Metadata Report for BODC Series Reference Number 1197912
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
AMT20 (JC053) Bio-Optics - Fast Repetition Rate Fluorometer (FRRF) Data Quality Report
During the start of the cruise there were problems with the Chelsea Technologies Group Ltd. (CTG) MKI FRRF sensor (s/n 182041, INDREF=338523) deployed on the FRRF optics rig. The battery charging plug was dislodged from the socket and board which was then replaced with the back of the CTG MKI FRRF sensor (s/n 182039).
The CTG sensor (s/n 182041) continued to have problems and after two profiles had corrupted data, the sensor was eventually replaced with a CTG MKI FRRF sensor (s/n 182042) for station JC05326 (27/10/2014).
Data Quality Report
Values marked -999 in the originator's data files have been converted to the appropriate absent data values using the flag 'N'.
Functional Absorption cross-section (light and dark)
Values outside the expected range of values (0-1600 A2Q-1) for these parameters have been flagged as suspect.
Photochemical efficiency {Fv/Fm}
Values outside the expected range of values (0-1) for these parameters have been flagged as suspect.
In-vivo fluorescence (chlorophyll)
Values outside the expected range of values (0-5) for these parameters have been 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
Chelsea Technologies Group FASTtracka MKI FRRF
The FASTtracka is a Fast Repetition Rate Fluorometer (FRRF) designed to measure the variable fluorescence of marine phytoplankton. It can be deployed on its own or integrated in moorings, profiling systems or in towed applications.
The operation mode comprises a rapid series of high frequency flashes (200 kHz), which enable the measurement of the absorption cross section of photosystem II (PSII), the rate of electron transport and the level of photochemical quenching. A 16 MHz clock microcontroller monitors the digital acquisition of the stimulated fluorescence and the excitation flashes, while simultaneously measuring Photosynthetic Active Radiation (PAR). These concurrent measurements allow for estimates of phytoplankton primary productivity to be made.
A comparison of ambient-irradiated and dark adapted phytoplankton samples is possible due to the optical head dual (light and dark) chamber design. All measurements are stored on an internal memory card with a 24 MB capacity and are downloaded through an RS232 connector.
Additional specifications include a maximum depth rating of 500 m and a chlorophyll-a sensitivity of 0.1 to 30 µg l-1.
Further information can be found in the manufacturer's specification sheet or the user guide.
RRS James Cook (JC053) AMT20 FRRF Sensor Profile Instrumentation II
Instrument | Serial number | Parameter |
---|---|---|
Chelsea Technologies Group Ltd. FRRF MKI sensor | 182042 | Plankton Physiology |
Druck Depth Sensor | Not supplied | Depth |
GE Druck PDCR/PTX 1830/1840 series presssure sensors
Basic Information
The PDCR 1830/1840 transducer (mV output) and PTX 1830/1840 transmitter (4-20 mA output) are fully submersible sensors for the measurement of hydrostatic liquid levels. IP68 rated for indefinite immersion in 700 mH2O.The Druck micromachined silicon element is sealed within an all-titanium pressure module assembly isolated from the media assembly. This is contained in a welded titanium body, terminated in an injection moulded cable assembly which features a Kevlar strain cord.
Pressure measurement
Operating Pressure Ranges | Units | |
---|---|---|
PDCR 1830/1840 (mV) | PTX 1830/1840 (mA) | Other units may be specified such as: feet, inches, Bar, mBar kPa, kg/cm |
0.75, 1.5 mH2O gauge, 3.5, 7, 10, 15, 20, 35, 50, 70, 100, 150, 200, 350, 600 mH2O gauge and absolute | Any zero based full scale from 0.75 to 600 mH2O gauge and 3.5 to 600 mH2O absolute |
Excitation Voltage | |
---|---|
PDCR 1830/1840 (mV) | PTX 1830/1840 (mA) |
10 V at 5 mA nominal | 9 to 30 V |
Output is fully ratiometric to supply within 2.5 V to 12 V limits | 9 to 28 V for intrinsically Safe Version |
Performance Specification
Accuracy | |
---|---|
Combined effects of Non-linearity, Hysteresis and Repeatability:
| |
Long-term Stability | |
±0.1% full scale typically per annum |
Operating Temperature Range (°C) | Compensated Temperature Range (°C) | ||
---|---|---|---|
Min | Max | Min | Max |
-20 | 60 | -2 | 30 |
Temperature Effects | |||
|
Zero Offset and Span Setting | |
---|---|
PDCR 1830/1840 | PTX 1830/1840 |
| Maximum: ±0.05 mA |
Additional Options
A: Lightning Surge Arrestor (PTX 1830/1840 only) | B: Intrinsically Safe Version | C: Alternative Pressure Connection | D: Improved Accuracy |
---|---|---|---|
Integral lightning protection assembly certified to standard IEC 61000-4-5 (level 4). | In place of the standard acetyl nose cone, a welded male pressure connection can be supplied. | An improved accuracy of ±0.06% full scale best straight line is available (±0.08% FS BSL for ranges below 1 mH2O (1.5 psi)) |
More information can be found in the manufacturer's specification sheet.
AMT20 (JC053) Bio-Optics - Fast Repetition Rate Fluorometer (FRRF) profiles
Data Acquisition and Analysis
These data originate from analysis of profiles collected from the FRRF sensor deployed on the optics rig on RRS James Cook between 12th October and 25th November 2010. Optics profiles were made at or within one hour of local solar noon and mostly deployed on the sunward side of the ship. The data was obtained from the upcast of the optics rig. There were problems with the sensor on the optics rig using the FRRF sensor (s/n 182041) but this was replaced with another FRRF sensor (s/n 182042) on the 27/10/2010.
The FRRF data were processed using V6 of the Sam Laney (WHOI) Matlab code as used in previous cruises.
The primary outputs of the FRRF data stream are the maximum fluorescence (Fm) and the ratio of the variable to maximum fluorescence (Fv/Fm). The final FRRF data product will consists of the phytoplankton physiological parameters binned to 2 m depth resolution.
BODC Data Processing Procedures
Data were submitted to BODC in 38 folders which were saved to the archive with accession number PML120226. Within these files there were 23 .csv binned files that were available for transfer. The files were provided to BODC with the following metadata: cruise, date, Julian Day, latitude and longitude. The light/dark Photosynthetically Active Range (PAR) irradiance channels were not loaded as these channels have been loaded to the database with the UV and AC9 profiles. The light/dark chamber turnover time for electron flow (tau) and light/dark chamber gain settings were not loaded to the database and are available upon request.
Parameter codes defined in BODC parameter dictionary were assigned to the variables as shown in the table below. No unit conversions were necessary as all the parameters were provided in the same units as in the BODC Parameter Dictionary.
Originator's Parameter | Description | Units | BODC Parameter Code | Description | Units | Comments |
---|---|---|---|---|---|---|
Depth | Depth data depth binned to (2 m) | m | DEPHPR01 | Depth below surface of the water body by profiling pressure sensor and converted to seawater depth using UNESCO algorithm | m | - |
FoD | Dark chamber fluorescence | Dimensionless | FOMIND01 | Minimum in-vivo fluorescence (chlorophyll) {Fo} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the dark chamber | Dimensionless | - |
FoL | Light chamber fluorescence | Dimensionless | FOMINL01 | Minimum in-vivo fluorescence (chlorophyll) {Fo} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the light chamber | Dimensionless | - |
FmL | Light chamber maximum fluorescence | Dimensionless | FMMAXL01 | Maximum in-vivo fluorescence (chlorophyll) {Fm} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the light chamber | Dimensionless | - |
FmD | Dark chamber maximum fluorescence | Dimensionless | FMMAXD01 | Maximum in-vivo fluorescence (chlorophyll) {Fm} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the dark chamber | Dimensionless | - |
Fv_FmD | Dark chamber ratio of variable to maximum fluorescence | Dimensionless | FVFMFR04 | Photochemical quantum efficiency {Fv/Fm} of the water body by in-situ fast repetition rate fluorometer (FRRF) and calculation from blank-corrected Fm and Fo fluorescence yields from the dark chamber | Dimensionless | - |
Fv_FmL | Light chamber ratio of variable to maximum fluorescence | Dimensionless | FVFMFR03 | Photochemical quantum efficiency {Fv/Fm} of the water body by in-situ fast repetition rate fluorometer (FRRF) and calculation from blank-corrected Fm and Fo fluorescence yields from the light chamber | Dimensionless | - |
sigmaL | Light chamber cross section of photosystem II | 10-20 m-2 photon-1 | SIGFRBL1 | Functional absorption cross-section {Sigma-PSII} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the light chamber | Angstrom squared per quantum | - |
sigmaD | Dark chamber cross section of photosystem II | 10-20 m-2 photon-1 | SIGFRBL2 | Functional absorption cross-section {Sigma-PSII} of the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the dark chamber | Angstrom squared per quantum | - |
Par(L) | Photosynthetically available radiation coincidental with Light Chamber acquisition | µW cm-2 | - | - | - | Parameter not loaded to the database |
Par(D) | Photosynthetically available radiation coincidental with Dark Chamber acquisition | µW cm-2 | - | - | - | Parameter not loaded to the database |
tauL | Light chamber turnover time for electron flow | µs | - | - | - | Parameter not loaded to the database |
tauD | Dark chamber turnover time for electron flow | µs | - | - | - | Parameter not loaded to the database |
gainL | Light chamber gain setting | Dimensionless | - | - | - | Parameter not loaded to the database |
gainD | Dark chamber gain setting | Dimensionless | - | - | - | Parameter not loaded to the database |
Project Information
Oceans 2025 Theme 10, Sustained Observation Activity 1: The Atlantic Meridional Transect (AMT)
The Atlantic Meridional Transect has been operational since 1995 and through the Oceans 2025 programme secures funding for a further five cruises during the period 2007-2012. The AMT programme began in 1995 utilising the passage of the RRS James Clark Ross between the UK and the Falkland Islands southwards in September and northwards in April each year. Prior to Oceans 2025 the AMT programme has completed 18 cruises following this transect in the Atlantic Ocean. This sustained observing system aims to provide basin-scale understanding of the distribution of planktonic communities, their nutrient turnover and biogenic export in the context of hydrographic and biogeochemical provinces of the North and South Atlantic Oceans.
The Atlantic Meridional Transect Programme is an open ocean in situ observing system that will:
- give early warning of any fundamental change in Atlantic ecosystem functionng
- improve forecasts of the future ocean state and associated socio-economic impacts
- provide a "contextual" logistical and scientific infrastructure for independently-funded national and international open ocean biogeochemical and ecological research.
The specific objectives are:
- To collect hydrographic, chemical, ecological and optical data on transects between the UK and the Falkland Islands
- To quantify the nature and causes of ecological and biogeochemical variability in planktonic ecosystems
- To assess the effects of variability in planktonic ecosystems on biogenic export and on air-sea exchange of radiatively active gases
The measurements taken and experiments carried out on the AMT cruises will be closely linked to Themes 2 and 5. The planned cruise track also allows for the AMT data to be used in providing spatial context to the Sustained Observation Activities at the Porcupine Abyssal Plain Ocean Observatory (SO2) and the Western Channel Observatory (SO10).
More detailed information on this Work Package is available at pages 6 - 9 of the official Oceans 2025 Theme 10 document: Oceans 2025 Theme 10
Weblink: http://www.oceans2025.org/
Data Activity or Cruise Information
Cruise
Cruise Name | JC053 (AMT20) |
Departure Date | 2010-10-12 |
Arrival Date | 2010-11-25 |
Principal Scientist(s) | Andrew Rees (Plymouth Marine Laboratory) |
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 |