Metadata Report for BODC Series Reference Number 1073619
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
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Problem Reports
No Problem Report Found in the Database
RSS James Clark Ross Cruise AMT8 CTD Data Quality Document
Downwelling sub-surface PAR irradiance
For downwelling PAR, some data points were beyond the maximum range of the parameter and so were flagged as suspect.
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
James Clark Ross Cruise AMT8 CTD Instrumentation
Sea-Bird Electronics 911plus CTD (with SBE9 CTD and SBE11 deck unit)
Fitted with secondary conductivity cell and temperature sensor
Rosette fitted with 12 30-litre Niskin water bottles
Wet Labs WETstar miniature fluorometer model 9707005, SN WS3S-303P
Wet Labs Cstar transmissometer model 9706011, SN CST-153R
Biospherical Instruments Inc. spherical PAR sensor model QSP-200L, SN4499
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.
WET Labs WETStar Fluorometers
WET Labs WETStar fluorometers are miniature flow-through fluorometers, designed to measure relative concentrations of chlorophyll, CDOM, uranine, rhodamineWT dye, or phycoerythrin pigment in a sample of water. The sample is pumped through a quartz tube, and excited by a light source tuned to the fluorescence characteristics of the object substance. A photodiode detector measures the portion of the excitation energy that is emitted as fluorescence.
Specifications
By model:
| Chlorophyll WETStar | CDOM WETStar | Uranine WETStar | Rhodamine WETStar | Phycoerythrin WETStar | |
|---|---|---|---|---|---|
| Excitation wavelength | 460 nm | 370 nm | 485 nm | 470 nm | 525 nm |
| Emission wavelength | 695 nm | 460 nm | 530 nm | 590 nm | 575 nm |
| Sensitivity | 0.03 µg l-1 | 0.100 ppb QSD | 1 µg l-1 | - | - |
| Range | 0.03-75 µg l-1 | 0-100 ppb; 0-250 ppb | 0-4000 µg l-1 | - | - |
All models:
| Temperature range | 0-30°C |
|---|---|
| Depth rating | 600 m |
| Response time | 0.17 s analogue; 0.125 s digital |
| Output | 0-5 VDC analogue; 0-4095 counts digital |
Further details can be found in the manufacturer's specification sheet, and in the instrument manual.
Biospherical Instruments Quantum Scalar Irradiance Profiling Sensor QSP-200
The QSP-200 is a submersible spherical radiance collector designed to ensure a uniform directional response over 3.7-pi steradians. The aluminium-encased optical light pipe funnels flux from the collector to a silicon photodetector that has a flat quantum response over the Photosynthetically Active Radiation (PAR) spectrum (400 - 700 nm).
The sensor can be coupled with other instruments and accessories, allowing for automatic data acquisition and digital display. The standard version has a depth rating of 1000 m and the QSP-200D includes the option of a 200 m depth transducer. The logarithmic output version (QSP-200L4S) is available for integration with CTD or STD and uses a shielded underwater cable. The QSP-200 has been superseded by the QSP-2300.
Specifications
| Wavelength | 400 to 700 nm |
| PAR Spectral Response | better than ± 8% within the specified wavelength |
| Directional response | ± 6% for 0 to 110° |
| PAR Dynamic Range | 1.4 x 10-5 to 0.5 µE cm-2 s-1 |
| Nominal sensitivity | 1 V = 1 x 1017 quanta cm-2 sec-1 |
| Noise level | < 1 mV |
| Maximum Noise Sensor Dark | < 100 µV RMS |
| Response Temperature Coefficient | < 0.15% °C-1 |
| Temperature Range | -2 to 35°C |
| Temperature coefficient of the dark signal | < 10 µV °C-1 |
| Depth rating | 1000 m |
Further details can be found in the manufacturer's specification sheet.
Paroscientific Absolute Pressure Transducers Series 3000 and 4000
Paroscientific Series 3000 and 4000 pressure transducers use a Digiquartz pressure sensor to provide high accuracy and precision data. The sensor comprises a quartz crystal resonator that responds to pressure-induced stress, and temperature is measured for thermal compensation of the calculated pressure.
The 3000 series of transducers includes one model, the 31K-101, whereas the 4000 series includes several models, listed in the table below. All transducers exhibit repeatability of better than ±0.01% full pressure scale, hysteresis of better than ±0.02% full scale and acceleration sensitivity of ±0.008% full scale /g (three axis average). Pressure resolution is better than 0.0001% and accuracy is typically 0.01% over a broad range of temperatures.
Differences between the models lie in their pressure and operating temperature ranges, as detailed below:
| Model | Max. pressure (psia) | Max. pressure (MPa) | Temperature range (°C) |
|---|---|---|---|
| 31K-101 | 1000 | 6.9 | -54 to 107 |
| 42K-101 | 2000 | 13.8 | 0 to 125 |
| 43K-101 | 3000 | 20.7 | 0 to 125 |
| 46K-101 | 6000 | 41.4 | 0 to 125 |
| 410K-101 | 10000 | 68.9 | 0 to 125 |
| 415K-101 | 15000 | 103 | 0 to 50 |
| 420K-101 | 20000 | 138 | 0 to 50 |
| 430K-101 | 30000 | 207 | 0 to 50 |
| 440K-101 | 40000 | 276 | 0 to 50 |
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.
James Clark Ross Cruise AMT8 CTD Processing
Originator's Processing
The CTD profiles were processed onboard using Sea-Bird's data processing software.
BODC data processing
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Reformatting
The data files were sent to BODC in Sea-Bird's data processing software output. All available channels were listed into ASCII format. Non-null channels were then converted to PXF, a BODC internal format. The data were processed from 1Hz averaged down- and upcast data. Sigma-theta was calculated and output from the raw data during the conversion to PXF format.
Parameters
Originator's Parameter Originator's Units Description BODC code BODC Units Comments Depth m Pressure PRESPR01 decibars Converted from depth to pressure during transfer to PXF Temperature °C Temperature TEMPCU01 °C - Temperature, 2 °C Temperature TEMPCU02 °C - Salinity - Salinity PSALCU01 - - Salinity, 2 - Salinity PSALCU02 - - Voltage 2 :
AMT801-AMT809
Voltage 0 :
AMT812-AMT862V Beam attenuation ATTNMS01 m-1 Calibrated to zero in clear water Voltage 3 :
AMT801-AMT809
Voltage 1 :
AMT812-AMT862V Fluorometer voltage FVLTWS01 V - Voltage 2 :
AMT812-AMT862V 2 pi-PAR meter voltage LVLTBD01 V - - - Calibrated fluorescence CPHLPS01 mg m-3 Calibrated against bottle extracted chl-a data - - Downwelling PAR irradiance IRRDPP01 µE m-2 s-1 Calculated from PAR meter voltage using manufacturer's coefficients - - Potential temperature POTMCV01 °C Computed using UNESCO POTEMP function (using primary T and S) - - Sigma-theta SIGTPR01 kg m-3 Computed using UNESCO SVAN function -
Screening
The PXF data were compared with the original data files to ensure that no errors had been introduced during the conversion process. The data channels were then screened on a graphics workstation using in-house visualisation software. This allows multiple channels to be viewed simultaneously. The start and end-points of the downcast were marked. The pressure ranges over which bottles were fired were also marked. The bottle firing events were identified by disturbances in CTD parameters on the upcast profiles. All spurious and null data were flagged with appropriate BODC quality control flags.The secondary temperature and salinity channels were used to aid screening of the primary channels only. The primary channels should be used in preference to the secondary channel as they have been quality controlled.
The following notes were made during the screening of AMT8 CTD data.
For AMT8001 to AMT8009, and AMT8019 the PAR voltage channel was all null.
For AMT8004, the transmissometer data appeared to be suspect between 375 - 400 db, temperature and salinity were flagged between 360-440 db and fluorescence was flagged from 375 db to the end of the downcast. For AMT8006 to AMT8008, the fluorescence signals were all 0.0 so flagged as supect.
For AMT8009, the fluorescence signal was null.
For AMT8014, there was a disturbance in the PAR voltage profile between 30 and 50 db; this was flagged as suspect.
For AMT8018, the transmissiometer signal was constant at a value of 5.0, and the fluorescence values appeared extremely high. Both channels were flagged as suspect.
For AMT8021, the sections between 15-30 db and 70-85 db in the PAR channel were flagged as suspect.
For AMT8025, the sections between 7-10 db and 15-20 db in the PAR channel were flagged as suspect.
For AMT8056, a disturbance in the transmissometer signal between 40-45 db was flagged as suspect. -
Loading into the BODC database
After the data had been screened and quality controlled, the data were loaded into the BODC database under the Oracle RDBMS.
Calibrations
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Pressure
The pressure sensor had a mean reading of -0.3 decibar while the CTD was logging in air - this was identified during BODC processing. A pressure correction was, therefore, applied to the data when they were listed from the BODC database.
PRESPR01(corr) = PRESPR01(raw) + 0.3 decibar (BODC calibration 1723).
-
Temperature
No reversing thermometer data were available for AMT8, so the CTD sensor data have not been calibrated against another data set. However, the Sea-Bird sensors were tested and calibrated before and after the cruise, and manufacturer's calibrations were applied during Sea-Bird processing. No further correction has been applied to the data at BODC.
-
Salinity
No bench salinometer data are available for AMT8, so no further calibration of the salinity channel is possible. Users should be aware that the data are uncalibrated and may not be accurate.
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Fluorometer
Chlorophyll-a sample data were available from different analysis techniques. At this stage, the CTD fluorometer has been calibrated against fluorometric assays carried out on acetone extracts. This ensures that calibration of all fluorometers, whether CTD or underway, has been carried out using the same technique throughout all AMT cruises to AMT11.
There were 225 samples which were compared with fluorometer voltage at bottle-firing pressures. Samples were removed from the calibration data set where the standard deviation of the CTD voltage over the bottle firing pressures was <0.01V. Some additional outlying samples were also removed. In general, there was a large degree of scatter in the relationship between fluorometer voltage and chlorophyll-a. The relationship also appeared to vary with time throughout the cruise. It was possible to identify 5 groups of casts for which the relationship was good.
The relationship between fluorometer data and chlorophyll-a in casts from AMT056 onwards was very poor and variable. The relationship from AMT8001 to AMT055 was good; this calibration has been applied to the whole cruise as no suitable calibration for the later casts could be found.
CPHLPS01 = 4.78 * FVLTWS01 - 0.0636 (BODC calibration 2564; r2 = 0.844; N = 173)
After the calibration was applied, the residuals were examined. The following points can be made about the data from AMT8056 onwards:
AMT8056 showed a cluster of data points (between 8 and 37db) where the predicted CTD value was too high.
AMT8058 had a very noisy fluorometer signal and the residuals were both negative and positive after the calibration was applied.
The predicted values for AMT8062 were too low.
The predicted data for AMT8059 and AMT8060 had low residuals associated with them so the calibration equation appeared to fit well for these casts. -
Beam attenuation coefficient
The Sea-Bird data files contained a transmissometer voltage channel. These data were converted to beam attenuation using the manufacturer's calibration information.
Beam attenuation = -1 / x * ln ((Vsig - Vd) / (Vref - Vd)),
where x is the pathlength (0.25m), Vsig is the output voltage, Vd is the blocked path reading (0.059), Vref is the output in clean water (4.678).
No transmissometer air readings were available from the cruise, so the data have not been corrected for possible source decay during the course of the cruise.
-
Irradiance
Irradiance = 10 lightmeter voltage * (104 * calibration factor), where the wet calibration factor = 2.53 * 10-4 µEinsteins cm-2sec-1.
Project Information
The Atlantic Meridional Transect (AMT) - Phase 1 (1995-2000)
Who was involved in the project?
The Atlantic Meridional Transect (AMT) programme was designed by and implemented as a collaboration between Plymouth Marine Laboratory (PML) and Southampton Oceanography Centre (SOC). The programme was hosted by Plymouth Marine Laboratory and involved additional researchers from UK and international universities throughout its duration.
What was the project about?
When AMT began in 1995 the programme provided a platform for international scientific collaboration, including the calibration and validation of SeaWiFs measurements and products. The programme provided an exceptional opportunity for nationally and internationally driven collaborative research and provided a platform for excellent multi-disciplinary oceanographic research. As an in situ observation system, the data collected by the AMT consortium informed on changes in biodiversity and function of the Atlantic ecosystem during this period of rapid change to our climate and biosphere.
The scientific aims were to assess:
- mesoscale to basin scale phytoplankton processes
- the functional interpretation of bio-optical signatures
- the seasonal, regional and latitudinal variations in mesozooplankton dynamics
When was the project active?
The first phase of the AMT programme ran from 1995 to 2000 and consisted of a total of 12 cruises. A second phase of funding allowed the project to continue for the period 2002 to 2006 with a further 6 cruises.
Brief summary of the project fieldwork/data
The AMT programme undertook biological, chemical and physical oceanographic research during the annual return passage of the RRS James Clark Ross between the UK and the Falkland Islands or the RRS Discovery between the UK and Cape Town, a distance of up to 13,500 km. This transect crossed a range of ecosystems from sub-polar to tropical and from euphotic shelf seas and upwelling systems to oligotrophic mid-ocean gyres. The transect route was covered north-south in September/October and south-north in April/May of each year.
The measurements of hydrographic and bio-optical properties, plankton community structure and primary production completed on the first 12 transects (1995-2000) represent the most coherent set of repeated biogeochemical observations over ocean basin scales. This unique dataset has led to several important discoveries concerning the identification of oceanic provinces, validation of ocean colour algorithms, distributions of picoplankton, identifying new regional sinks of pCO2 and variability in rates of primary production and respiration.
Who funded the project?
The programme was funded by the Natural Environment Research Council (NERC) and further support was received from the National Aeronautics and Space Administration (NASA) with equipment and funding from the Sea-viewing Wild Field-of-view Sensor (SeaWiFS) project.
Data Activity or Cruise Information
Cruise
| Cruise Name | JR19990425 (AMT8, JR41, JR42) |
| Departure Date | 1999-04-25 |
| Arrival Date | 1999-06-07 |
| Principal Scientist(s) | Nigel Rees (Plymouth Marine Laboratory), Tim A Minshull (University of Southampton School of Ocean and Earth Science) |
| Ship | RRS James Clark Ross |
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 |
