the data, the originator converted the calibrated dissolved oxygen data from mg/l to µmol/kg using the following formula:

[µmol/kg] = (([mg/l]/1.42903) * 44660)/(sigma_theta + 1000)

References

Inall M. E. et al., 2012. RRS Discovery Cruise D376 Swansea to Southampton FASTNEt Cruise to the Celtic Sea Shelf Edge. Internal Report No 277. Scottish Association for Marine Science.

D376 CTD Processing undertaken by BODC

The 2 db-bin averaged (despiked and calibrated) CTD data from D376 were chosen for ingestion into the BODC database. These files contained the primary salinity and temperature channels (from the sensors within the CTD package, not those on the vane), together with dissolved oxygen processed to WOCE standards, alongside concurrent fluorometer and transmissometer data.

The data were reformatted to the standard BODC format, a subset of NetCDF, with variables mapped to suitable BODC parameter codes. The following table shows this mapping:

Flag mapping

As part of the reformatting process standard WOCE flags were mapped to corresponding BODC data quality flags. The following table shows the mapping between these flags. Definitions of BODC flags are available in the flag data document.

The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, and missing data marked by both setting the data to an appropriate absent data value and setting the quality control flag.

The data, together with appropriate 'usage' metadata, are banked at BODC where they are available for long term future use by the community.

Project Information

Fluxes Across Sloping Topography of the North East Atlantic (FASTNEt)

Background

The FASTNEt consortium was funded to deliver NERC's Ocean Shelf Edge Exchange Programme. Commencing in October 2011, this four year study aims to couple established observational techniques, such as moorings and CTDs, with the very latest in autonomous sampling initiatives - including use of Autosub Long Range and gliders. With the aid of novel model techniques, these observations will be utilised to construct a new paradigm of Ocean/Shelf exchange.

Shelf edge regions mark the gateway between the world's deep oceans and shallower coastal seas, linking terrestrial, atmospheric and oceanic carbon pools and influencing biogeochemical fluxes. Shelf edge processes can influence near-shore productivity (and fisheries) and ultimately affect global climate.

FASTNEt brings together researchers from multiple UK organisations. Further collaboration has been established with five Project Partners: the UK Met Office, Marine Scotland Science, Agri-Food and Biosciences Institute, Marine Institute Ireland and Scripps Institution of Oceanography.

Scientific Objectives

• To determine the seasonality of physical gradients and exchange across the shelf edge by deploying new observational technologies (gliders, Autosub Long Range) and established techniques (long term moorings, drifters)
• To quantify key exchange mechanisms and to collect new data targeted at testing and improving high resolution models of the shelf edge, by carrying out detailed process studies in contrasting regions of the shelf edge of the NE Atlantic margin
• To develop a new parameterisation of shelf edge exchange processes suitable for regional-scale models, using improved resolution numerical, and new empirical models constrained by the observations
• To test the new parameterisations in a regional model in the context of making an assessment of inter-annual variability of ocean-shelf exchange.

Fieldwork

Three survey sites on the UK shelf edge have been selected for FASTNEt. These are a) the Celtic Sea shelf edge, b) Malin shelf and c) North Scotland shelf. Fieldwork is centred around two research cruises. The first, to the Celtic Sea, on RRS Discovery in June 2012. The second cruise visits the Malin shelf on RRS James Cook, during summer 2013. In addition to these dedicated cruises, opportunist cruise activity to the North Scotland shelf has been agreed with project partner Marine Scotland Science. Autonomous technologies will complement observations made during the cruises and provide knowledge of seasonal and inter-annual variability in exchange processes.

Instrumentation

Types of instruments/measurements:

• Gliders
• Autosub Long Range
• Drifter buoys
• Scanfish
• Microstructure profilers
• Moored CTD/CT loggers and ADCPs
• Shipboard measurements: CTD, underway, nutrients (and other discrete sampling), LADCP, ADCP.

Contacts

Data Activity or Cruise Information

Cruise

Complete Cruise Metadata Report is available here

Fixed Station Information

Fixed Station Information

FASTNEt CTD Station A12

Station A12 was a CTD Station which was occupied repeatedly during FASTNEt cruise D376.

In total 12 casts were performed between 18/06/2012 and 19/06/2012, with the CTD package returning briefly to deck between casts in order for the ship to reposition.

The nominal position of Station A12 was 49.2° N, 8.5° W.

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:

SeaDataNet Quality Control Flags

The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:

Appendix 1: FASTNEt CTD Station A12

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.