USGS OFR 2012-1178: Profile Measurements and Data From the 2011 Optics, Acoustics, and Stress In Situ (OASIS) Project at the Martha's Vineyard Coastal Observatory, Appendix D

U.S. Geological Survey Open-File Report 2012-1178

Profile Measurements and Data From the 2011 Optics, Acoustics, and Stress In Situ (OASIS) Project at the Martha's Vineyard Coastal Observatory

Appendix 4. Nonstandard Data

This appendix describes data from the U. S. Geological Survey (USGS) 2011 Optics, Acoustics, and Stress In Situ (OASIS) Project at the Martha's Vineyard Coastal Observatory (MVCO) that are distributed in nonstandard formats. These include data from all the sensors on the arm because they have a variable-depth frame of reference and data from the acoustic doppler velocimeters (ADVs) and pulse-coherent acoustic doppler profiler (PCADP) mounted on the tripod, for which we provide raw burst data. These measurements have been converted to engineering units in Earth coordinates and stored in netCDF files using the EPIC convention (see Abbreviations and Symbols) without other editing, spike removal, or filtering. This allows users to analyze the data with the methods they consider suitable. Data distributed here include the following (for a complete description of the instruments, refer to Instrumentation section; numbers in parentheses are USGS mooring identification numbers):

unmodified burst data from the green, yellow, and blue ADVs (9105, 9106, and 91013 respectively)

unmodified burst data from the PCADP (9104)

data from the LISST-100X laser particle sizer (9109)

images from the LISST-HOLO particle imaging system

data from the YSI multiparameter sonde (91011)

data from the ABSS acoustic backscatter sensors (91012)

data from the IG-20 accelerometers recorded by the Modtronix and the Moxa (9108 and 91014, respectively)

time-series data acquired by the University of Maine AC-9 spectral absorption and beam attenuation meter and BB2F spectral backscattering instrument mounted on the USGS tripod by collaborators Emmanuel Boss and James Loftin of the University of Maine (no USGS mooring numbers)

Tripod Frame Mounted Instruments

Green ADV (9105) and Yellow ADV (9106)

Burst data from the green and yellow SonTek ADVs mounted on the tripod frame are nonstandard because velocity, acoustic backscatter, optical backscatter, and optical transmission are in unedited, raw form. No despiking or data cleanup was performed. This is indicated by "raw" in the filename.

Profiling Arm Instruments

The absolute and relative elevation of the instruments on the arm changed continuously during sampling. Elevation above the seafloor was calculated (appendix 1) for each sensor using (1) the arm angle and the mounting position of the sensors combined with (2) the elevation of the arm hinge, which changed slightly during the deployment as the tripod feet scoured into the seafloor. The elevation of the arm hinge was determined from the range-to-boundary measurements ("brange" variable) made by the PCADP mounted on the tripod crossbar next to the arm hinge. The main contributions to uncertainty in the sensor elevation estimates arise from (1) variations in brange associated with small topographic changes on the bottom and (2) small tilts in the tripod on the axis perpendicular to the arm motion. The elevation estimates are accurate within 5 centimeters (cm). Sampling time has been corrected for some instruments based on the assumption that any clock drift noted during the deployment was linear. The largest clock drift noted was 17 seconds (s); most instruments were within 3 s of universal time at the end of the deployment. The variable "mab" is elevation in meters above the seabed and the variable "dnc" is time (in The MathWorks, Matlab datenum format) corrected for clock drift. Files with these additional nonstandard variables are indicated by filenames with the "_eltcorr" suffix.

Blue ADV (91013)

Burst data from the blue SonTek ADV mounted on the profiling arm are nonstandard because velocity, acoustic backscatter, optical backscatter, and optical transmission are preserved in their uneditted, raw form. No despiking or data cleanup was performed. This is indicated by "raw" in the filename. Additionally, these data were collected from the profiling arm and have a variable elevation above the seafloor.

LISST-100X (9109)

LISST-100X data are nonstandard because they were collected from the profiling arm and have a variable elevation above the seafloor.

LISST-HOLO (91010)

The LISST-HOLO outputs grayscale images in portable greymap (pgm; see http://netpbm.sourceforge.net/doc/pgm.html for information on pgm format). No USGS standard has been established for LISST-HOLO images; for this reason, and because the images were collected from the moving arm and have a variable elevation above the seafloor, they are nonstandard.

YSI Multiparameter Sonde (91011)

YSI data are nonstandard because they were collected from the profiling arm and have a variable elevation above the seafloor.

ABSS Acoustic Backscatter System (91012)

ABSS data are nonstandard because they were collected from the profiling arm and have a variable elevation above the seafloor.

Modtronix Data (9108)

Data measured by sensors on the Modtronix (including IG-20 two-axis inclinometer and three-axis accelerometer data used to monitor arm movement) and recorded by the Moxa are nonstandard because they are unique to this experiment, and because they were collected from the profiling arm and have a variable elevation above the seafloor.

IG-20 Data From the Instrument Package on the End of the Arm (91014)

Data from the IG-20 two-axis inclinometer and three-axis accelerometer recorded by the Moxa are nonstandard because they are unique to this experiment and because they were collected from the profiling arm and have a variable elevation above the seafloor.

University of Maine Data

Optical Data

These data were collected using two instruments, a 10-cm path length AC-9 spectral absorption and beam attenuation meter and a BB2F spectral backscattering meter and fluorometer. The AC-9 was processed as described in Slade and others (2010). In summary, sea water was sampled for 25 minutes (min) (pumped from the hose intake near the end of the arm), and then, using an underwater switch, the water was pumped for 5 min through a 0.2-millimeter (mm) filter. The filtered samples were interpolated linearly in time and subtracted from the total measurements, producing particulate absorption and attenuation estimates that were independent of calibration. The particulate absorption values were corrected for scattering using the third method of Zaneveld and others (1994) that involved removing a spectrum similar in shape to the scattering spectra (estimated as the difference of attenuation minus absorption) and assuming absorption at 715 nanometers (nm) to be zero. All data were binned to 1-min bins.

The instruments produced data at 6 hertz (Hz) (AC-9) and 2 Hz (BB2F). The data were binned using a 1-min median bin to remove statistically poorly sampled large spike values. Variability in the data for each 1-min bin was quantified using the standard deviation of the measurements (which does include the spikes).

Beyond uncertainties associated with scattering correction (about 20 percent in blue wavelengths), we can use the differences in dissolved spectra to get a sense of how much dissolved content changed between its measurements (and hence the uncertainties in particulate attenuation and absorption). Mean and median changes in dissolved were smaller than the instrument resolution at 412 nm (which had the largest deviation of all wavelengths) and the standard deviation was 0.03 per meter (m^-1). For comparison the fifth percentile was 0.1 m^-1 (standard deviation 0.74 m^-1) and the median was 0.18 m^-1 (standard deviation 1.04 m^-1) for absorption or attenuation at 412 nm (where the errors are largest due to increase in dissolved absorption from red to blue wavelengths).

The particulate backscattering coefficient was derived from the BB2F as in Boss and others (2004). We measured the dark currents on our system and used WETLabs slope parameters to obtain the volume scattering function at 117 degrees. We removed the contribution of salt water and multiplied by a non-dimensional parameter (χ factor; Boss and Pegau, 2001) of 1.12 to obtain the particulate backscattering coefficient. We estimate the uncertainty in particulate backscattering coefficient to be approximately 10 percent (Boss and Pegau, 2001).

Derived Quantities

Chlorophyll a (Chl) was estimated from particulate absorption (a_p) by computing the absorption line-height at 676 nm and assuming a chlorophyll-normalized absorption of 0.014 square meters per milligram of chlorophyll (Boss and others, 2007):

Chl =

a_p(676)-39/65(a_p(650))

0.014

(4-1)

where

a_p	particulate absorption at the wavelength specified in parentheses and
Chl	chlorophyll a, determined in milligrams per cubic meter

Size tendency of particles (γ) was estimated from a power-law fit to the beam-attenuation spectra (for example, Boss and others, 2001). For a power-law distribution of particles, γ is related monotonically to the slope of the particle size distribution.

Particulate backscattering ratios in coastal environments (varying from 0.005 for phytoplankton and organic particles to 0.03 for quartz sediments, for example, Twardowski and others (2001) and Boss and others (2004)) provide estimates of particle composition. We computed the ratios at wavelengths of 532 nm and 650 nm by dividing the particulate backscattering coefficients by the corresponding AC-9-derived particulate scattering coefficient (calculated as particulate attenuation minus particulate absorption).

References Cited

Boss, E., and Pegau, W.S., 2001, Relationship of light scattering at an angle in the backward direction to the backscattering coefficient: Applied Optics, v. 40, p. 5503-5507.

Boss, E., Collier, R., Larson, G., Fennel, K., and Pegau, W.S., 2007, Measurements of spectral optical properties and their relation to biogeochemical variables and processes in Crater Lake National Park, OR: Hydrobiologia, v. 574, p. 149-159.

Boss, E., Pegau, W.S., Lee, M., Twardowski, M.S., Shybanov, E., Korotaev, G., and Baratange, F., 2004, Particulate backscattering ratio at LEO 15 and its use to study particle composition and distribution: Journal of Geophysical Research, v. 109, no. C0101410, 10 p.

Boss, E., Twardowski, M.S., and Herring, S., 2001, Shape of the particulate beam attenuation spectrum and its inversion to obtain the shape of the particulate size distribution: Applied Optics, v. 40, p. 4885-4893.

Fishman, M.J. and Friedman, L.C. (eds), 1989. Techniques of water-resources investigations of the U.S. Geological Survey, chapter A1 methods for determination of inorganic substances in water and fluvial sediments, third edition, book 5, p. 443. U. S. Geological Survey, Reston, VA. http://pubs.usgs.gov/twri/twri5-a1/pdf/twri_5-A1_n.pdf.

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, v. 27, no. 10, p. 1733-1746.

Twardowski M.S., Boss, E., MacDonald, J.B., Pegau, W.S., Barnard, A.H., and Zaneveld, J.R.V., 2001, A model for estimating bulk refractive index from the optical backscattering ratio and the implications for understanding particle composition in case I and case II waters: Journal of Geophysical Research, v. 106, no. C7, p. 14129-14142.

Traykovski, P., Richardson, M.D., Mayer, L.A., and Irish, J.D., 2007, Mine burial experiments at the Martha's Vineyard Coastal Observatory: IEEE Journal of Ocean Engineering, v. 32, no. 1, p. 150-166.

Zaneveld, J.R.V., Kitchen, J.C. and Moore, C.C., 1994, Scattering error correction of reflecting tube absorption meters, in Jafee, J.S., ed., Ocean Optics, 12, Bergen, Norway, June 13-15, 1994: SPIE, proceedings, v. 2258, p. 44-55.

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