Metadata Report for BODC Series Reference Number 1734745
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
JC088 Scanfish Survey Data Quality Report
This is a limited dataset and only 20 minutes of scanfish survey data were recorded, this was due to instrument failure. BODC M flags were added to the data in two cases:
- If individual data channels exhibited negative values.
- If the data value corresponded with a negative pressure value. This applied to much of the start and end of the time series.
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.
Instrument Description RRS James Cook JC088 Scanfish data
CTD unit and auxiliary sensors
The scanfish CTD was deployed with a Sea-Bird 911 plus unit in addition to a Chelsea Aquatracka III Fluorometer, Turner Cyclops C7 Fluorometer, and Oxygen SBE 43 sensor. The CTD sensors and Turner fluorometer were sited on the left side of the Scanfish-II EIVA A/S wing body with the Aquatracka fluorometer on the right.
The scanfish was fitted with the following scientific sensors:
Sensor | Serial Number | Last calibration date |
---|---|---|
Temperature Sensor | 2919 | 15 February 2013 |
Conductivity Sensor | 2841 | 27 July 2012 |
Digiquartz Pressure Sensor | 90573 | 10 November 2010 |
SBE 43 Oxygen Sensor | 1882 | 2 August 2011 |
Chelsea Aquatracka Mk III Fluorometer | 06-5706-001 | 12 June 2013 |
Turner Cyclops C7 Fluorometer | 2100432 | 12 June 2013 |
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.
Turner Designs Cyclops-7 Submersible Sensors
The Cyclops-7 series of sensors is designed for integration into multi-parameter platforms, providing measurements of in vivo chlorophyll-a, cyanobacteria (phycocyanin and phycoerythrin), rhodamine and fluorescein dyes, optical brighteners, coloured dissolved organic matter (CDOM), crude oil and refined fuels, BTEX (benzene, toluene, ethylbenzene, and xylenes) or turbidity.
The voltage output of the sensor can be correlated with in situ concentration by calibration with a standard of known concentration. The excitation wavelength varies, depending on the environmental variable of interest, with visible wavelengths being used for chlorophyll, rhodamine, fluorescein and cyanobacteria; UV being used for CDOM, oil, optical brighteners and refined fuels; and IR being used for turbidity. The photodiode detector operates over the range 300-1100 nm. Custom optics over the range 260-900 nm are also available.
The Cyclops-7 operates over an ambient temperature range of 0 to 50°C and a water temperature range of -2 to 50°C. It has a depth rating of 600 m and displays a linearity of 0.99 R2 over the full range.
Specifications
Application | Minimum detection limit | Dynamic range |
---|---|---|
Chlorophyll-a | 0.025 µg L-1 | 0 to 500 µg L-1 |
CDOM | 0.4 ppb QS* | 0 to 2500 ppb QS* |
Crude Oil | 0.02 ppb QS* | 0 to 1500 ppb QS* |
Cyanobacteria | 150 cells mL-1 | 0 to 150000 cells mL-1 |
Optical Brighteners | 1 ppb QS* | 0 to 15000 ppb QS* |
Fluorescein Dye | 0.01 ppb | 0 to 500 ppb |
Rhodamine Dye | 0.01 ppb | 0 to 1000 ppb |
Turbidity | 0.05 NTU | 0 to 3000 NTU |
Refined Fuels | 2 ppb NS** | 0 to 10000 ppb NS** |
BTEX | 0.1 ppm | > 2500 ppm |
*QS - Quinine Sulphate
**NS - 1,5 Napthalene Disulfonic Disodium Salt
Further details can be found in the manufacturer's specification sheet.
JC088 Scanfish Processing undertaken by BODC
Data arrived at BODC in a single ASCII (.cnv) file output from Seasave software and representing data collected from the scanfish survey conducted during JC088. This was reformatted to BODC's internal QXF format.
Measured variables
The following table shows the mapping of the measured variables within the ASCII files to the appropriate BODC parameter codes. These variables were collected directly from the sensors attached to the scanfish, and processed using SBE Data Processing version 7.21h software.
Originator' Variable | Units | Description | BODC Parameter Code | Units | Comments |
---|---|---|---|---|---|
Pressure | dbar | Pressure exerted by water body | PRESPR01 | dbar | - |
Temperature | °C | Temperature of water body | TEMPPR01 | °C | - |
Conductivity | S/m | Electrical conductivity of water body | CNDCPR01 | S/m | - |
Fluorescence | ug/l | Concentration of fluorescein per unit volume of the water body | FSCEINXX | µg l | - |
Chlorophyll | ug/l | Concentration of chlorophyll-a per unit volume of the water body | CHPLPR01 | µg m3 | - |
Oxygen | mg l | Concentration of oxygen {O2} per unit volume of the water body | DOXYSU01 | µmol l | - |
Latitude | deg | Latitude north (WGS84) | ALATGP01 | deg | - |
Longitude | deg | Longitude east (WGS84) | ALONGP01 | deg | - |
Derived variables
The following table shows the mapping of the derived variables within the ASCII file and those derived by BODC to the appropriate BODC parameter codes. Salinity and depth were computed by SBE Data Processing Version 7.21h software from various measured variables mentioned above.
Originator' Variable | Units | Description | BODC Parameter Code | Units | Comments |
---|---|---|---|---|---|
Salinity | - | Practical salinity of water body | PSALPR01 | - | - |
Depth | m | Depth below surface of the water body | DEPHPR01 | m | Derived by SBE Data Processing Version 7.21h software using a GPS feed |
Density | - | Sigma-theta of the water body by CTD | SIGTPR01 | Kg m-3 | Derived during reformatted to BODC's internal QXF format |
The reformatted data were visualised using the in-house EDSERPLO software. Suspect data were marked by adding an appropriate quality control flag, and missing data marked by both setting the data to an appropriate value and setting the quality control flag.
Other variables
BODC also hold the following variables provided by the Originator which have not been ingested.
Originator' Variable | Comments |
---|---|
Density | Derived by SBE Data Processing Version 7.21h software |
Depth | Generated from a single fixed latitude (lat=55.3983) |
Potential Temperature | Derived by SBE Data Processing Version 7.21h software and aligned to depth generated from a single fixed latitude (lat=55.3983) |
Salinity | Derived by SBE Data Processing Version 7.21h software and aligned to depth generated from a single fixed latitude (lat=55.3983) |
Density | Derived by SBE Data Processing Version 7.21h software and aligned to depth generated from a single fixed latitude (lat=55.3983) |
Originators Processing RRS James Cook JC088 Scanfish data
Sampling Strategy
The RRS James Cook JC088 was the second of two cruises funded by the NERC Consortium grant for the Fluxes Across the Sloping Topography of the North East Atlantic (FASTNEt) project. Led by the Scottish Association for Marine Science, JC088 was a 26 day cruise setting sail from Govan on 28 June 2013 and returning to Southampton on 24 July 2013.
A single scanfish tow-yo survey was carried out during the cruise. The scanfish was deployed and recovered on 1 July 2013 where it was generally 'flown' at tow speeds of 6 knots, 650 m behind the ship from depths of 1-5 m below the surface to 100-120 m, with a cycling time of every 2 minutes.
The instrument was recovered shortly after the fifth dive following the link to the instrument being lost. A leak was discovered in the pressure case of the instrument unit and the scanfish was not able to be used for the remainder of the cruise.
Data Processing
Following the recovery of the scanfish the data were saved to the deck unit PC and transferred over the ship network to a Unix data disk. Seasave version 7.22 software was used for the acquisition of the data from CTD and SBE Data processing version 7.21h software used to perform all processing steps.
Raw data files were converted from engineering units to produce files containing the 24Hz down and up cast data using the DATCNV program. A low-pass filter was then run on all data via the FILTER program, with the pressure channel being filtered with a time constant of 0.5 seconds. It was necessary to apply shifts equal to 0.5 seconds to the temperature and conductivity sensor outputs using ALIGNCTD, due to fast horizontal movement of the instrument during tow-yo surveys. The effect of thermal inertia on conductivity cells was removed by CELLTM and data were averaged using time with a 1 s bin size for up and downcasts using BINAVERAGE. Depth, potential temperature, salinity and potential density were all calculated by DERIVE and finally the binary files were converted into ASCII format files by ASCIIOUT.
At the end of the SBE processing routine the time series of scanfish CTD data were aligned with the ship GPS navigation data to produce the bottom relief profiles during scanfish tow-yo transects.
The ASCII .cnv file was de-spiked against main outliers using sorting for pressure, temperature and conductivity columns and resorted again using scan number column data.
References
Inall, M. E., (2013) 'Cruise JC088 Glasgow to Southampton FASTNEt Cruise to the Malin Shelf Edge', Internal Report No xxx, Scottish Association for Marine Science.
Available - Cruise JC088 Internal Report
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
Collaborator | Organisation |
---|---|
Prof. Mark Inall (lead) | Scottish Association for Marine Science, U.K |
Dr. Jason Holt | National Oceanography Centre, U.K |
Dr. Peter Miller | Plymouth Marine Laboratory, U.K |
Dr. Mattias Green | Bangor University, U.K |
Prof. Jonathan Sharples | University of Liverpool, U.K |
Dr. Vasyl Vlasenko | University of Plymouth, U.K |
Data Activity or Cruise Information
Cruise
Cruise Name | JC088 |
Departure Date | 2013-06-28 |
Arrival Date | 2013-07-24 |
Principal Scientist(s) | Mark E Inall (Scottish Association for Marine Science) |
Ship | RRS James Cook |
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 |