Metadata Report for BODC Series Reference Number 1826200
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Open Data supplied by Natural Environment Research Council (NERC)
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JC088 MSS90 Microstructure Profiler Instrumentation
Two microstructure profilers were deployed during the JC088 cruise. The profilers deployed were a ISW Microstructure sensor named MSS90 (serial number 042) and MSS90-D (serial number 054).
Both of the instruments deployed were similar versions of the ISW Wassermesstechnik manufactured MSS90. Each instrument contained essentially the same electronics and sensors and only differed in terms of the pressure housing and accompanying winches used for deployment and recovery.
The standard operating depth of the MSS90 is 500 m and this applied to MSS90 (serial number 042). The MSS90-D profiler (serial number 054) has undergone modification to enable operation in up to 4000 m water depth.
The MSS90 sensor configuration is detailed in the following table:
|Shear 1||ISW 6014|
|Shear 2||ISW 6015 (changed to 6016 after station BM3).|
|ISW-SST NTC (°C)||Sea and Sun Technology|
|Dissolved Oxygen (%)||Oxyguard, DO522M18|
|Fluorescence (µg/l)||Turner Cyclops|
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.
|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.
Originator's Processing RRS James Cook JC088 MSS - Microstructure profiler data
The following information contains extracts from the JC088 cruise report.
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. JC088 was a 26 day cruise sailing on 28 June 2013 from King George V Dock, Govan to the Malin Shelf edge where inline and bedframe mooring were deployed before returning to Southampton on 24 July 2014.
The MSS is a vertically profiling instrument package equipped with a variety of sensors that primarily include microstructure shear, temperature and standard CTD sensors.
Two releases of fluorescein dye tracer were made in order to directly observe secondary circulation associated with recruitment to the bottom Ekman layer (release #1) and adjustment of the slope current to a topographic feature (canyon) (release #2).
The primary instrument used to track the fluorescein dye was the ISW Microstructure Sensor, MSS90. The MSS90 was instrumented with a Turner Cyclops-7 fluorometer, detecting fluorescein in the concentration range 0-5 or 0-50 µg/l.
Due to the rapid deployment and recovery of the MSS90 as compared to the CTD rosette, the MSS90 was also used to extend CTD sections A and B to a position close to the Irish and Scottish coats, respectively.
Two similar versions of the ISW Wassermesstechnik manufactured MSS90 (MSS054 and MSS042) were used during the dye release experiments.
During JC088 the winch was located on the port quarter and the MSS deployed over the stern. Profiling was conducted whilst underway at approximately one knot and to a depth that varied depending on initial release depth. Both instruments were ballasted to fall at a speed of approximately 0.7 - 1.0 m s-1. Data were acquired using the Sun and Sea Technology software, Standard Data Acquisition (SDA). Postprocessing and conversion of binary data to engineering units was performed using MSS-Pro (supplied by ISW).
In addition to the standard downwards profiling, the up-cast during which the MSS was recovered to the surface was also recorded due to the valid data provided for fluorescence.
Two of the principal CTD sections (A and B) were extended inshore using the PU (Plymouth University) MSS. The same procedure was employed as during the dye tracking whereby the vessel slowed to one knot. Two profiles were obtained at each location after allowing the conductivity cell sufficient time to equilibrate.
Due to deployment issues both SAMS (MSS054) and Plymouth University (MSS042) were used within each experiment. The breakdown of when each instrument were used is as follows:
- Dye experiment 1 - MSS054 profile 1 to 276 and 410 to 515.
- Dye experiment 1 - MSS042 profile 278 to 409 and 516 to 537.
- Dye experiment 2 - MSS042 profile 2 to 14.
- Dye experiment 2 - MSS054 profile 15 to 363.
Gaps in these records are explained by corrupt or discarded data files. The problems were largely due to failure of the cable termination attaching the cable to the MSS. Water penetration caused subsequent interruptions in power supply to the profiler and data transmission back to the deck unit.
A correction for salinity was applied to both of the MSS profiles after initial analysis revealed differences between each instrument and also that of the ship's underway system. For the MSS042 instrument, a constant offset of 0.015 was added to each measurement. For the MSS054 instrument, a spline-fit was generated for the difference between the underway system. This was achieved through interpolating the spline calibration values across the time domain of the entire experiment, and subtracting each of the interpolated values from the measured values.
The spline calibrated values are -
|Date / Time||offset for MSS054|
Processing by BODC of RRS James Cook JC088 MSS - Microstructure profiler data
Data from 2 microstructure profilers (MSS90 (Plymouth) and MSS90-D (SAMS)) arrived at BODC in four Matlab structured files. The four files included data during both of the dye releases and included the up and down cast of the profiler.
During BODC transfer, the data collated in the .MAT files were split per profile and the underway navigation file was used to obtain the latitude and longitude.
The raw ASCII .tob files were also supplied. The raw files will not be transferred but are available on request. Please note these raw .tob files contain uncorrected salinty data and hence parameters derived using salinity are not to be trusted.
The .MAT files were reformatted to BODC's internal QXF (netCDF) format and the following table shows how the variables within the files were mapped to appropriate BODC parameter codes:
|Originator's Variable||Units||Description||BODC Parameter Code||Units||Comment|
|S = in-situ corrected Salinity||Pss||Practical salinity of the water body by conductivity cell and computation using UNESCO 1983 algorithm||PSALPR01||Dimensionless||Equal units - no conversion required|
|T = in-situ Temperature||°C||Temperature of the water body||TEMPPR01||°C||-|
|Dye = recorded level of dye||µg/L||Concentration of fluorescein per unit volume of the water body by fluorometry||FSCEINXX||µg/L||-|
|Press = Pressure||Decibars||Pressure (spatial co-ordinate) exerted by the water body by profiling pressure sensor and corrected to read zero at sea level||PRESPR01||Decibars||-|
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.
Due to the large volume of the dataset only a light screening process has taken place. The overall quality of the data is at the discretion of the end user.
Sea and Sun Technology MSS 90 Microstructure Profiler
A multiparameter probe used to measure micro-scale water stratification as well as the intensity of small scale turbulence in the water column in marine and limnic environments. The instrument can be used for free sinking or rising measurements. The instruments sinking or rising velocity can be adjusted by a combination of weights and buoyancy elements. It has a depth rating of approximately 500 m, samples at 1024 Hz and is equipped with high resolution micro-structure and turbulence sensors (temperature, current shear) and standard CTD sensors (temperature, conductivity, pressure). All microstructure channels have a response time of less than 12 ms. The unit includes internal sensors to control for vibrations and tilt internally.
The system comprises the profiler, a winch, a probe interface and data acquisition computer. Additional sensors, such as oxygen and optical scattering, can be attached to the profiler. The instrument can support up to a maximum of nine sensors.
There are two different models available which have the same electronic and sensor equipment, with the difference relating to the size and weight of the instruments, see the table below for further details. The shear sensor data quality of the MSS90L is however superior due to the higher mass and stability.
|Technical Data/Dimensions||MSS 90||MSS 90L|
|Depth range||500 m||500 m|
|Weight in water||10 kg||12.5 kg|
|Depth range||500 m||500 m|
|Length of housing||1 m||1.25 m|
|Standard sensor equipment||Pressure, temperature and conductivity |
2 x Shear
Temperature microstructure sensor FP07
Acceleration sensor for measuring the profiler vibration
|Pressure, temperature and conductivity |
2 x Shear
Temperature microstructure sensor FP07
Acceleration sensor for measuring the profiler vibration
|Optional sensors||Turbidity |
|Sampling rate||1024 s-1||1024 s-1|
|Resolution||16 Bit||16 Bit|
|Housing||Seamless drawn titanium tube||Seamless drawn titanium tube|
|Channels response time||<12 ms||<12 ms|
Further details can be found in the manufacturer's manual.
Fluxes Across Sloping Topography of the North East Atlantic (FASTNEt)
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.
- 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.
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.
Types of instruments/measurements:
- Autosub Long Range
- Drifter buoys
- Microstructure profilers
- Moored CTD/CT loggers and ADCPs
- Shipboard measurements: CTD, underway, nutrients (and other discrete sampling), LADCP, ADCP.
|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|
|Principal Scientist(s)||Mark E Inall (Scottish Association for Marine Science)|
|Ship||RRS James Cook|
Complete Cruise Metadata Report is available here
No Fixed Station Information held for the Series
The following single character qualifying flags may be associated with one or more individual parameters with a data cycle:
|<||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.)|
|E||End of CTD Down/Up Cast|
|G||Non-taxonomic biological characteristic uncertainty|
|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|
|O||Improbable value - user quality control|
|0||no quality control|
|2||probably good value|
|3||probably bad value|
|6||value below detection|
|7||value in excess|
|A||value phenomenon uncertain|
|Q||value below limit of quantification|