Metadata Report for BODC Series Reference Number 861574

• 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

Originator comments on data quality

Two new SBE43 dissolved oxygen sensors, purchased during summer 2003, were used throughout the cruise. Neither performed well. There was always an offset of ~1 ml l^-1 between the readings from the two instruments. While the overall level of the secondary sensor looked the better of the two, this one also suffered markedly from pressure hysteresis with an offset of up to 0.3 ml l^-1 between downcast data (when the sensor was being loaded) and upcast data (when it was being unloaded). During stops in the upcast, when niskin bottles were being fired, the reading from the secondary sensor relaxed to a value intermediate between the down and up trace. The primary sensor showed much less hysteresis, but never recorded oxygen levels close to saturation, even at the surface in open water. Since no underway Winkler titrations were performed, processing of the data will have to await the post-cruise calibration of the sensors by Sea-Bird. Although the final absolute oxygen concentrations are likely to be subject to relatively large errors, the main motivation for recording the data was to help quantify mixing within the main pycnocline. For this, relative changes in concentration through the water column are most important. Any future users of the sensors who require accurate absolute concentrations are advised to ensure that there is a Winkler titration system available on board.

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.

Instrument Description

CTD unit and auxiliary sensors

A total of 44 CTD casts were undertaken during JR84, using a CTD configuration including:

• 12-way CTD frame with 12 by 10L Niskin bottles
• Sea-Bird 9/11 plus CTD system
• two Sea-Bird 43 Oxygen sensors
• Tritech PA200/20-5 Altimeter
• Chelsea Aquatracka MKIII Fluorometer
• dual Sea-Bird temperature and conductivity sensors
• Sea-Bird SBE35 Deep Ocean Standards Thermometer

Data were logged at 24 Hz onto a PC running SEASAVE Win32 V 5.25, Sea-Bird's data acquisition software. The instrumentation serial numbers and calibration dates were as follows:

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.

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.

BODC Processing

The data arrived at BODC in the following formats:

• Raw Sea-Bird files
• 24Hz resolution pstar files
• 2db resolution pstar files

The decision was taken by BODC to load the 2db resolution pstar files as these represent the final calibrated data produced by the originator. All three original data formats are available upon request from BODC. There were 43 2db pstar files representing all CTD profiles from JR84 excluding station 18 that was aborted at 40 db and repeated with station 19 (a full depth profile). These were reformatted to the internal QXF format using BODC transfer function 360. The following table shows how the variables within the pstar files were mapped to 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, missing data by both setting the data to an appropriate value and setting the quality control flag.

General Data Screening carried out by BODC

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 unfeasible values
• Inconsistencies between related information, for example:
  • Times for instrument deployment and for start/end of data series
  • Length of record and the number of data cycles/cycle interval
  • Parameters expected and the parameters actually present in the data cycles
• Originator's comments on meter/mooring performance and data quality

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

Data cycles are inspected using time or depth series plots of all parameters. Currents are additionally inspected using vector scatter plots and time series plots of North and East velocity components. These presentations undergo intrinsic and extrinsic screening to detect infeasible values within the data cycles themselves and inconsistencies as seen when comparing characteristics of 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 data values will not be altered.

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

• Spurious data at the start or end of the record.
• Obvious spikes occurring in periods free from meteorological disturbance.
• A sequence of constant values in consecutive data cycles.

If a large percentage of the data is affected by irregularities then a Problem Report will be written rather than flagging the individual suspect values. Problem Reports are also used to highlight irregularities seen in the graphical data presentations.

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

• Maximum and minimum values of parameters (spikes excluded).
• The occurrence of meteorological events.

This intrinsic and extrinsic 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 making are not introduced.

Originator's Data Processing

Sampling strategy

A total of 44 CTD casts were completed during the cruise to the Pine Island Glacier (PIG) on the western side of the Antarctic Peninsula. All casts, with the exception of stations 2, 18, 42, 43, and 44, were full depth profiles. Cast 18 was aborted at 40 decibar and repeated with a full depth cast in station 19. Rosette bottles were fired throughout the profile on most casts to obtain independent salinity samples for calibration. Samples were not taken from cast 15 because the samples were spoiled by the ingestion of a jellyfish by the CTD frame. The CTD included a SBE35 high-precision thermometer to obtain independent temperature profiles for use in calibration.

Water samples were taken for post-cruise determination of Oxygen 18 isotope values and Radon content. Stations that were sampled for these quantities are listed in the cruise report.

Data Processing

Data processing steps are described in detail in the JR84 cruise report, they will be summarised here. Data file naming by the data originator is of the form CCctdNNN.EXT where CC is the cruise number , NNN is the station number and EXT is the file type extension.

Raw data files output from Sea-Bird seasave were:

• CCctdNNN.dat (raw data file)
• CCctdNNN.con (configuration file)
• CCctdNNN.bl (bottle information file)
• CCctdNNN.hdr (header information file)

Sea-Bird data processing software steps were as follows:

1. Data conversion module run to apply instrumental calibration coefficients to the raw data and to convert the binary file to ASCII format. CCctdNNN.cnv is output.
2. Cell thermal mass module run to re-derive pressure and conductivity taking into account cell thermal lag and pressure effects. The files CCctdNNNtm.cnv and CCctdNNN.ros are output.

SBE35 data were manually downloaded from the instrument in a separate process. The SBE35 data were refomatted and saved as CCsbeNNN files. Discrete salinity sample values were entered into an ASCII format file with filename CCsamNNN.txt.

The remaining CTD data processing steps used the National Oceanography Centre, Southampton (NOCS) pstar Fortran routines as follows:

1. 84seactd0 converts the data from ASCII format to pstar.
2. 84seactd1 requires that the SBE35 data have been transferred and downloaded, four output files are produced:
   • CCctdNN.bottle (CTD data at bottle firing points)
   • CCctdNNN.samp (CTD data at bottle firing points with SBE35 and discrete salinity sample data)
   • CCsamNNN.dif (temperature and salinity calibration residual values)
   • sampNNN.bot (raw salinity sample values)
   The fileCCctdNNN.cond containing salinity sample conductivity values is also produced.
3. 84seactd2 plotted salinity profiles with discrete samples for quality control of the sample data.
4. ctdoff produced the mean conductivity residual and standard deviation for calibration.
5. 84seactd3 applied the conductivity residual and re-derived salinity. CCctdNNN.cal files were produced.
6. 84seactd4 produced the final calibrated CCctdNNN.24Hz and CCctdNNN.2db data products.
7. 84seactd5 applied the calibration to the raw data which created files CCctdNNN.cbottle, CCctdNNN.csamp and CCctdNNN.cdif

Field calibrations

Calibration was part of the pstar processing steps already outlined and used discrete water samples taken from the CTD rosette. A list of the bottles excluded from the calibration and the reasons for exclusion are on pages 42 and 43 of the cruise report. Duplicate salinity samples were also taken for comparison at the start of the cruise. The salinity difference between the 36 duplicate samples was 0.00011. The calibration applied was time-dependent with the values applied by CTD station as listed on p43 of the cruise report. The calibration was checked for a pressure dependency with none identified.

A comparison of the SBE35 data against the CTD data was undertaken but no calibration applied. The offsets between the SBE35 thermometer and the primary temperature cell showed that for 516 samples the mean offset was 0.00296°C, with the SBE 35 being lower. Comparison of the SBE35 with the secondary temperature cell showed that for 516 samples the mean offset was slightly lower at 0.00257°C.

Project Information

AutoSub Under Ice (AUI) Programme

AutoSub was an interdisciplinary Natural Environment Research Council (NERC) thematic programme conceived to investigate the marine environment of floating ice shelves with a view to advancing the understanding of their role in the climate system.

The AUI programme had the following aims:

• To attain the programme's scientific objectives through an integrated programme based on interdisciplinary collaborations and an international perspective
• To develop a data management system for the archiving and collation of data collected by the programme, and to facilitate the eventual exploitation of this record by the community
• To provide high-quality training to develop national expertise in the use of autonomous vehicles in the collection of data from remote environments and the integration of such tools in wider programmes of research
• To stimulate and facilitate the parameterising of sub-ice shelf processes in climate models, and to further demonstrate the value of autonomous vehicles as platforms for data collection among the wider oceanographic and polar community

Following the invitation of outline bids and peer review of fully developed proposals, eight research threads were funded as part of AUI:

Physical Oceanography

• ISOTOPE: Ice Shelf Oceanography: Transports, Oxygen-18 and Physical Exchanges.
• Evolution and impact of Circumpolar Deep Water on the Antarctic continental shelf.
• Oceanographic conditions and processes beneath Ronne Ice Shelf (OPRIS).

Glaciology and Sea Ice

• Autosub investigation of ice sheet boundary conditions beneath Pine Island Glacier.
• Observations and modelling of coastal polynya and sea ice processes in the Arctic and Antarctic.
• Sea ice thickness distribution in the Bellingshausen Sea.

Geology and Geophysics

• Marine geological processes and sediments beneath floating ice shelves in Greenland and Antarctica: investigations using the Autosub AUV.

Biology

• Controls on marine benthic biodiversity and standing stock in ice-covered environments.

The National Oceanography Centre Southampton (NOCS) hosted the AUI programme with ten further institutions collaborating in the project. The project ran from April 2000 until the end of March 2005, with some extensions to projects beyond this date because of research cruise delays. The following cruises were the fieldwork component of the AUI project:

Table 1: Details of the RRS James Clark Ross AUI cruises.

All the cruises utilised the AutoSub autonomous, unmanned and untethered underwater vehicle to collect observations beneath sea-ice and floating ice shelves. AutoSub can be fitted with a range of oceanographic sensors such as:

• Conductivity Temperature Depth (CTD) instruments
• Acoustic Doppler Current Profillers (ADCP)
• A water sampler
• Swath bathymetry systems
• Cameras

In addition to use of AutoSub during each cruise measurements were taken from ship. These varied by cruise but included:

• Ship underway measurements and sampling for parameters such as:
  • Salinity
  • Temperature
  • Fluorescence
  • Oxygen 18 isotope enrichment in water
  • Bathymetry using a swath bathymetry system
• Full-depth CTD casts for with observations of samples taken for parameters such as:
  • Salinity
  • Temperature
  • Fluorescence
  • Optical transmissivity
  • Dissolved oxygen
  • Oxygen 18 isotope enrichment in water
  • Water CFC content
• Sea floor photography and video using the WASP system
• Sea floor sampling with trawls/rock dredges
• Sea ice observations (ASPeCt), drifters and sampling

The AutoSub project also included numerical modelling work undertaken at University College London, UK.

The project included several firsts including the first along-track observations beneath an ice shelf using an autonomous underwater vehicle. The AutoSub vehicle was developed and enhanced throughout this programme and has now become part of the NERC equipment pool for general use by the scientific community. Further information for each cruise can be found in the respective cruise reports (links in Table 1).

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: