Metadata Report for BODC Series Reference Number 1224942

Metadata Summary

Data Description

Data Category Multiple data types -ship
Instrument Type
WETLabs C-Star transmissometer  transmissometers
WETLabs ECO Triplet  fluorometers; optical backscatter sensors
WETLabs ac-s in-situ spectrophotometer  transmissometers
Instrument Mounting research vessel
Originating Country United Kingdom
Originator Mr Giorgio Dall'Olmo
Originating Organization Plymouth Marine Laboratory
Processing Status banked
Project(s) -

Data Identifiers

Originator's Identifier AMT22_SEABASS.TXT
BODC Series Reference 1224942

Time Co-ordinates(UT)

Start Time (yyyy-mm-dd hh:mm) 2012-10-15 00:20
End Time (yyyy-mm-dd hh:mm) 2012-11-20 14:50
Nominal Cycle Interval 600.0 seconds

Spatial Co-ordinates

Start Latitude 43.23720 N ( 43° 14.2' N )
End Latitude 46.56430 S ( 46° 33.9' S )
Start Longitude 20.28660 W ( 20° 17.2' W )
End Longitude 53.57580 W ( 53° 34.5' W )
Positional Uncertainty 0.0 to 0.01 n.miles
Minimum Sensor Depth 5.5 m
Maximum Sensor Depth 5.5 m
Minimum Sensor Height -
Maximum Sensor Height -
Sea Floor Depth -
Sensor Distribution Fixed common depth - All sensors are grouped effectively at the same depth which is effectively fixed for the duration of the series
Sensor Depth Datum Approximate - Depth is only approximate
Sea Floor Depth Datum -


BODC CODE Rank Units Short Title Title
LAMBIN01 0 Nanometres Wavelength Wavelength of electromagnetic radiation measurement
AADYAA01 1 Days Date(Loch_Day) Date (time from 00:00 01/01/1760 to 00:00 UT on day)
AAFDZZ01 1 Days Time(Day_Fract) Time (time between 00:00 UT and timestamp)
ACYCAA01 1 Dimensionless Record_No Sequence number
ALATZZ01 1 Degrees Lat Latitude north
ALONZZ01 1 Degrees Lon Longitude east
ABSPXAC9 2 per metre absorb_cwoffset_2D Absorbance of electromagnetic radiation (unspecified single wavelength) {light absorbance} by the water body by transmissometer and calibration to read zero in clear water
ATTNXAC9 2 per metre attn_cwoffset_2D Attenuation (unspecified single wavelength) per unit length of the water body by transmissometer and calibration to read zero in clear water
BB117XXX 2 per metre AttenBS_2D_117deg Attenuation due to backscatter (unspecified single wavelength at 117 degree incidence) by the water body [particulate >unknown phase] by in-situ optical backscatter measurement

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

AMT22 RRS James Cook (JC079) Inherent optical properties - Data Quality Report

The data were screened using the BODC in-house software, Edserplo. Date were flagged in accordance with BODC flagging procedure.

The data had a few spikes across parameters which were flagged as 'M' and were considered to be possible bubbles by the data originator. Negative values that occurred through the dataset for optical parameters were flagged as M. Cycle numbers that had spikes flagged 'M' are given in the table below. Data that exceeded the Null value (-9.00) for ATTNXAC9 at cycle number 853 were flagged as N.

Parameter Cycle Numbers Flagged
BB117XXX 438, 854, 1413, 2984, 3059, 3163, 3312, 2984
ATTNXAC9 (ac-s - wavelengths to 730) 853, 1266, 1267, 1413, 2807, 2808, 2809, 2984,3059, 3163, 3312
ABSPXAC9 (C-Star - wavelengths 526 and 651) 2984, 3163, 3312
ABSPXAC9 854,1266, 1267, 1413, 2807, 2808, 2809, 2984, 3163, 3312

The entire bin at wavelength 730 nm the particulate absorption spectrum (ABSPXAC9) was set to zero by the originator's code. These data were flagged as 'M' as the values are either zero, negative or too small to fit within parameter's LFM.

The raw data is available upon request.

Data Access Policy

Public domain 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.

The recommended acknowledgment is

"This study uses data from the data source/organisation/programme, provided by the British Oceanographic Data Centre and funded by the funding body."

Narrative Documents

WETLabs ac-s in-situ spectrophotometer

The WETLabs ac-s in-situ spectrophotometer is based on the ac-9 flow through sensor offering increased spectral resolution of in-situ absorption and beam attenuation. The ac-s can have 80 (+/- 5) wavelength outputs with a range of 400-730 nm. The ac-s consists of a 10 or 25 cm pathlength, a 4nm resolution, an accuracy of 0.001 - 10 m -1 , an operational temperature range of 0 - 30 °C and an operational depth rating of 500 m.



Diamater 10.4 cm
Length 79 cm
Weight in air 5.9 kg
Weight in water 0.8 kg


Input Voltage 10-35 VDC
Output RS232, RS485
Current draw 0.83 A @12 V nominal
Connector MCBH6MP


Temperature range 0 - 30°C
Depth rating 500 m


Spectral range 400 - 730 nm
Bandpass (FWHM), nm 400: 10-18
450: 10-16
550: 10-15
650: 10-18
730: 10-25
Pathlength, cm 10 or 25
Beam cross-section 8 mm dia. (nominal)
Linear dispersion 6 - 7.0 nm/mm
Resolution 4 nm
Precision, 400 to 449 nm ±0.003 m -1 typ., 0.006 m -1 max @ 1 Hz
±0.005 m -1 typ., 0.012 m -1 max @ 4 Hz
Precision, 450 to 730 nm ±0.0005 m -1 typ., 0.0015 m -1 max @ 1 Hz
±0.001 m -1 typ., 0.003 m -1 max 4 1 Hz
Accuracy 0.001 - 10 m -1

For more information see the manufacturer's brochure or user guide .

WETLabs C-Star transmissometer

This instrument is designed to measure beam transmittance by submersion or with an optional flow tube for pumped applications. It can be used in profiles, moorings or as part of an underway system.

Two models are available, a 25 cm pathlength, which can be built in aluminum or co-polymer, and a 10 cm pathlength with a plastic housing. Both have an analog output, but a digital model is also available.

This instrument has been updated to provide a high resolution RS232 data output, while maintaining the same design and characteristics.


Pathlength 10 or 25 cm
Wavelength 370, 470, 530 or 660 nm

~ 20 nm for wavelengths of 470, 530 and 660 nm

~ 10 to 12 nm for a wavelength of 370 nm

Temperature error 0.02 % full scale °C -1
Temperature range 0 to 30°C
Rated depth

600 m (plastic housing)

6000 m (aluminum housing)

Further details are available in the manufacturer's specification sheet or user guide .

AMT22 RRS James Cook (JC079) Inherent optical properties - Instrumentation

Instrument Serial number Parameter Wavelength (nm)
WET Labs C-star(526_nm) Transmissometer CST687G ATTNXAC9 526
WET Labs C-star(650 nm) Transmissometer CST686R ATTNXAC9 650
WET Labs ECO-BB3 BB3-349 BXXXVSF 470 and 526
WET Labs ac-s in-situ Spectrophotometer ACS-007 ATTNXAC9 Every 5 nm from 400 to 750 nm
WET Labs ac-s in-situ Spectrophotometer ACS-007 ABSPXAC9 Every 5 nm from 400 to 750 nm

AMT22 RRS James Cook (JC079) Inherent optical properties - Data Processing Documentation

Originator's Processing

Measurements and Methods

Optical measurements were conducted on water passing through the ship's non-toxic flow-through system.

The data were processed as described by Dall'Olmo (Dall'Olmo et al. 2009, Dall'Olmo et al., 2012) with the use of a 0.2 µm cartridge filter in order to provide a baseline for the absorption and attenuation measurements. The C-star and AC-s optical measurements were averaged into 1-min time intervals before further processing. To compute particulate beam attenuation and absorption coefficients ( c p and a p , respectively), the median values of the beam attenuation and absorption coefficients measured during each of the 0.2-µm filtration times were linearly and piecewise interpolated between hours and subtracted from the bulk measurements. This procedure allowed the determination of calibration-independent particulate beam-attenuation and absorption coefficients, with the uncertainties determined mostly by the instrument precision (Boss et al., 2007).

Originator's Quality Control

AC-s c p and a p spectra were further processed to:


No calibration files were provided for these AC-s and Cstar data, because these data were derived using the filter-no-filter technique (Dall'Olmo et al., 2009, 2012; Slade et al., 2010). The following scaling factors and uncertainties are given below:

Wavelength (nm) Scaling factor (1/(m sr counts)) Uncertainty (%)
470 7.4033x10 -6 8.3
526 4.2179x10 -6 8.4

Wall effects (bb_{wall} see Dall'Olmo et al., 2009) were derived from two measurements of 0.2-um filtered MilliQ water during the cruise. These wall effects were:

Wavelength (nm) Wall effect (1/m) Uncertainty (1/m)
470 3.7029x10 -4 0.8327x10 -4
526 3.1437x10 -4 0.5218x10 -4

Dark counts were also determined during the cruise:

Wavelength (nm) Average dark count Standard Deviation
470 56.65 1.29
526 51.29 1.12

BODC Processing

The data were received by email as a zipped text file. The data were then transferred to the BODC format and loaded to the database.

Parameter codes defined in the BODC parameter dictionary were assigned to the variable as shown in the table below:

Originator's Parameter Name Originator's Units BODC Parameter Code BODC Units BODC Description
lat degrees (+ve N) ALATZZ01 Latitude north Degrees
lon degrees (+ve E) ALONZZ01 Longitude east Degrees
cp (particulate beam-attenuation co-efficient) 1/m ATTNXAC9 per metre Attenuance (unspecified single wavelength) per unit length of the water body by transmissometer and calibration to read zero in clear water
ap (particulate beam-absorption co-efficient) 1/m ABSPXAC9 per metre Light absorbance (unspecified single wavelength) by the water body by transmissometer and calibration to read zero in clear water
bbp (particulate backscattering coefficient) 1/m BSXXXVSF per metre Attenuance due to backscatter (unspecified single wavelength) in the water body by scattering photometer and computation from volume scatter data
wavelength nm LAMBIN01 Nanometres Wavelength of electromagnetic radiation measurement

N.B. The same parameter was used for the C-Star (cp526 and cp651) attenuation co-efficients as the AC-s attenuation co-efficients.


Once transferred the reformatted data were imported into the BODC in-house visualisation software, Edserplo.Data were appropriately flagged and double checked for any anomalous results. Further details are given in the data quality report.


Dall'Olmo G., Westberry T. K., Behrenfeld M. J., Boss E. and Slade, W. H., (2009). Significant contribution of large particles to optical backscattering in the open ocean. Biogeosciences, 6, pp. 947-967.

Dall'Olmo G., Boss E., Behrenfeld M. J., and Westberry T. K. (2012). Particulate optical scattering coefficients along an Atlantic Meridional Transect. Optics Express, 20, pp. 21532-21551.

Slade W. H., Boss E., Dall'Olmo G., Langner M. R., Loftin J., Behrenfeld M. J., Roesler C., and Westberry T. K. (2010). Underway and moored methods for improving accuracy in measurement of spectral particulate absorption and attenuation. Journal of Atmospheric and Oceanic Technology, 27(10), pp. 1733-1746.

Project Information

No Project Information held for the Series

Data Activity or Cruise Information


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