Dataset: PAR

Name: Large particulate matter concentration, biovolume, and sized distribution in the Pacific Ocean from 2015-04-11 to 2015-06-18 measured by the Underwater Vision Profiler 5 (UVP5) on the P16N Repeat Hydrography cruise aboard the NOAA Ship Ronald H. Brown
Published: 2021-04-27
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.787432.2

Spatial Extent: N:56.29027 E:-149.86171 S:-16.95559 W:-153.23287

Temporal Extent: 2015-04-11 - 2015-06-18

Project:

Variability in particle size distributions, sinking velocities, and fluxes in the northern Gulf of Alaska (GoA Particles)

Principal Investigator:

Andrew M.P. McDonnell (University of Alaska Fairbanks, UAF)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-04-27

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Large particulate matter concentration, biovolume, and sized distribution in the Pacific Ocean from 2015-04-11 to 2015-06-18 measured by the Underwater Vision Profiler 5 (UVP5) on the P16N Repeat Hydrography cruise aboard the NOAA Ship Ronald H. Brown

Abstract:

This dataset includes large particulate matter concentration, biovolume, and sized distribution in the Pacific Ocean from 2015-04-11 to 2015-06-18 measured by the Underwater Vision Profiler 5 (UVP5) on the P16N Repeat Hydrography cruise aboard the NOAA Ship Ronald H. Brown.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-04-27	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.787432.2	2021-07-09

Description

The Underwater Vision Profiler (UVP5) is an underwater camera system that was designed to record the vertical distributions of large aggregates and zooplankton (> 102 µm) down to 6000 m. Two units that consist of red-light emitting diodes (LEDs) illuminate (in 100 µsecond flashes) an area of 4 X 20 cm which provides a volume sampling of ~1L per frame. The UVP5 was mounted on the bottom of each CTD rosette and collected data on each CTD cast (data are collected during the down cast). The methodology generally follows Picheral et al., 2010.

Methods & Sampling

The Underwater Vision Profiler 5 (UVP5) was utilized to collect in situ images of particles and plankton across the 2015 P16N repeat hydrography transect from French Polynesia (17°S) to the northern Gulf of Alaska shelf (56.3°N), primarily along the 151°W and 152°W meridians. The UVP5 was integrated within the conductivity temperature depth (CTD) rosette, and several images per second were acquired during the downcasts, resulting in a total of 171 vertical profiles from both legs of the cruise, most spanning from the surface down to near the bottom. The UVP captured in situ images of particles and plankton in a mixed processing mode in which particles were sized, counted, and tabulated in real time during the profile. Subsequent processing bins these particle counts into discrete, pre-defined size bins ranging from 102 µm to >26 mm in equivalent spherical diameter. Particle biovolume was also computed for each size bin. All data contained here is inclusive of both living and non-living particles and plankton.

Supplemental file "file_header_uvp5_sn009_2015_p16n_BCO-DMO_PAR.txt" contains additional metadata from the original file header.

Known Problems:
Some profiles did not extend to the full depth of the CTD cast because of problems with the rechargeable lithium ion battery onboard the UVP.

Data Processing Description

The UVP5 software acquires and processes images in real time. The gain, shutter and LED pulses are controlled and the background image is removed. Images are acquired and processed to get size and grey level for each image. Size information on all detected particles is stored and images of individual particles and plankton larger than 500 µm in equivalent spherical diameter are segmented and saved for later identification. Image post processing and metadata creation is accomplished with the Zooprocess software. Tabulated particle data are used to sum the number and volume of particles within predefined size and depth bins, allowing for the computation of the Datasets. Data and images have been uploaded to the Ecotaxa website (http://ecotaxa.obs-vlfr.fr/) which serves as a tool for particle and zooplankton identification with machine learning and human verification, as well as a repository for all globally collected UVP data. Data files for particle and zooplankton abundances are exported from the Ecotaxa particle module in detailed Ocean Data View (ODV) format, and reformatted for submission to BCO-DMO. The size distribution data is reported in non-differential forms (simply the concentration of particles in each size bin) as well as on a numeric and particle volume basis assuming all particles are spherical. The size bin limits are defined in equivalent spherical diameter (ESD), where ESD = (4 Sm π-1)-0.5 where Sm is the projected area of each particle in mm² and the particle concentrations are reported for each size bin defined by the log-transformed center of each size bin in µm. The biovolume is computed as the sum of the individual spherical volumes of each particle issued from the calibrated ESD.

This dataset was prepared using the scripts archived in this Github repository: https://github.com/britairving/UVP_submission_formatting. This repo has been forked by BCO-DMO to ensure a copy of the code is available. This can be accessed at https://github.com/BCODMO/UVP_submission_formatting. A .zip file of the code is also attached to this dataset as a Supplemental File.

BCO-DMO Processing Notes:
-added conventional header with dataset name, PI name, version date;
- added ISO_DateTime_UTC field with times formatted following ISO8601 conventions;
- renamed fields to comply with BCO-DMO naming conventions;
- replaced "-9999.000000" with "nd" to indicate "no data".

Data Files

File
par.csv (Comma Separated Values (.csv), 46.26 MB) MD5:0005351fc871e61e7d1bec9f426037aa Primary data file for dataset ID 787432

Supplemental Files

File
file_header_uvp5_sn009_2015_p16n_BCO-DMO_PAR.txt (Octet Stream, 1.66 KB) MD5:a5b7ad00a9811207794b2c5de657e3b1 Original header of the data file "uvp5_sn009_2015_p16n_PAR", containing deployment information (location, date, time), instrument information, and uncertainty equations.
UVP Data Submission Formatting Repo filename: UVP_submission_formatting-1.0.zip (ZIP Archive (ZIP), 80.78 KB) MD5:b3f6c50ec61d75a64dfed6ab0c8cd484 Code used to prepare data for submission to BCO-DMO; associated with datasets 787966 and 787432. PI: Andrew McDonnell. Also available from BCO-DMO Github at https://github.com/BCODMO/UVP_submission_formatting

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1459835

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
RB1503_leg1	P16N 33RO20150410 P16N_leg1 rb1503_leg1 P16N/1	2015-04-10	NOAA Ship Ronald H. Brown	Jessica Cross (Chief Scientist) Samantha Siedlecki (Co-Chief Scientist)	data info
RB1503_leg2	P16N 33RO20150525 P16N_leg2 P16N/2 2015_P16N_leg2 rb1503_leg2 RB1503	2015-05-25	NOAA Ship Ronald H. Brown	Alison Macdonald (Chief Scientist) Sabine Mecking (Co-Chief Scientist) Christian Blair Lewis (Contact)	data info

Instruments

Underwater Vision Profiler

Supplied Name: Underwater Vision Profiler 5 (UVP5)

Supplied Description:

Underwater Vision Profiler 5 (UVP5), Manufactured by Hydroptic serial number sn009

Instrument Type

Generic Name: Underwater Vision Profiler

Acronym: UVP

Generic Description:

A description of the UVP instrument can be found in the following publication: Picheral, M., L. Guidi, L. Stemmann, D. M. Karl, G. Iddaoud, and G. Gorsky. 2010. The Underwater Vision Profiler 5: An advanced instrument for high spatial resolution studies of particle size spectra and zooplankton. Limnol. Oceanogr. Meth. 8: 462-473. (access the PDF at URL: http://cmore.soest.hawaii.edu/cmoredata/LMO/Guidi/Picheral_2010.pdf)

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
station	Site	unitless	station
profile	Profile name	unitless	cast
UVP_rawfilename	Raw file name from UVP	unitless	file_name
ISO_DateTime_UTC	Date and time (UTC); formatted to ISO8601 standard: YYYY-MM-DDThh:mm:ssZ Format: %Y-%m-%dT%H:%M:%S%Z	unitless	ISO_DateTime_UTC
date	Date Format: %Y%m%d	unitless	date
time	Time (UTC) Format: %H:%M:%S	unitless	time
lat	Latitude in decimal degrees (positive values = North)	decimal degrees North	lat
lon	Longitude in decimal degrees (positive values = East)	decimal degrees East	lon
bin_depth	Depth, midpoint of 5m depth bin	meters (m)	depth
volume	Total volume of water sampled within each depth bin	liters (L)	volume
abundance_102_128_um	Abundance of particles with an equivalent spherical diameter between 102-128 micrometers	number/L	abundance
abundance_128_161_um	Abundance of particles with an equivalent spherical diameter between 128-161 micrometers	number/L	abundance
abundance_161_203_um	Abundance of particles with an equivalent spherical diameter between 161-203 micrometers	number/L	abundance
abundance_203_256_um	Abundance of particles with an equivalent spherical diameter between 203-256 micrometers	number/L	abundance
abundance_256_323_um	Abundance of particles with an equivalent spherical diameter between 256-323 micrometers	number/L	abundance
abundance_323_406_um	Abundance of particles with an equivalent spherical diameter between 323-406 micrometers	number/L	abundance
abundance_406_512_um	Abundance of particles with an equivalent spherical diameter between 406-512 micrometers	number/L	abundance
abundance_512_645_um	Abundance of particles with an equivalent spherical diameter between 512-645 micrometers	number/L	abundance
abundance_645_813_um	Abundance of particles with an equivalent spherical diameter between 645-813 micrometers	number/L	abundance
abundance_0p813_1p02_mm	Abundance of particles with an equivalent spherical diameter between 0.813-1.02 millimeters	number/L	abundance
abundance_1p02_1p29_mm	Abundance of particles with an equivalent spherical diameter between 1.02-1.29 millimeters	number/L	abundance
abundance_1p29_1p63_mm	Abundance of particles with an equivalent spherical diameter between 1.29-1.63 millimeters	number/L	abundance
abundance_1p63_2p05_mm	Abundance of particles with an equivalent spherical diameter between 1.63-2.05 millimeters	number/L	abundance
abundance_2p05_2p58_mm	Abundance of particles with an equivalent spherical diameter between 2.05-2.58 millimeters	number/L	abundance
abundance_2p58_3p25_mm	Abundance of particles with an equivalent spherical diameter between 2.58-3.25 millimeters	number/L	abundance
abundance_3p25_4p1_mm	Abundance of particles with an equivalent spherical diameter between 3.25-4.1 millimeters	number/L	abundance
abundance_4p1_5p16_mm	Abundance of particles with an equivalent spherical diameter between 4.1-5.16 millimeters	number/L	abundance
abundance_5p16_6p5_mm	Abundance of particles with an equivalent spherical diameter between 5.16-6.5 millimeters	number/L	abundance
abundance_6p5_8p19_mm	Abundance of particles with an equivalent spherical diameter between 6.5-8.19 millimeters	number/L	abundance
abundance_8p19_10p3_mm	Abundance of particles with an equivalent spherical diameter between 8.19-10.3 millimeters	number/L	abundance
abundance_10p3_13_mm	Abundance of particles with an equivalent spherical diameter between 10.3-13 millimeters	number/L	abundance
abundance_13_16p4_mm	Abundance of particles with an equivalent spherical diameter between 13-16.4 millimeters	number/L	abundance
abundance_16p4_20p6_mm	Abundance of particles with an equivalent spherical diameter between 16.4-20.6 millimeters	number/L	abundance
abundance_20p6_26_mm	Abundance of particles with an equivalent spherical diameter between 20.6-26 millimeters	number/L	abundance
abundance_gt26_mm	Abundance of particles with an equivalent spherical diameter greater than 26 millimeters	number/L	abundance
biovolume_102_128_um	Biovolume of particles with an equivalent spherical diameter between 102-128 micrometers	mm^3/L	biovolume
biovolume_128_161_um	Biovolume of particles with an equivalent spherical diameter between 128-161 micrometers	mm^3/L	biovolume
biovolume_161_203_um	Biovolume of particles with an equivalent spherical diameter between 161-203 micrometers	mm^3/L	biovolume
biovolume_203_256_um	Biovolume of particles with an equivalent spherical diameter between 203-256 micrometers	mm^3/L	biovolume
biovolume_256_323_um	Biovolume of particles with an equivalent spherical diameter between 256-323 micrometers	mm^3/L	biovolume
biovolume_323_406_um	Biovolume of particles with an equivalent spherical diameter between 323-406 micrometers	mm^3/L	biovolume
biovolume_406_512_um	Biovolume of particles with an equivalent spherical diameter between 406-512 micrometers	mm^3/L	biovolume
biovolume_512_645_um	Biovolume of particles with an equivalent spherical diameter between 512-645 micrometers	mm^3/L	biovolume
biovolume_645_813_um	Biovolume of particles with an equivalent spherical diameter between 645-813 micrometers	mm^3/L	biovolume
biovolume_0p813_1p02_mm	Biovolume of particles with an equivalent spherical diameter between 0.813-1.02 millimeters	mm^3/L	biovolume
biovolume_1p02_1p29_mm	Biovolume of particles with an equivalent spherical diameter between 1.02-1.29 millimeters	mm^3/L	biovolume
biovolume_1p29_1p63_mm	Biovolume of particles with an equivalent spherical diameter between 1.29-1.63 millimeters	mm^3/L	biovolume
biovolume_1p63_2p05_mm	Biovolume of particles with an equivalent spherical diameter between 1.63-2.05 millimeters	mm^3/L	biovolume
biovolume_2p05_2p58_mm	Biovolume of particles with an equivalent spherical diameter between 2.05-2.58 millimeters	mm^3/L	biovolume
biovolume_2p58_3p25_mm	Biovolume of particles with an equivalent spherical diameter between 2.58-3.25 millimeters	mm^3/L	biovolume
biovolume_3p25_4p1_mm	Biovolume of particles with an equivalent spherical diameter between 3.25-4.1 millimeters	mm^3/L	biovolume
biovolume_4p1_5p16_mm	Biovolume of particles with an equivalent spherical diameter between 4.1-5.16 millimeters	mm^3/L	biovolume
biovolume_5p16_6p5_mm	Biovolume of particles with an equivalent spherical diameter between 5.16-6.5 millimeters	mm^3/L	biovolume
biovolume_6p5_8p19_mm	Biovolume of particles with an equivalent spherical diameter between 6.5-8.19 millimeters	mm^3/L	biovolume
biovolume_8p19_10p3_mm	Biovolume of particles with an equivalent spherical diameter between 8.19-10.3 millimeters	mm^3/L	biovolume
biovolume_10p3_13_mm	Biovolume of particles with an equivalent spherical diameter between 10.3-13 millimeters	mm^3/L	biovolume
biovolume_13_16p4_mm	Biovolume of particles with an equivalent spherical diameter between 13-16.4 millimeters	mm^3/L	biovolume
biovolume_16p4_20p6_mm	Biovolume of particles with an equivalent spherical diameter between 16.4-20.6 millimeters	mm^3/L	biovolume
biovolume_20p6_26_mm	Biovolume of particles with an equivalent spherical diameter between 20.6-26 millimeters	mm^3/L	biovolume
biovolume_gt26_mm	Biovolume of particles with an equivalent spherical diameter greater than 26 millimeters	mm^3/L	biovolume

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Dataset: PAR