Dataset: CTD
Deployment: TT043

Beam Attenuation Coefficient, Light Scattering, Fluorescence protocols

Wilford Gardner, Jan Gundersen, Mary Jo Richardson.
Texas A&M University

Data Reduction Scheme

	The primary purpose for measuring the beam attenuation
in JGOFS programs is to determine the concentration and distribution of
particulate matter (PM) or particulate organic carbon (POC) in the
water with continuous profiling rather than with limited discrete
samples.  Towards this end, a 25 cm Sea Tech Transmissometer was
interfaced with the University of Washington's SeaBird CTD for all
Arabian Sea cruises. Transmissometer data were analyzed for the five
process cruises (TN043, TN045, TN049, TN050 and TN054) that occupied a
standard set of stations.  Data from the raw CTD files were binned at 2
db intervals through SeaBird's SEASOFT program, which has a spike
removal subroutine which we have tested and found to remove
transmissometer data spikes properly.  The data were corrected for
factory and field air calibrations. Beam transmission was converted to
beam attenuation coefficients using c=-(1/r)*ln(%Tr/100) where c=beam
attenuation coefficient (m^-1), r=beam path length (m), and Tr=% beam
transmission.

The Arabian Sea data set presented some challenges because 1-4
different transmissometers were used on any given cruise, complicating
the data calibration.  It is impractical to do a proper bench or air
calibration prior for each CTD cast since the deck of the ship is not
always a clean environment and atmospheric conditions can change
rapidly and affect the air readings.  One calibration method is to
compare the beam attenuation at depth where the particle concentration
is relatively invariant.  The primary concern is ensuring that the
optical windows are uniformly clean, which is best determined by
comparing adjacent profiles.  Unfortunately, many of the CTD casts
extended only to 150 m or less, which was usually shallower than the
particle minimum. Furthermore, the stations covered a wide geographic
area, so it is more likely that the particle minimum at depth could
vary.  The primary method for comparing the beam attenuation signal to
particulate matter (PM) concentration or particulate organic carbon
(POC) concentration is to filter water samples and determine the dry
weight using stable filters (0.4 um pore size Poretics filters in this
case), or the amount of organic carbon on a glass fiber filter (0.7 um
nominal pore size).  The beam c data for those bottle depths (chosen as
the cp value of the 2 db bin within which the sample depth fell) are
then regressed against PM or POC using a Model II regression to
determine the intercept  where the concentration of particles in the
water equals zero. Theoretically this value should be 0.364 since the
transmissometers are set at the factory to read 0.364 in particle-free
water.  PM was filtered on four of the five cruises where beam c was
analyzed.  POC was measured on the one cruise for which no PM
measurements were made (TN049) as well as most of the other cruises.

In order to determine the attenuation specific to particulate matter,
the attenuation due to water must be subtracted from the beam c values
( cp = c -  cw).  Practically, cw is determined as the minimum
attenuation measured during each cruise. It must be noted that this
minimum attenuation value is  the "cleanest" water observed and is not
particle free. Thus, the regressions of the cp data versus particle
concentrations must be adjusted.

  A prediction of the PM concentration can be obtained from the
resulting equations for each cruise:

    TN043 ->    PM = 602 * cp      (r^2 = 0.86)
    TN045 ->    PM = 483 * cp      (r^2 = 0.87)
    TN050 ->    PM = 687 * cp      (r^2 = 0.92)
    TN054 ->    PM = 615 * cp      (r^2 = 0.86)

PM is in ug/Kg, and cp is attenuation per meter.

Note that these are Model II regressions so the equations are the same
if PM is regressed versus cp or vice versa. For comparison,
the relationships between particle concentration and attenuation in
surface waters of previous JGOFS programs were:

    PM = 1022*cp 	North Atlantic Bloom Exp.
    PM = 451*cp 	EqPac Spring Time Series
    PM = 647*cp 	EqPac Fall Time Series



Chlorophyll

	Chlorophyll-a fluorescence distribution in the Arabian Sea was
determined, in-situ, with a SeaTech Fluorometer. The fluorometer was
interfaced with the Sea-Bird CTD, and the data were acquired in the
same format as the transmissometer data. The Fluorometer is a standard
irradiation/emission system. When chlorophyll a is excited by blue
light (425 nm), it will fluoresce at a peak wavelength of 685 nm (red
light).  The emission detector is filtered to a peak response in order
to make the measurement insensitive to the excitation source. The
amount of fluoresced light detected is converted to a voltage range of
0 to 5 volts.  A signal gain of 10x was used, setting sensitivity to
3mg chl-a m^-3. The fluorometer is set to sample with a three second time
constant to smooth the data. A baffle has been placed in front of the
emission detector in an attempt to make it insensitive to ambient light
(SeaTech Fluorometer Manual). The SEASOFT software converts the
measured voltage into a relative chlorophyll-a value using the
equation:

		[volts * signal gain/5] + offset = mg chl-a m^-3

	These relative values were calibrated using discreet
chlorophyll samples (taken by various JGOFS scientists and analyzed
onboard the ship using a Turner Fluorometer). There is a good (r^2 =
0.90) linear correlation between fluorometer-determined chlorophyll-a
fluorescence, and the chlorophyll-a  concentrations determined using a
Turner fluorometer. Regressions were made for each cruise individually,
but the correlations (based on the standard deviation of the slope and
intercept) were improved when data from cruises TN049, TN050, and TN054
were combined. Prior to TN049, chlorophyll samples were taken from the
Trace-Metal rosette, which contained no CTD or fluorometer for accurate
depth or fluorescence measurements. We attempted a comparison between
standard CTD/fluorometer profiles made close in time to the Trace-Metal
casts on which chlorophyll measurements were made, but the lack of
accurate depths or water density for the discreet samples plus the
temporal variability between casts introduced too much scatter for a
useful correlation. There were too few chlorophyll a measurements made
on the standard CTD casts during TN043 and TN045 to independently
calibrate the fluorometer. This added to the appeal of a general
calibration for the fluorescence signal for all cruises, though we
recognize that data for two cruises were not included.  We emphasize
for future work that it is necessary to have a fluorometer and CTD on
the rosette at the time chlorophyll samples are being taken in order to
accurately calibrate the fluorescence signal. Furthermore continuous
profiles from a fluorometer provide higher resolution than discreet
samples alone.

	 Slightly different slopes and intercepts were observed in the
fluorescence/chlorophyll correlations for samples above and below the
chlorophyll maximum. Therefore the depth of the chlorophyll maximum was
determined by visual inspection of each profile (to avoid confusion
with individual spikes) and the samples were divided into two
categories, separated at a depth 10 m beneath the maximum fluorescence
value. The assumption (substantiated by inspection of the data) is that
chlorophyll-containing particles within the subsurface chlorophyll
maximum are more similar to those above the maximum than below. A model
II linear regression on each group of data indicated a very slight
difference in slopes between the two groups, but a substantial offset
in the intercepts. This results in a difference in the concentration of
predicted chlorophyll based on the fluorescence above and below the
chlorophyll maximum. Similar differences in chlorophyll fluorescence
above and below the chlorophyll maximum were noticed by Pak et
al.(1988). Equations are provided here for both regions in the Arabian Sea.

 	Above the depth of the chlorophyll maximum:
		Chl a  = 0.357*Fl + 0.078    (r^2 = 0.86)

	Below the depth of the chlorophyll maximum:
                Chl a = 0.389*Fl - 0.05      (r^2 = 0.93)

LSS - SeaTech Light Scattering Sensor

	Light scattering due to particles was monitored using a SeaTech
Light Scattering Sensor (LSS). The LSS projects light from two 880 nm
(infrared) LEDs into a sampling volume that varies depending upon the
concentration of particulate matter, but that is roughly the shape of a
stretched balloon. Back-scattered light from the particulate matter is
measured by a detector. The range on the LSS was set to 0 - 33 mg/l.
The amount of light detected is scaled to a 0-5 volt output, but in the
Arabian Sea most values were less than 0.5 volts.  The LSS output
depends upon the nature of the particulate matter and will vary with
changes in particle size distribution, shape, index of refraction,
organic/inorganic content etc. Therefore the LSS requires site-specific
calibration. The LSS was interfaced with the SeaBird CTD and the data
were handled in the same format as the transmissometer and fluorometer
data.

<pre>
<h2>Beam Attenuation Coefficient, Light Scattering, Fluorescence protocols
Wilford Gardner, Jan Gundersen, Mary Jo Richardson.
Texas A&M University</h2>

<b>Data Reduction Scheme</b>

The primary purpose for measuring the beam attenuation
in JGOFS programs is to determine the concentration and distribution of
particulate matter (PM) or particulate organic carbon (POC) in the
water with continuous profiling rather than with limited discrete
samples. Towards this end, a 25 cm Sea Tech Transmissometer was
interfaced with the University of Washington's SeaBird CTD for all
Arabian Sea cruises. Transmissometer data were analyzed for the five
process cruises (TN043, TN045, TN049, TN050 and TN054) that occupied a
standard set of stations. Data from the raw CTD files were binned at 2
db intervals through SeaBird's SEASOFT program, which has a spike
removal subroutine which we have tested and found to remove
transmissometer data spikes properly. The data were corrected for
factory and field air calibrations. Beam transmission was converted to
beam attenuation coefficients using c=-(1/r)*ln(%Tr/100) where c=beam
attenuation coefficient (m^-1), r=beam path length (m), and Tr=% beam
transmission.

The Arabian Sea data set presented some challenges because 1-4
different transmissometers were used on any given cruise, complicating
the data calibration. It is impractical to do a proper bench or air
calibration prior for each CTD cast since the deck of the ship is not
always a clean environment and atmospheric conditions can change
rapidly and affect the air readings. One calibration method is to
compare the beam attenuation at depth where the particle concentration
is relatively invariant. The primary concern is ensuring that the
optical windows are uniformly clean, which is best determined by
comparing adjacent profiles. Unfortunately, many of the CTD casts
extended only to 150 m or less, which was usually shallower than the
particle minimum. Furthermore, the stations covered a wide geographic
area, so it is more likely that the particle minimum at depth could
vary. The primary method for comparing the beam attenuation signal to
particulate matter (PM) concentration or particulate organic carbon
(POC) concentration is to filter water samples and determine the dry
weight using stable filters (0.4 um pore size Poretics filters in this
case), or the amount of organic carbon on a glass fiber filter (0.7 um
nominal pore size). The beam c data for those bottle depths (chosen as
the cp value of the 2 db bin within which the sample depth fell) are
then regressed against PM or POC using a Model II regression to
determine the intercept where the concentration of particles in the
water equals zero. Theoretically this value should be 0.364 since the
transmissometers are set at the factory to read 0.364 in particle-free
water. PM was filtered on four of the five cruises where beam c was
analyzed. POC was measured on the one cruise for which no PM
measurements were made (TN049) as well as most of the other cruises.

In order to determine the attenuation specific to particulate matter,
the attenuation due to water must be subtracted from the beam c values
( cp = c - cw). Practically, cw is determined as the minimum
attenuation measured during each cruise. It must be noted that this
minimum attenuation value is the "cleanest" water observed and is not
particle free. Thus, the regressions of the cp data versus particle
concentrations must be adjusted.

A prediction of the PM concentration can be obtained from the
resulting equations for each cruise:

TN043 -> PM = 602 * cp (r^2 = 0.86)
TN045 -> PM = 483 * cp (r^2 = 0.87)
TN050 -> PM = 687 * cp (r^2 = 0.92)
TN054 -> PM = 615 * cp (r^2 = 0.86)

PM is in ug/Kg, and cp is attenuation per meter.

Note that these are Model II regressions so the equations are the same
if PM is regressed versus cp or vice versa. For comparison,
the relationships between particle concentration and attenuation in
surface waters of previous JGOFS programs were:

PM = 1022*cp North Atlantic Bloom Exp.
PM = 451*cp EqPac Spring Time Series
PM = 647*cp EqPac Fall Time Series

<b>Chlorophyll</b>

Chlorophyll-a fluorescence distribution in the Arabian Sea was
determined, in-situ, with a SeaTech Fluorometer. The fluorometer was
interfaced with the Sea-Bird CTD, and the data were acquired in the
same format as the transmissometer data. The Fluorometer is a standard
irradiation/emission system. When chlorophyll a is excited by blue
light (425 nm), it will fluoresce at a peak wavelength of 685 nm (red
light). The emission detector is filtered to a peak response in order
to make the measurement insensitive to the excitation source. The
amount of fluoresced light detected is converted to a voltage range of
0 to 5 volts. A signal gain of 10x was used, setting sensitivity to
3mg chl-a m^-3. The fluorometer is set to sample with a three second time
constant to smooth the data. A baffle has been placed in front of the
emission detector in an attempt to make it insensitive to ambient light
(SeaTech Fluorometer Manual). The SEASOFT software converts the
measured voltage into a relative chlorophyll-a value using the
equation:

[volts * signal gain/5] + offset = mg chl-a m^-3

These relative values were calibrated using discreet
chlorophyll samples (taken by various JGOFS scientists and analyzed
onboard the ship using a Turner Fluorometer). There is a good (r^2 =
0.90) linear correlation between fluorometer-determined chlorophyll-a
fluorescence, and the chlorophyll-a concentrations determined using a
Turner fluorometer. Regressions were made for each cruise individually,
but the correlations (based on the standard deviation of the slope and
intercept) were improved when data from cruises TN049, TN050, and TN054
were combined. Prior to TN049, chlorophyll samples were taken from the
Trace-Metal rosette, which contained no CTD or fluorometer for accurate
depth or fluorescence measurements. We attempted a comparison between
standard CTD/fluorometer profiles made close in time to the Trace-Metal
casts on which chlorophyll measurements were made, but the lack of
accurate depths or water density for the discreet samples plus the
temporal variability between casts introduced too much scatter for a
useful correlation. There were too few chlorophyll a measurements made
on the standard CTD casts during TN043 and TN045 to independently
calibrate the fluorometer. This added to the appeal of a general
calibration for the fluorescence signal for all cruises, though we
recognize that data for two cruises were not included. We emphasize
for future work that it is necessary to have a fluorometer and CTD on
the rosette at the time chlorophyll samples are being taken in order to
accurately calibrate the fluorescence signal. Furthermore continuous
profiles from a fluorometer provide higher resolution than discreet
samples alone.

Slightly different slopes and intercepts were observed in the
fluorescence/chlorophyll correlations for samples above and below the
chlorophyll maximum. Therefore the depth of the chlorophyll maximum was
determined by visual inspection of each profile (to avoid confusion
with individual spikes) and the samples were divided into two
categories, separated at a depth 10 m beneath the maximum fluorescence
value. The assumption (substantiated by inspection of the data) is that
chlorophyll-containing particles within the subsurface chlorophyll
maximum are more similar to those above the maximum than below. A model
II linear regression on each group of data indicated a very slight
difference in slopes between the two groups, but a substantial offset
in the intercepts. This results in a difference in the concentration of
predicted chlorophyll based on the fluorescence above and below the
chlorophyll maximum. Similar differences in chlorophyll fluorescence
above and below the chlorophyll maximum were noticed by Pak et
al.(1988). Equations are provided here for both regions in the Arabian Sea.

Above the depth of the chlorophyll maximum:
Chl a = 0.357*Fl + 0.078 (r^2 = 0.86)

Below the depth of the chlorophyll maximum:
Chl a = 0.389*Fl - 0.05 (r^2 = 0.93)

<b>LSS - SeaTech Light Scattering Sensor</b>

Light scattering due to particles was monitored using a SeaTech
Light Scattering Sensor (LSS). The LSS projects light from two 880 nm
(infrared) LEDs into a sampling volume that varies depending upon the
concentration of particulate matter, but that is roughly the shape of a
stretched balloon. Back-scattered light from the particulate matter is
measured by a detector. The range on the LSS was set to 0 - 33 mg/l.
The amount of light detected is scaled to a 0-5 volt output, but in the
Arabian Sea most values were less than 0.5 volts. The LSS output
depends upon the nature of the particulate matter and will vary with
changes in particle size distribution, shape, index of refraction,
organic/inorganic content etc. Therefore the LSS requires site-specific
calibration. The LSS was interfaced with the SeaBird CTD and the data
were handled in the same format as the transmissometer and fluorometer
data.
</pre>