Metadata Report for BODC Series Reference Number 1197186


Metadata Summary

Data Description

Data Category Fluorescence or pigments
Instrument Type
NameCategories
Chelsea Instruments FASTtracka I Fast Repetition Rate Fluorometer  active fluorometers
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Tim Smyth
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Project(s) -
 

Data Identifiers

Originator's Identifier AMT22_OPT023_FRRF_CAST1_121030
BODC Series Reference 1197186
 

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2012-10-30 13:58
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 2.0 metres
 

Spatial Co-ordinates

Latitude 2.92103 N ( 2° 55.3' N )
Longitude 25.66053 W ( 25° 39.6' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor Depth 1.0 m
Maximum Sensor Depth 209.0 m
Minimum Sensor Height 3450.3 m
Maximum Sensor Height 3658.3 m
Sea Floor Depth 3659.3 m
Sensor Distribution Variable common depth - All sensors are grouped effectively at the same depth, but this depth varies significantly during the series
Sensor Depth Datum Instantaneous - Depth measured below water line or instantaneous water body surface
Sea Floor Depth Datum Chart reference - Depth extracted from available chart
 

Parameters

BODC CODE Rank Units Short Title Title
ACYCAA01 1 Dimensionless Record_No Sequence number
DEPHPR01 1 Metres CmpDep Depth below surface of the water body by profiling pressure sensor and converted to seawater depth using UNESCO algorithm
FMMAXD01 1 Dimensionless FRRF_Fm_blankCorr_dark 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
FMMAXL01 1 Dimensionless FRRF_Fm_blankCorr_light 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
FOMIND01 1 Dimensionless FRRF_Fo_blankCorr_dark 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
FOMINL01 1 Dimensionless FRRF_Fo_blankCorr_light 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
FVFMFR03 1 Dimensionless FRRF_FvFm_BlankCorr_light Photochemical quantum efficiency {Fv/Fm} in 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
FVFMFR04 1 Dimensionless FRRF_FvFm_BlankCorr_dark Photochemical quantum efficiency {Fv/Fm} in 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
SIGFRBL1 1 Angstrom squared per quantum FRRF_sigma_blankCorr_light Functional absorption cross-section {Sigma-PSII} in the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the light chamber
SIGFRBL2 1 Angstrom squared per quantum FRRF_sigma_blankCorr_dark Functional absorption cross-section {Sigma-PSII} in the water body by in-situ fast repetition rate fluorometer (FRRF) and derivation from the blank-corrected raw data from the dark chamber
 

Definition of Rank

  • Rank 1 is a one-dimensional parameter
  • Rank 2 is a two-dimensional parameter
  • Rank 0 is a one-dimensional parameter describing the second dimension of a two-dimensional parameter (e.g. bin depths for moored ADCP data)

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 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 (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