Dataset: Video Plankton Recorder raw data

Name: VPR data from R/V Oceanus OC469-01, OC471-01 in the NW Atlantic: Woods Hole to Barbados from 2010-2011 (Trichodesmium project)
Published: 2022-06-22
Keywords: biota, oceans

Cite This Dataset

Project:

Quantification of Trichodesmium spp. vertical and horizontal abundance patterns and nitrogen fixation in the western North Atlantic (Trichodesmium)

Program:

Ocean Carbon and Biogeochemistry (OCB)

Principal Investigator:

Dennis J. McGillicuddy (Woods Hole Oceanographic Institution, WHOI)

Co-Principal Investigator:

Cabell S. Davis (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Sonya T. Dyhrman (Lamont-Doherty Earth Observatory, LDEO)

Dr John Waterbury (Woods Hole Oceanographic Institution, WHOI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-06-22

Restricted:

Validated:

Yes

Current State:

Final no updates expected

VPR data from R/V Oceanus OC469-01, OC471-01 in the NW Atlantic: Woods Hole to Barbados from 2010-2011 (Trichodesmium project)

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Description

The raw VPR data file collection organized by cruise.

Cruise ID

Listing of Files in Compressed tar

Compressed tar of VPR Data Files

OC469 - 8 casts
28 GB

vpr_dirs.ls.txt (40 KB)
vpr1.filelist.txt (2.5 MB)
vpr3.filelist.txt (85 KB)
vpr4.filelist.txt (3.8 MB)
vpr5.filelist.txt (1 KB)
vpr6.filelist.txt (155 KB)
vpr7.filelist.txt (3.3 MB)
vpr8.filelist.txt (1.36 MB)

vpr_dirs.tar.gz (14 MB)
vpr1.tar.gz (2.2 GB)
vpr3.tar.gz (92 MB)
vpr4.tar.gz (2.9 GB)
vpr5.tar.gz (135 KB)
vpr6.tar.gz (.24 GB)
vpr7.tar.gz (6.1 GB)
vpr8.tar.gz (1.9 GB)

OC471 - 16 casts
150 GB

basic directory structure
vpr_dirs.filelist.txt (127 KB)

data files for rois from individual VPR tows
vpr1.filelist.txt (7.7 MB)
vpr2.filelist.txt (4.8 MB)
vpr3.filelist.txt (5.0 MB)
vpr4.filelist.txt (6.0 MB)
vpr5.filelist.txt (6.5 MB)
vpr6.filelist.txt (14.8 MB)
vpr7.filelist.txt (12.1 MB)
vpr8.filelist.txt (5.4 MB)
vpr9.filelist.txt (13.2 MB)
vpr10.filelist.txt (12.5 MB)
vpr11.filelist.txt (8.2 MB)
vpr12.filelist.txt (7.2 MB)
vpr14.filelist.txt (2.3 MB)
vpr15.filelist.txt (6.5 MB)
vpr16.filelist.txt (10.1 MB)

basic directory structure
vpr_dirs.tar.gz (189 MB)

data files for rois from individual VPR tows
VPR-1: vpr1.tar.gz (7.3 GB)
VPR-2: vpr2.tar.gz (4.8 GB)
VPR-3: vpr3.tar.gz (5 GB)
VPR-4: vpr4.tar.gz (6.3 GB)
VPR-5: vpr5.tar.gz (7.1 GB)
VPR-6: vpr6.tar.gz (16.5 GB)
VPR-7: vpr7.tar.gz (16 GB)
VPR-8: vpr8.tar.gz (7.3 GB)
VPR-9: vpr9.tar.gz (18.7 GB)
VPR-10: vpr10.tar.gz (16.9 GB)
VPR-11: vpr11.tar.gz (11 GB)
VPR-12: vpr12.tar.gz (9.2 GB)
VPR-14: vpr14.tar.gz (2.9 GB)
VPR-15: vpr15.tar.gz (7.8 GB)
VPR-16: vpr16.tar.gz (12.9 GB)

Hint: To work with the raw files files, make a separate subdirectory for the cruise and download the compressed data file tar files to that cruise subdirectory. Then decompress and unpack only the .tar.gz files for that cruise into that cruise subdirectory. For example, to work with the VPR data files from OC469, on a linux system:

mkdir OC469; cd OC469
download all the .tar.gz files for cruise OC469
gunzip OC469_vpr.tar.gz
tar -xvf OC469_vpr.tar

After the OC469 tar file is unpacked, it will require about 28 GB of disk space (the Total size noted in column (1), and you should have a collection of subdirectories similar to those listed above for OC469 VPR file set.

Contact:

Anyone trying to use these raw VPR files is encouraged to contact either Dennis McGillicuddy with any questions.

Dennis McGillicuddy
Applied Ocean Physics & Engineering
Woods Hole Oceanographic Institution
MS #11, Bigelow 209A
Woods Hole, Ma. 02543

mcgillic@whoi.edu
Office Phone: +1 508 289 2683
http://www.whoi.edu/profile.do?id=dmcgillicuddy

Methods & Sampling

Each VPR tow (VPR1, VPR2, VPR3, etc.) has a subdirectory that includes:

a VPRstartup_readme.txt file and these subdirectories:
/calibration
/processed
/rois
/trois

Data Processing Description

The images (.TIFF files) were extracted from video using Matlab-based software. The data are raw; no processing has been applied.

BCO-DMO Data Manager Notes:
* Version 1 2014-04-08 replaced by Version 2 2022-06-22
* [2022-06-22] Fixed broken link in metadata and data since it was broken due to a missing a slash between the cruise and filename "OC471vpr16.filelist.txt" -> "OC471/vpr16.filelist.txt"

Data Files

File
vpr_filelist_tricho.csv (Comma Separated Values (.csv), 6.86 KB) MD5:0401eba3e9493885da3272516ca16934 Primary data file for dataset ID 511466

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-0925284

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
OC469-01		2010-10-02	R/V Oceanus	Dennis J. McGillicuddy (Chief Scientist)	data info
OC471-01		2011-04-23	R/V Oceanus	Dennis J. McGillicuddy (Chief Scientist)	data info

Instruments

Video Plankton Recorder

Supplied Name: VPR

Supplied Description:

Instrument Type

Generic Name: Video Plankton Recorder

Acronym: VPR

Generic Description:

The Video Plankton Recorder (VPR) is a video-microscope system used for imaging plankton and other particulate matter in the size range from a few micrometers to several centimeters. The VPR is essentially an underwater microscope. It consists of four video cameras (with magnifying optics) synchronized at 60 fields per second (fps) to a red-filtered 80 W xenon strobe (pulse duration = 1 microsecond). The current lens on each camera can be adjusted to provide a field of view between 5 mm and 10 cm. Use of higher magnification lenses is currently being explored for viewing protozoans (less than 1 micrometer resolution). The four cameras are set for concentric viewing fields so that a range of up to four magnifications can be viewed simultaneously, allowing a wide size range of plankton to be sampled. Depth of field is adjusted by the lens aperture setting, and the volume sampled in each video field ranges from about 1 ml to 1 liter, depending on lens settings. The cameras have been configured for stereoscopic viewing as well.A strobe on the other arm illuminates the imaged volume and flashes 60 times per second, producing 60 images per second of the particles and plankton in the water. The images are then saved internally on a computer hard disk and later plotted.

Deployment: Most commonly, the VPR is mounted in a frame and lowered into the water from the stern of the ship. Sometimes, a CTD also is mounted next to the VPR to collect depth, temperature, and salinity information at the same time as each video image. The instrument is lowered down through the water to a maximum depth of 350 meters to generate a profile of plankton/particle abundance and taxon group along with temperature and salinity. In addition to the towed configuration for mapping plankton distributions, it is possible to deploy the VPR in a fixed position (on a mooring) for viewing plankton swimming behaviors in two or three dimensions. The VPR instrument system has been used in both configurations, and deployment on ROVs has been proposed.

This definition was taken from the WHOI Ocean Instruments Web site and from a US GLOBEC Newsletter.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
cruise_id	cruise identification	unitless	cruise_id
num_casts	number of VPR casts available	unitless	no_bcodmo_term
size_unpacked	size of files for whole cruise VPR's once uncompressed	gigabytes	no_bcodmo_term
file_lists	text file listing of compressed VPR files; one file per cast	unitless	no_bcodmo_term
file_list_size	download size of text files	megabytes	no_bcodmo_term
compressed_files	name and link for compressed VPR file; one file per cast	unitless	no_bcodmo_term
compressed_files_size	download size of compressed files	KB=kilobytes; MB=megabytes; GB=gigabytes	no_bcodmo_term

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Database

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Dataset: Video Plankton Recorder raw data