Metadata Report for BODC Series Reference Number 1108584


Metadata Summary

Data Description

Data Category Fluorescence or pigments
Instrument Type
NameCategories
Chelsea Instruments FASTtracka I Fast Repetition Rate Fluorometer  active fluorometers
GE Druck PTX and PCDR 1830 and 1840 series level pressure sensors  sea level recorders
Instrument Mounting lowered unmanned submersible
Originating Country United Kingdom
Originator Dr Tim Smyth
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Project(s) Oceans 2025 Theme 10 SO1:AMT
 

Data Identifiers

Originator's Identifier AMT18_OPT028_FRRF_CAST1_081105
BODC Series Reference 1108584
 

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2008-11-05 14:40
End Time (yyyy-mm-dd hh:mm) -
Nominal Cycle Interval 2.0 metres
 

Spatial Co-ordinates

Latitude 38.76446 S ( 38° 45.9' S )
Longitude 38.46238 W ( 38° 27.7' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor Depth 1.0 m
Maximum Sensor Depth 183.0 m
Minimum Sensor Height 5050.52 m
Maximum Sensor Height 5232.52 m
Sea Floor Depth 5233.52 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

Data Quality Report for FRRF profiles from cruise JR20081003

Data Quality Report

Values marked -999 in the originator's data files have been converted to the appropriate absent data value for all channels.

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.


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 .

AMT18 Bio-Optics - Fast Repetition Rate Fluorometer (FRRF) profiles instrumentation

Instrument Description

Instrument Serial Number Parameter
Chelsea FRRF 182043 Phytoplankton physiology
Chelsea PAR sensor 046058 PAR
Druck Depth sensor 2500106 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 mH 2 O gauge, 3.5, 7, 10, 15, 20, 35, 50, 70, 100, 150, 200, 350, 600 mH 2 O gauge and absolute Any zero based full scale from 0.75 to 600 mH 2 O gauge and 3.5 to 600 mH 2 O 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:

  • Standard: ±0.1% full scale best straight line maximum
  • Option D: ±0.06% full scale best straight line maximum (±0.08% full scale best straight line maximum for 1 mH 2 O and below).
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
  • ±0.3% full scale Temperature Error Band for 3.5 mH 2 O range and above
  • ±0.6% full scale Temperature Error Band for ranges below 3.5 mH 2 O range and above

 

Zero Offset and Span Setting
PDCR 1830/1840 PTX 1830/1840
  • Typical: ±1.5 mV
  • Maximum: ±3 mV
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 .

AMT18 Bio-Optics - Fast Repetition Rate Fluorometer (FRRF) profiles processing

Data Acquisition and Analysis

These data originate from analysis of profiles collected from the FRRF sensor deployed on the optics rig on RRS James Clark Ross between 3rd October and 10th November 2008. The optics rig was deployed from the starboard aft quarter of the ship using the capston on 180 m of 6 mm dyneema generally at solar noon. Deployment was generally on the sunward side of the ship. The rig was lowered at a rate of 0.5 ms -1 down to 180 m depth and the upcast was carried out at 0.1ms -1 . Upon recovery, data from the FRRF were downloaded from using hyperterminal.

The data from the FRRF were processed using V6 of the Sam Laney (WHOI) Matlab code. 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. This was done once in the middle of the transect.

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 consists of the phytoplankton physiological parameters binned to 2 m depth resolution.

BODC Data Processing Procedures

Data were submitted to BODC in 24 csv files and saved to the archive with accession number PML090110. The files were provided to BODC with the following metadata: cruise, Julian Day (Light/Dark), depth, latitude and longitude. Light/Dark photosynthetically available radiation channels were not loaded to the database as these channels hav been loaded to the database with the UV and AC9 profiles. Light/Dark chamber turnover time for electron flow (tau) and Light/Dark chamber gain settings were not loaded to the database and are available on 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:

The specific objectives are:

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 JR20081003 (AMT18, JR218)
Departure Date 2008-10-03
Arrival Date 2008-11-10
Principal Scientist(s)E Malcolm S Woodward (Plymouth Marine Laboratory)
Ship RRS James Clark Ross

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