Metadata Report for BODC Series Reference Number 1917178
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
Data Description |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Data Identifiers |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time Co-ordinates(UT) |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Spatial Co-ordinates | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Parameters |
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Problem Reports
No Problem Report Found in the Database
RRS Discovery Cruise AMT27 (DY084) CTD Data Quality Document
Temperature, salinity, potential temperature and sigma-theta: Entrainment features were visible in a number of casts, both in the frame mounted (primary) and vane mounted (secondary channels). These features were apparent throughout the thermocline/pycnocline and continued down to varying depths. The level of entrainment can be indicated by a variation between data points of around 0.2 to 0.3 °C in the temperature, of 0.04-0.05 in the salinity and 0.02 kg m-3in sigma-theta. Overall, the primary temperature, salinity and density channels were deemed to be of better quality and were retained for banking in the NODB, while secondary channels were discarded.
Fluorescence: In circumstances where data were collected at pressures typically > 150 dbar, negative concentrations were frequently visible. These were flagged as anomalous. These resulted from the chlorophyll calibration being optimised for the euphotic zone, in particular the fluorescence/chlorophyll maximum.
Dissolved oxygen concentration and oxygen saturation: Several casts exhibited strong variability. All oxygen channels were flagged for the whole of CTD cast 000, 001, and 020 (BODC file references: 41300, 41400 and 43300 respectively).
Attenuance and transmissance: Casts 2-14 had large sections of values outside the parameter range (0-400 m-1) and (0-100%) which were flagged as anomalous. There were also some large spikes which were flagged in casts 47, 61 and 64. These may have occurred due to a suspect manufacturer's calibration. Although the values should be teated with caution, the shape of the profiles are still representative of the parameter.
Down and up-welling PAR irradiance: Optics casts were taken pre-dawn and at solar noon. Therefore, for almost half the casts, the PAR values are negligible as they were recorded in the dark.
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
| Housing | Plastic or titanium |
| Membrane | 0.5 mil- fast response, typical for profile applications 1 mil- slower response, typical for moored applications |
| Depth rating | 600 m (plastic) or 7000 m (titanium) 10500 m titanium housing available on request |
| Measurement range | 120% of surface saturation |
| Initial accuracy | 2% of saturation |
| Typical stability | 0.5% per 1000 h |
Further details can be found in the manufacturer's specification sheet.
RRS Discovery DY084 CTD Instrumentation
A Sea-Bird 911 plus CTD system was used on cruise DY084. This was mounted on a SBE-32 carousel water sampler holding 24 10-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:
| Parameter | Range | Initial accuracy | Resolution at 24 Hz | Response time |
|---|---|---|---|---|
| Temperature | -5 to 35°C | 0.001°C | 0.0002°C | 0.065 sec |
| Conductivity | 0 to 7 S m-1 | 0.0003 S m-1 | 0.00004 S m-1 | 0.065 sec (pumped) |
| Pressure | 0 to full scale (1400, 2000, 4200, 6800 or 10500 m) | 0.015% of full scale | 0.001% of full scale | 0.015 sec |
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:
| Excitation | Chlorophyll a | Rhodamine | Fluorescein | Turbidity |
|---|---|---|---|---|
| Wavelength (nm) | 430 | 500 | 485 | 440* |
| Bandwidth (nm) | 105 | 70 | 22 | 80* |
| Emission | Chlorophyll a | Rhodamine | Fluorescein | Turbidity |
| Wavelength (nm) | 685 | 590 | 530 | 440* |
| Bandwidth (nm) | 30 | 45 | 30 | 80* |
* 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 Log Quantum Cosine Irradiance Sensor QCP-2300 & QCP-2350
The QCP-2300 is a submersible cosine-collector radiometer designed to measure irradiance over Photosynthetically Active Radiation (PAR) wavelengths. It features a constant (better than ±10%) quantum response from 400 to 700 nm with the response being sharply attenuated above 700 nm and below 400 nm.
The sensor is a blue-enhanced high stability silicon photovoltaic detector with dielectric and absorbing glass filter assembly. The output is a DC voltage typically between 0 and 5 VDC that is proportional to the log of the incident irradiance.
The QCP-2300 is specifically designed for integration with 12-bit CTD systems and dataloggers requiring a limited-range of signal input.
Specifications
| Wavelength | 400 to 700 nm |
| PAR Spectral Response | better than ± 10% over 400-700 nm |
| Cosine Directional Response | ± 5% 0 to 65°; ± 10% 0 to 85° |
| Noise level | < 1 mV |
| Temperature Range | -2 to 35 °C |
| Depth Range (standard) | 1000 m |
Further details can be found in the manufacturer's manual.
.WETLabs Single-angle Backscattering Meter ECO BB
An optical scattering sensor that measures scattering at 117°. This angle was determined as a minimum convergence point for variations in the volume scattering function induced by suspended materials and water. The measured signal is less determined by the type and size of the materials in the water and is more directly correlated to their concentration.
Several versions are available, with minor differences in their specifications:
- ECO BB(RT)provides analog or RS-232 serial output with 4000 count range
- ECO BB(RT)D adds the possibility of being deployed in depths up to 6000 m while keeping the capabilities of ECO BB(RT)
- ECO BB provides the capabilities of ECO BB(RT) with periodic sampling
- ECO BBB is similar to ECO BB but with internal batteries for autonomous operation
- ECO BBS is similar to ECO BB but with an integrated anti-fouling bio-wiper
- ECO BBSB has the capabilities of ECO BBS but with internal batteries for autonomous operation
Specifications
| Wavelength | 471, 532, 660 nm |
| Sensitivity (m-1 sr-1) | 1.2 x 10-5 at 470 nm 7.7 x 10-6 at 532 nm 3.8 x 10-6 at 660 nm |
| Typical range | ~0.0024 to 5 m-1 |
| Linearity | 99% R2 |
| Sample rate | up to 8Hz |
| Temperature range | 0 to 30°C |
| Depth rating | 600 m (standard) 6000 m (deep) |
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
| Pathlength | 10 or 25 cm |
| Wavelength | 370, 470, 530 or 660 nm |
| Bandwidth | ~ 20 nm for wavelengths of 470, 530 and 660 nm ~ 10 to 12 nm for a wavelength of 370 nm |
| Temperature error | 0.02 % full scale °C-1 |
| Temperature range | 0 to 30°C |
| Rated depth | 600 m (plastic housing) 6000 m (aluminum housing) |
Further details are available in the manufacturer's specification sheet or user guide.
Originator Data Processing of CTD casts from cruise DY084 (AMT27)
Sampling Strategy
A total of 78 CTD casts and one shakedown CTD were performed during DY084 to obtain profiles of the water column from a range of sensors including pressure, temperature, conductivity, oxygen, fluoresence, PAR, turbidity, transmittance, and attenuance. CTDs were deployed pre-dawn at ~4:30am and noon ~12:30pm ship time each day, until 21st October when deployment times switched to 3:00am and 10:30am ship time, weather permitting. profiles were down to 500m depth twice a day, and every 4th day to 1000m with an additional 1000m cast after the pre-dawn.
Data Processing
The Sea-bird data collection software Seasave-Win32 recorded the raw data output from the CTD casts. Processing the raw data occurred daily, following the BODC recommended guidelines using SBE Data Processing-Win32 v7.26.7. Subsequently, the following processing routines were run to convert the raw CTD data into CNV files, each routine is named after each stage in brackets <>:
- Data conversion - converted raw binary Sea-Bird files to ASCII files (CNV) containing the 24 Hz data for up and down casts <DatCnv>.
- Generation of bottle files for each cast containing the mean values of all the variables at the time of bottle firing events <Bottle Summary>.
- Using the CNV files, processing routines were applied to remove pressure spikes <WildEdit>.
- The oxygen sensor was then shifted relative to the pressure by 2 seconds, to compensate for the lag in the sensor response time <AlignCTD> .
- The effect of thermal 'initia' on the conductivity cells was removed <CellTM>.
- The surface soak for each cast was identified using <Seaplot> and removed manually, then <LoopEdit> was run to minimise the marked wake effect linked to ship rolling observed on recent cruises.
- Salinity and oxygen concentration were re-derived amd density (sigma-theta) values were derived after the corrections for sensor lag and thermal inertia had been applied <Derive>.
- The CTD files produced from Sea-Bird processing were converted from 24Hz ascii files into 1 dbar downcast files for calibration and visualisation on-board <BinAverage>.
- Removal of the initial salinity and oxygen channels produced at the DatCnv stage, along with the conductivity, voltage and altimeter channels from the 1-dbar downcast files <Strip>.
prior to processing the xmlcon files were checked to against the instrument calibration sheets to ensure the correct set up details were used.
Data were then processed using the Mexec processing suite (a set of Matlab and shell scripts developed by Brian King (NOC) and updated by numerous users, including substantial recent updates by Yvonne Firing). All CTD processing and calibration for JC159 was executed using Mexec v3.2.
Calibrations
Collation of the sensor values at bottle firing generated by the
To generate a calibration, an offset between the discrete water sample measurement (salinity/oxygen) and the nominal value from the sensor at bottle firing was calculated. Outliers were identified using plots of offset against the discrete sample values and a linear regression was applied.
Where the regression was strong and significant the calibration equation was derived by rearranging the regression equation:
Offset = a * Discrete sample + b
Where: offset = Discrete sample - Sensor value
To give: Calibrated value = 1/(1-a) * Sensor value + b/(1-a)
Where the regression was not significant the mean value of the offset was applied. All calibration datasets are available upon request from BODC post cruise.
Salinity
The salinity channels were calibrated against bench salinometer measurements from five samples on average collected from CTD casts every few days. Further details of these measurements can be found in the NMF-SS cruise report section.
For salinity sensor 1, there was a weak but significant relationship between bench salinity and offset (n = 101; r2 = 0.162; p < 0.001). However, applying a regression did not improve the dataset nor did applying the mean offset.
The secondary CTD salinity sensor was calibrated against discrete salinity measurements. The regression of bench salinity against offset was not significant or strong (n = 108; r2 = 0.00385; p >0.05) so the mean offset was applied to these data.
Calibrated secondary salinity = uncalibrated salinity - 0.00234
Oxygen
Calibration of the SBE 43 oxygen sensor against discrete oxygen Winkler titration measurements used five depths collected from the pre-dawn and noon CTDs. The CTD oxygen sensor recorded anomalous values on the shakedown cast and on CTD001, so data from these casts were not included in the calibration. The oxygen sensor operated without problem throughout the remainder of the cruise.
Several data points did not fit the pattern observed with the data from the other casts and so were excluded from the calibration data set. There was a strong, significant relationship between the offset and the discrete oxygen data, so that the trend below was applied to the CTD oxygen data.
The calibration equation:
Calibrated O2 (in µmol/l) = 1.1004 * sensor O2 (in µmol/l) - 5.9485 (n = 314; r2 = 0.887; p < 0.001);
Fluorometer
118 Niskin samples from 44 stations were filtered for chlorophyll A which were analysed ashore. These measurements were used to calibrate the fluorometer.
The CTD temperature, transmittance, and turbidity sensors were not calibrated. Temperature sensor differences were stable throughout the cruise.
RRS Discovery DY084 CTD BODC Processing
The CTD data were supplied to BODC as 79 .txt files 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.
| Originator's variable | Units | BODC Code | Units | Comments |
|---|---|---|---|---|
| Pressure | dbar | PRESPR01 | dbar | - |
| Temperature_1 | °C | TEMPST01 | °C | - |
| Temperature_2 | °C | TEMPST02 | °C | - |
| Beam_Transmission | % | POPTDR01 | % | - |
| Beam_Attenuation | m-1 | ATTNDR01 | m-1 | - |
| Fluorescence | µg L-1 | CPHLPM01 | mg m-3 | Units are equivalent, no conversion required |
| PAR_Irradiance_1 | µE m-2 sec-1 | IRRUUV01 | µE m-2 s-1 | - |
| PAR_Irradiance_2 | µE m-2 sec-1 | IRRDUV01 | µE m-2 s-1 | - |
| Turbidity | m-1 sr-1 | BB117NIR | m-1 nm-1 sr-1 | - |
| Salinity_1 | PSU | PSALST01 | PSU | - |
| Salinity_2 | PSU | PSALST02 | PSU | - |
| Salinity2_calibrated | µmol L-1 | PSALCC02 | µmol L-1 | - |
| Oxygen | µmol L-1 | DOXYSU01 | µmol L-1 | - |
| Oxygen_Calibrated | µmol L-1 | DOXYSC01 | µmol L-1 | - |
| - | - | OXYSSU01 | % | Calculated during transfer from DOXYSU01 |
| - | - | OXYSSC01 | % | Calculated during transfer from DOXYSC01 |
| - | - | SIGTPR01 | kg m-3 | Calculated during transfer |
| - | - | POTMCV01 | °C | Calculated during transfer |
ODV flags applied during originators processing were transferred as 'L' flags.
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, except for the calibrated second sensor salinity, have been removed from the final file but can also be provided on request.
Project Information
No Project Information held for the Series
Data Activity or Cruise Information
Cruise
| Cruise Name | DY084 (AMT27, DY085) |
| Departure Date | 2017-09-23 |
| Arrival Date | 2017-11-05 |
| Principal Scientist(s) | Andrew Rees (Plymouth Marine Laboratory), Phyllis Lam (University of Southampton School of Ocean and Earth Science) |
| Ship | RRS Discovery |
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:
| Flag | Description |
|---|---|
| Blank | Unqualified |
| < | 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.) |
| D | Thermometric depth |
| E | End of CTD Down/Up Cast |
| G | Non-taxonomic biological characteristic uncertainty |
| H | Extrapolated value |
| 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 |
| N | Null value |
| O | Improbable value - user quality control |
| P | Trace/calm |
| Q | Indeterminate |
| R | Replacement value |
| S | Estimated value |
| T | Interpolated value |
| U | Uncalibrated |
| W | Control value |
| X | Excessive difference |
SeaDataNet Quality Control Flags
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
| Flag | Description |
|---|---|
| 0 | no quality control |
| 1 | good value |
| 2 | probably good value |
| 3 | probably bad value |
| 4 | bad value |
| 5 | changed value |
| 6 | value below detection |
| 7 | value in excess |
| 8 | interpolated value |
| 9 | missing value |
| A | value phenomenon uncertain |
| B | nominal value |
| Q | value below limit of quantification |
