Metadata Report for BODC Series Reference Number 1197395
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 James Cook (JC079) AMT22 FRRF Data Quality Report
Data Quality Report
The FRRF instruments were changed on the 24 October 2012.
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)
(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
These data have no specific confidentiality restrictions for users. However, users must acknowledge data sources as it is not ethical to publish data without proper attribution. Any publication or other output resulting from usage of the data should include an acknowledgment.
If the Information Provider does not provide a specific attribution statement, or if you are using Information from several Information Providers and multiple attributions are not practical in your product or application, you may consider using the following:
"Contains public sector information licensed under the Open Government Licence v1.0."
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 (JC079) AMT22 FRRF Sensor Profile Instrumentation II
24th October 2012 to 19th November 2012
Instrument | Serial number | Parameter |
---|---|---|
Chelsea Technologies Group Ltd. FastTracka MK I Fluorometer | 182039 | Plankton physiology |
Druck Depth Sensor | Not supplied | Depth |
AMT22 (JC079) 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 10th October and 24th November 2012. Optics profiles were made at or within one hour of local solar noon and mostly deployed on the sunward side of the ship. Upon recovery, data from the FRRF were downloaded using hyperterminal.
The FRRF data were processed using V6 of the Sam Laney (WHOI) Matlab code as used in previous AMT cruises. This required the FRRF to be characterised using 0.2 µm filtered water, at each of the gain settings (0, 1, 4, 16, 64, 256) for both the light and dark chambers, in a black bucket. During this cruise there were difficulties using Sam Laney's code. In addition to this the Chelsea Technologies Group (CTG) FastTracka MK I Fluorometer was swapped with a different (CTG) FastTracka MK I sensor on the 24th October 2012.
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 .csv files and saved to the archive with accession number PML140007. The files were provided to BODC with the following metadata: cruise, date, Julian Day, latitude and longitude. The light/dark Photosynthetically Active Range (PAR) 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 but 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 with the same units as 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
No Project Information held for the Series
Data Activity or Cruise Information
Cruise
Cruise Name | JC079 (AMT22) |
Departure Date | 2012-10-10 |
Arrival Date | 2012-11-24 |
Principal Scientist(s) | Glen A Tarran (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 |