Metadata Report for BODC Series Reference Number 1928650

• 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

CTD data from cruise JR18002 Quality Report

Screening and Quality Control

During BODC quality control, data were screened using in house visualisation software. The data were screened and any obvious outliers and spikes were looked at in closer detail and flagged if necessary.

Improbable value ('M') flags were applied to the POPTDR01 channel where the values were >100%.

AHSFZZ01

This channel has been flagged where values are constant or increase with depth. The altimeter only collects good data within 100 m of the seabed and these instances of constant values or increases with depth occur more than 100 m from the seabed.

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.

JR18002 CTD Instrumentation

A Sea-Bird 911 plus CTD system was used on cruise JR18002. This was mounted on a SBE-32 carousel water sampler holding 24 12-litre Niskin bottles. The CTD was fitted with the following scientific sensors:

Some calibration dates are unavailable.

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.

Chelsea Technologies Group Aquatracka MKIII fluorometer

The Chelsea Technologies Group Aquatracka MKIII is a logarithmic response fluorometer. Filters are available to enable the instrument to measure chlorophyll, rhodamine, fluorescein and turbidity.

It uses a pulsed (5.5 Hz) xenon light source discharging along two signal paths to eliminate variations in the flashlamp intensity. The reference path measures the intensity of the light source whilst the signal path measures the intensity of the light emitted from the specimen under test. The reference signal and the emitted light signals are then applied to a ratiometric circuit. In this circuit, the ratio of returned signal to reference signal is computed and scaled logarithmically to achieve a wide dynamic range. The logarithmic conversion accuracy is maintained at better than one percent of the reading over the full output range of the instrument.

Two variants of the instrument are available, both manufactured in titanium, capable of operating in depths from shallow water down to 2000 m and 6000 m respectively. The optical characteristics of the instrument in its different detection modes are visible below:

* The wavelengths for the turbidity filters are customer selectable but must be in the range 400 to 700 nm. The same wavelength is used in the excitation path and the emission path.

The instrument measures chlorophyll a, rhodamine and fluorescein with a concentration range of 0.01 µg l^-1 to 100 µg l^-1. The concentration range for turbidity is 0.01 to 100 FTU (other wavelengths are available on request).

The instrument accuracy is ± 0.02 µg l^-1 (or ± 3% of the reading, whichever is greater) for chlorophyll a, rhodamine and fluorescein. The accuracy for turbidity, over a 0 - 10 FTU range, is ± 0.02 FTU (or ± 3% of the reading, whichever is greater).

Further details are available from the Aquatracka MKIII specification sheet.

Biospherical Instruments QCP-2350 [underwater] PAR sensor

A cosine-corrected PAR quantum irradiance profiling sensor. For use in underwater applications with 24 bit ADC systems. Measures light available for photosynthesis on a flat surface. Operation is by a single channel compressed analog output voltage that is proportional to the log of incident PAR (400-700 nm) irradiance. The sensor is designed for operation in waters to depths of up to 2,000 m (standard) or 6,800 m (optional).

For more information, please see this document: https://www.bodc.ac.uk/data/documents/nodb/pdf/Biospherical_QCP2300_QCP2350_Apr2014.pdf

Tritech Digital Precision Altimeter PA200

This altimeter is a sonar ranging device that gives the height above the sea bed when mounted vertically. When mounted in any other attitude the sensor provides a subsea distance. It can be configured to operate on its own or under control from an external unit and can be supplied with simultaneous analogue and digital outputs, allowing them to interface to PC devices, data loggers, telemetry systems and multiplexers.

These instruments can be supplied with different housings, stainless steel, plastic and aluminum, which will limit the depth rating. There are three models available: the PA200-20S, PA200-10L and the PA500-6S, whose transducer options differ slightly.

Specifications

Common specifications are presented below

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

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.

Specifications

Further details are available in the manufacturer's specification sheet or user guide.

JR18002 ORCHESTRA CTD Data: Processing by BODC

The CTD data were supplied to BODC as 71 NetCDF files, containing both upcast and downcast data, and were converted to the BODC internal format.

During transfer the originator's variables were mapped to unique BODC parameter codes. The following table shows the parameter mapping.

Following transfer the data were screened using BODC in-house visualisation software. Improbable data values were assigned the appropriate BODC data quality flag. Missing data values, where present, were changed to the missing data value and assigned a BODC data quality flag.

Second sensor parameters have been removed from the final file but can be provided on request.

JR18002 ORCHESTRA Originator's CTD Data Processing

Sampling Strategy

A Sea-Bird Scientific SBE9plus CTD was mounted on a rosette with a SBE32 carousel water sampler and 24 12-litre Niskin bottles, and connected via a sea cable to a SBE11plus deck unit. In total, 71 CTD casts were completed on cruise JR18002 to produce full depth vertical profiles of temperature, salinity and dissolved oxygen concentration. These stations were along the WOCE SR1b line.

Operation was normal on the 71 stations conducted during the cruise, except for CTD 23 when the rosette was smashed on the ship's hull during recovery, due to an outstanding wave that suddenly rocked the ship; the impact sheared Niskin 19 from the frame and it was lost.

More information on the CTD configuration can be found here.

Originator's processing

Data were recorded using Seasave version 7.22.3 (Sea-Bird Scientific). After each cast, BAS_SVP was run. This prepares a sound velocity profile and a CTD listing for transmission to the UK Met Office. Then, three operations were run through the SBE Data Processing version 7.22.2 software.
The SBE data processing module Datcnv was used to convert the hex file to ascii (.cnv and .ros files).
Run/Align CTD was run using the program setup file AlignCTD.psa. It inputs an X.cnv file and outputs an X align.cnv file. It aligns parameter data in time, relative to pressure. This ensures that calculations of salinity, dissolved oxygen concentration and other parameters are made using measurements from the same parcel of water.
Run/Cell Thermal Mass)was run using the program setup file CellTM.psa. It inputs an X align.cnv file and outputs an X align ctm.cnv file. It uses a recursive filter to remove conductivity cell thermal mass effects from the measured conductivity.

SBE35 temperature data were uploaded using SeaTerm after finishing a cast or, for later stations with multiple casts at one site, for several casts at once. SBE35 temperature data can be logged when a Niskin bottle is fired. If the SBE35 is set to 8 samples, it requires approximately 13 seconds to make a measurement, calculated as 8 * 1.1 seconds plus an overhead; the procedure followed for bottle firing was therefore to wait 30 s for equilibration, fire a bottle, and wait 15 s to ensure the SBE35 measurement had been taken. Data are stored internally and must be downloaded at the CTD deck unit as a separate process from the CTD data transfer. The SBE35 data are then transferred as a collection of ASCII files. The SBE35 cable was damaged by handling lines during deployment or recovery of the rosette in the early casts, so the SBE35 was removed before cast 11 and refitted, with a new cable, on cast 23.

Further processing was conducted using the Mexec software suite v3.2:

Niskin sample data were read in to files also containing the CTD data at bottle firing times using smallscript load botcaldata.m. As sample data accumulated, we compared sample and CTD data, as well as individual sample values with smoothed, gridded profiles, to detect sample or Niskin flags that needed to be changed (either undetected bad values or bad Niskins, or Niskins flagged as questionable that looked fine). Flags assigned in the laboratory were usually not lowered based on this analysis. Inspection of profiles aboard the ship led to the assignment of bad or questionable flags to 41 salinity, 56 oxygen, 13 DIC, 17 alkalinity, 1 nitrate+nitrite, 2 silicate, and 3 phosphate values (these totals do not include values that were flagged because the Niskin was bad or questionable).

This initial quality control procedure was carried out using two functions:

• msam_checkbottles_01([a:b], var, sr1b) plots one sample of the type var for a range of stations [a:b], alongside residuals from the CTD values (for salinity and oxygen) or from the mapped values (for other quantities). Already flagged points are marked, and points for further investigation are selected using the GUI interface.
• msam_checkbottles_02(n, var) plots profiles of several sample types for a single station n, as well as neigbouring stations values and the CTD/mapped profiles.

A record of all post-comparison flag alterations was kept in the text document bottle_data_flags.txt within the CTD data directory. For oxygen and salinity, some good samples may yet be inappropriately flagged as questionable if they were taken at points in the profile with strong gradients/high variability. To detect these flags on bottles, the script ctd evaluate sensors.m plots their values against both the the CTD at firing times and the CTD 1 Hz data stream. Where the latter shows variance encompassing the bottle sample value, the 3 or 4 flag may be altered. Flags in bottle_data_flags.txt are applied to data files by running msam_02b.m. At the conclusion of this process only those results with 2 flags were used for calibration purposes.

Temperature, salinity, and oxygen were calibrated, using ctd_evaluate_sensors.m to compare calibration (SBE35 or bottle sample analysis values) with CTD data and determine calibration functions.

Temperature calibration

Comparisons between 1334 SBE35 readings and values recorded by each of the two CTD temperature sensors showed an apparent scale factor in addition to pressure dependence and, for sensor two, a very small drift in time. The calibration functions used were:

T_1,cal = T₁(1.00016) + interp([0, 800, 5000], [0.1,-0.2, 0.0] x 10^-3, p) + 1 x 10^-5,
T_2,cal = T₂(1.00017) + interp([0, 2000, 5000], [-1,-1.3,-1.8] x 10^-3, p) - n x 10^-5 + 2.8 x 10^-4, where p is pressure and n is station number, and interp(a, b, c) indicates linear interpolation of b(a) to c. The existence of very similar best fit scale factors for each sensor may be a cause for concern, but the correction is quite small in any case.

Conductivity calibration
Conductivities (at Niskin bottle firing temperatures) calculated from 441 good bottle salinity analyses were compared with the two CTD sensors. The calibrations applied were:

C_1,cal = C₁(1 + interp([0, 1800, 5000], [-0.8,-2.0,-1.5] x 10^-3, p) + 6 x 10^-4/35),
C_2,cal = C₂(1 + interp([0, 1500, 5000], [-1.8,-2.8,-4.5] x 10^-3, p)/35).

These conductivity scale factors are approximately equivalent to adding the quantity in curly brackets to salinity.

Oxygen calibration

Using the calibrated salinity and temperature to compute density and convert oxygen concentrations to µmol kg^-1, 444 good dissolved oxygen values were compared with the corresponding CTD readings. Scale and additive dependence on CTD oxygen, pressure, station number, and temperature were considered; simple functions of pressure seemed to reduce the bottle-CTD differences without over-fitting, resulting in a final calibration of:

O_cal = O(interp([0, 5000], [1.036, 1.062], p) + 3n x 10^-5) + interp([0, 500, 5000], [-1.50.5 - 0.9], p).

Please see the cruise report for further detail.

The processed data were supplied to BODC for banking.

Problems

On stations 36 to 39, the primary CTD gave bad values for several hundred meters. Secondary sensors looked fine and were set as main sensor for those stations. Subsequently, the secondary sensor was set as the main sensor for all stations (and earlier stations were reprocessed) because it was more reliable overall and was also the sensor the oxygen was plumbed into.

For station 15, automatic out-of-range editing was applied at the mctd_02a.m stage, and the cell thermal mass correction applied after that. For stations 29, 36, 39, and 40-43, automatic out-of-range editing was applied at the mctd rawedit.m stage. In the case of stations 36 and 39, this was to remove obvious stretches of bad temperature and conductivity data. For the others, relatively small negative pressures were leading to values outside the permitted range for the subsequent GSW calculations, so the minimum allowed pressure was set to -1.495.

Project Information

Radium in Changing Environments: A Novel Tracer of Iron Fluxes at Ocean Margins (RaCE:TraX)

Background

Radium in Changing Environments: A Novel Tracer of Iron Fluxes at Ocean Margins (RaCE:TraX) is a NERC (Natural Environment Research Council) funded project which involves using Radium (Ra) as a tracer to better understand the cycling of Iron (Fe) in the marine environment.

This project aims to answer three key questions to fill the gaps in our knowledge of the Fe cycle:

• How much Fe comes from continental shelf sediments?
• How much Fe is supplied by glacial meltwater?
• How rapidly is Fe scavenged from the metal-rich fluids at hydrothermal vents?

NERC Grant Reference NE/P017630/1 'Radium in Changing Environments: A Novel Tracer of Iron Fluxes at Ocean Margins'.

Participants

This project was a collaboration between AL Annett, University of Southampton (Lead Principal Investigator) and additional project members and cruise participants from the University of Southampton and the University of Bristol.

Fieldwork

Data has been collected on the James Clark Ross cruise JR18002

RaCE:TraX aim for this cruise was to measure Ra and Actinium (Ac) isotope ratios from samples across the Drake passage, to be used along with samples from the Western Antarctic Peninsula (Cruise JR18003) to determine the origin of Fe in the Antarctic Circumpolar Current.

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: