Metadata Report for BODC Series Reference Number 1192065

• 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

Maximum Instrument Depth Greater Than Sea Floor Depth

CTD/XBT Data

It is possible for the maximum depth of a CTD/XBT cast to exceed the estimated sea floor depth at a given location.

The depth of a CTD unit is calculated from its measurements of pressure using an algorithm which makes assumptions about the density profile of the water column and XBT depth is often estimated from an assumed descent rate. Similarly, total water depth is calculated from the two-way travel time of sound waves through the water column making assumptions about the velocity of the sound waves. All of these calculations may contain errors, and the depth of a CTD/XBT unit may therefore appear to be below the sea floor.

Other Instrument Types

It is possible that instrument depths are taken from instantaneous measurements whereas water depth is read from a chart or corrected to a datum, such as mean sea level. If this occurs and the instrument depth has been read at high tide it is possible that an instrument mounted on the sea floor will have a depth half of the tidal range below the sea floor depth.

JC088 CTD Data Quality Report

Transmittance

The Chelsea/Seatech transmissometer was last calibrated on 11th June 2012 and it is not known if any field calibrations were applied. For the following casts, the transmissometer data includes values that exceed 100% transmittance:

• 001, 006, 011, 012, 013, 025, 026, 027, 040, 046, 059, 060, 061, 063

As the affected casts are distributed throughout the cruise, all of the transmittance data should therefore be considered to be a relative measure. Transmission values exceeding 100% have been flagged as suspect ('M').

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

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.

Specifications

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

JC088 CTD Instrumentation Description

CTD unit and auxiliary sensors

The CTD system used on cruise JC088 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). Data were recorded using a Sea-Bird 11plus deck unit using Firmware version 5.

The package was fitted with the following scientific sensors

A fast CT sensor was additionally deployed on the CTD package during 15 unspecified casts for comparison with the CTD sensors in support of a project developing sensors for use on gliders.

The discrete salinity samples collected from water bottles on the CTD were analysed in the ship's temperature-controlled room using a Guildline Autosal8400 salinometer (serial number 60839). Dissolved oxygen concentrations from further water samples were determined using a titration technique.

References

Inall M. E. et al., 2013. RRS James Cook Cruise JC88 Glasgow to Southampton FASTNEt Cruise to the Malin Shelf Edge. Internal Report No xxx. Scottish Association for Marine Science.

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.

BODC CTD Screening

BODC screen both the series header qualifying information and the parameter values in the data cycles themselves.

Header information is inspected for:

• Irregularities such as infeasible values
• Inconsistencies between related information. For example:
  • Deepest CTD data cycle is significantly greater than the depth of the sea floor.
  • Times of the cruise and the start/end of the data series.
  • Length of the record, number of data cycles, cycle interval, clock error and the period over which data were collected.
  • Parameters stated as measured and the parameters actually present in the data series.
• Originator's comments on instrument/sampling device performance and data quality.

Documents are written by BODC highlighting irregularities that cannot be resolved.

Data cycles are inspected using depth series plots of all parameters. These presentations undergo screening to detect infeasible values within the data cycles themselves and inconsistencies when comparing adjacent data sets displaced with respect to depth, position or time.

Values suspected of being of non-oceanographic origin may be tagged with the BODC flag denoting suspect value.

The following types of irregularity, each relying on visual detection in the time series plot, are amongst those that may be flagged as suspect:

• Spurious data at the start or end of the record where the instrument was recording in air
• Obvious spikes occurring in the data due electrical problems
• Constant, or near-constant, data channels

If a large percentage of the data is affected by irregularities, deemed abnormal, then instead of flagging the individual suspect values, a caution may be documented.

The following types of inconsistency are detected automatically by software:

• Data points with values outside the expected range for the parameter, as defined by the BODC parameter usage vocabulary.

Inconsistencies between the characteristics of the data set and those of its neighbours are sought, and where necessary, documented. This covers inconsistencies in the following:

• Maximum and minimum values of parameters (spikes excluded).
• Anomalous readings due to the CTD package being bounced through temperature and/or salinity gradients.

This screening of the parameter values seeks to confirm the qualifying information and the source laboratory's comments on the series. In screening and collating information, every care is taken to ensure that errors of BODC's making are not introduced.

JC088 CTD BODC Data Processing

The data arrived at BODC in 73 ASCII format files representing all of the CTD casts taken during the cruise. These were reformatted to BODC's internal file format which is a NetCDF subset. The following table shows how the variables within the *.CTD files were mapped to appropriate BODC parameter codes:

The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag. There were no missing data.

JC088 CTD Originator Processing

Sampling Strategy

A total of 73 CTD casts were performed during the cruise, which sailed between Glasgow (UK) and Southampton (UK) via the Malin shelf edge. Upon deployment, the CTD package was typically 'soaked' at a depth of ten metres to allow the pumps to switch on. The package was then brought back up close to the surface (2 to 5m) before starting the cast. The Niskin bottles were fired on the way up, and the CTD package was stopped for at least 30 seconds before firing to allow the sensors to settle.

The primary and secondary temperature and conductivity sensors were in close agreement.

Data Processing

The CTD data were processed according to the standards described in the SAMS CTD data Processing Protocol (Dumont and Sherwin, 2008, SAMS internal report No 257 ), using Seabird Data Processing version 7.21f and Matlab R2012a. Raw data files were converted from engineering units to binary .cnv files using the DATCNV program. Variables exported were scan number, pump status, Julian day, latitude, longitude, pressure [db], depth [m], temperature0 [ITS-90, deg C], conductivity0 [mS/cm], temperature1 [ITS-90, deg C], conductivity1 [mS/cm], oxygen [mg/l], altimeter [m], fluorescence [µg/l], beam transmission [%],beam attenuation [1/m], turbidity [m ^-1/sr], primary PAR, secondary PAR. 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 major spikes in the data, before AlignCTD advanced the conductivities by 0.073 seconds to address an apparent lag between temperature and conductivity sensors. Similarly, oxygen was advanced relative to pressure by five 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.

Some large "spikes" lasting a few seconds were observed in the data from both of the conductivity and temperature sensors, predominantly in the thermocline area. A possible explanation was described in the D352 cruise report, whereby the spikes arise from variable CTD fall rate leading to inefficient flushing of the CTD package. The WILDEDIT and LOOPEDIT programs proved inefficient in removing those spikes, and were therefore manually removed in the MATLAB despiking routine. This explains the sometimes irregular data interval observed on the 24 Hz dataset. For bin-averaged data, the Sea Bird software interpolates any missing values, and data users should therefore use caution when interpreting the data.

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

Calibrations

Salinity

A total of 129 salinity samples were collected and analysed, including a few duplicate samples. The Autosal and the SeaBird values were in very good agreement. A few outliers were removed (4 for the primary sensor, and 6 for the secondary), where the difference between the Autosal and CTD values was greater than 2 standard deviations from the average. The following calibration equations were established and applied to the CTD data for the cruise.

y = 0.9987x + 0.0481 , R² = 0.9999 (primary salinity)

y = 0.9983x + 0.0621 , R² = 1.000 (secondary salinity)

Dissolved oxygen

A total of 468 samples were collected to calibrate the dissolved oxygen sensor on the CTD. A few outliers were removed (20 points in total), 75% of which occurred on samples taken from cast 001. The following calibration equation was established and applied to the CTD oxygen data for the cruise

y = 0.927x - 4.5318 , R² = 0.9811

Data archival

The data originator produced several versions of the CTD data set for JC088:

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

• 24 Hz despiked, non-calibrated CTD data

• 2db-bin averaged despiked, non-calibrated CTD data

• 1m-bin averaged despiked, non-calibrated CTD data

• 1s-bin averaged despiked, calibrated (oxygen and salinity) CTD data

• 24 Hz despiked, primary and secondary salinities calibrated CTD data

• 2db-bin averaged despiked, calibrated (salinity and oxygen) WOCE-formatted CTD data

The last two versions of the data 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. The 24 Hz archived version contains additional parameters including PAR, fluorescein fluorescence, turbidity and altimeter data: these will not be processed any further by BODC but are available on request in the original supplied format.

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., 2013. RRS James Cook Cruise JC88 Glasgow to Southampton FASTNEt Cruise to the Malin Shelf Edge. Internal Report No xxx. Scottish Association for Marine Science.

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

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:

SeaDataNet Quality Control Flags

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