http://lod.bco-dmo.org/id/dataset/718403
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2017-10-31
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Holographic images from LISST-Holo system while deployed on the AUV Honey Badger (Wave Glider) during a deployment in the North Pacific gyre in 2015 (MAGI project)
2018-01-05
publication
2018-01-05
revision
BCO-DMO Linked Data URI
2018-01-05
creation
http://lod.bco-dmo.org/id/dataset/718403
Tracy A. Villareal
University of Texas at Austin
principalInvestigator
Dr Cara Wilson
National Oceanic and Atmospheric Administration - Southwest Fisheries Science Center
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Villareal, T. A., Wilson, C. (2018) Holographic images from LISST-Holo system while deployed on the AUV Honey Badger (Wave Glider) during a deployment in the North Pacific gyre in 2015 (MAGI project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-01-05 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/718403 [access date]
Holographic Images from LISST-Holo system Dataset Description: <p>This dataset includes holographic images from a LISST-Holo Submersible Digital Holographic Camera during an AUV Honey Badger deployment in the North Pacific gyre in 2015. I&nbsp;Image metadata, cell counts (e.g. number of Hemiaulus cells in aggregate form), and all raw holographic images are in the&nbsp;RAW.zip (12GB) file.</p>
<p>Software for further processing the raw holographic images provided here is available at the Sequoia Scientific, Inc. <a href="https://www.sequoiasci.com/product/lisst-holo/" target="_blank">LISST-Holo page</a> The following montage and depth images can be created for every raw image using the LISST-Holo software.</p>
<p><img alt="holographic images" src="https://datadocs.bco-dmo.org/d3/data_docs/MAGI/LISST_Holo/example.png" style="height:230px; width:822px" /></p> Methods and Sampling: <p>The LISST-Holo Submersible Digital Holographic Camera from&nbsp;Sequoia Scientific, Inc. was mounted on in a tow fish deployed on a 10 m tether behind the sub-body of the AUV Honey Badger.&nbsp;Holographic images were acquired in bursts every 6 hours.&nbsp; During each burst, 15 images&nbsp;were taken in 5 seconds.</p>
<p>The software "Batch-Holo" was used to generate the biovolume from particles with an equivalent spherical diameter of 11.094-58.1 microns.&nbsp; See "Parameters" section for more details.</p>
<p>Hemiaulus and Rhizosolenia cells were identified by hand. Each image was viewed using the "Holo_Detail" software and any Hemiaulus or Rhizosolenia cells were counted.</p>
<p>The manual and specifications for the LISST-Holo system, and software used in this dataset are available on the instrument page.&nbsp; The software can be obtained from the&nbsp;Sequoia Scientific, Inc.&nbsp;<a href="https://www.sequoiasci.com/product/lisst-holo/" target="_blank">LISST-Holo&nbsp;page</a>.</p>
<p>The calculation of cells per liter was done using the following the following formula:</p>
<p><img alt="formula" src="https://datadocs.bco-dmo.org/d3/data_docs/MAGI/LISST_Holo/formula.png" style="height:154px; width:505px" /></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1430048 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1430048
completed
Tracy A. Villareal
University of Texas at Austin
361-749-6732
Marine Science Institute and Dept. of Marine Science 750 Channel View Dr.
Port Aransas
TX
78373
USA
tracyv@austin.utexas.edu
pointOfContact
Dr Cara Wilson
National Oceanic and Atmospheric Administration - Southwest Fisheries Science Center
1-831-648-5337
NOAA/NMFS/SWFSC Environmental Research Division 1352 Lighthouse Ave.
Pacific Grove
CA
93950
USA
cara.wilson@noaa.gov
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Raw_thumbnail
Imagename_raw
CTDTime
CTDTime_ISO
latitude
longitude
timeStamp
Date
holoNum
holoNum_difs
hemiCells
hemiChains
hemiAggs
hemiCellsINAggs
RhizoCells
smBV
qtrTimeStamp
qtrDate
qtrHCells
qtrHCellsPL
qtrHChains
qtrHAggs
qtrHAggPL
qtrHAggCells
qtrHAggCellsPL
PercHAgg
qtrRCells
qtrRCellsPL
qtrsmBV_SUM_ulL
qtrsmBV_MEAN_ulL
QtrLat
QtrLong
GPCTD
LISST-Holo
theme
None, User defined
file_link
file_name
Date and time
ISO_DateTime_UTC
latitude
longitude
date
sample description
abundance
biovolume
featureType
BCO-DMO Standard Parameters
Sea-Bird Glider Payload CTD
Sequoia LISST Digital Holographic Particle Imaging System
instrument
BCO-DMO Standard Instruments
HoneyBadger2015
service
Deployment Activity
North Pacific Ocean
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Long Duration AUVs as tools to explore Mesoscale feature aggregate interactions (MAGI)
https://osprey.bco-dmo.org/project/505589
Long Duration AUVs as tools to explore Mesoscale feature aggregate interactions (MAGI)
<p><em>NSF award abstract:</em><br />
Remote areas of the ocean are difficult to sample for short-lived or episodic features. This project will use a new sampling platform, the Wave Glider, and provide a continuous presence in the central North Pacific gyre. The six month duration of the mission will allow repeated sampling as well as spatial coverage previously unavailable. This mission will incorporate phytoplankton specific sensors as well as a set of optical sensors that will provide information on distribution, physiology and aggregation of a unique diatom-nitrogen fixing cyanobacterium symbiosis. When completed, this program will have generated the first data sets that follow these diatom blooms over extended periods in the region. Access to this instrumentation was facilitated by the PacX challenge, an international competition to produce high quality research from long-duration autonomous vehicles in the North and South Pacific Ocean. As a result of winning that competition, the principal investigator has been awarded the use of 6 months of the Honey Badger Wave Glider time in 2014. The Wave Glider is a wave-powered surface vessel capable of extended duration missions. In order to maximize this the principal investigator will outfit the glider with advanced sensors to quantify zones of intense diatom activity and aggregation along mesoscale features in the Pacific (Project MAGI: Mesoscale feature-AGregate Interactions).</p>
<p>Note: This project is funded by an NSF RAPID award.</p>
<p>
<a href="http://dmoserv3.whoi.edu/data_docs/MAGI/crew_pics/MAGI_crew.jpg" target="_blank"><img alt="Honey Badger Team" src="https://datadocs.bco-dmo.org/d3/data_docs/MAGI/crew_pics/thumbs/MAGI_crew.jpg" style="height:387px; width:600px" /></a><br />
The Honey Badger Team, image courtesy of Tracy Villareal</p>
<p><a href="http://dmoserv3.whoi.edu/data_docs/MAGI/crew_pics/P1030457.jpeg" target="_blank"><img alt="" src="https://datadocs.bco-dmo.org/d3/data_docs/MAGI/crew_pics/thumbs/P1030457.jpg" style="height:450px; width:600px" /></a><br />
Honey Badger, image courtesy of Tracy Villareal</p>
MAGI
largerWorkCitation
project
eng; USA
oceans
North Pacific Ocean
-156.0326
-144.84739
19.99956
29.46362
2015-06-01
2015-10-30
Eastern N. Pacific central gyre
0
BCO-DMO catalogue of parameters from Holographic images from LISST-Holo system while deployed on the AUV Honey Badger (Wave Glider) during a deployment in the North Pacific gyre in 2015 (MAGI project)
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/719089.rdf
Name: Raw_thumbnail
Units: unitless
Description: <p>Reduced size image thumbnail (.jpg) of the raw holographic image for display purposes. Formatted as html with a link to larger size thumbnail.</p>
http://lod.bco-dmo.org/id/dataset-parameter/719090.rdf
Name: Imagename_raw
Units: unitless
Description: <p>Image name of the holographic raw .pgm image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719091.rdf
Name: CTDTime
Units: unitless
Description: <p>Timestamp from data recorded from the CTD (UTC) in format yyyy-mm-dd HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/719092.rdf
Name: CTDTime_ISO
Units: unitless
Description: <p>Timestamp from data recorded in the CTD based on the ISO 8601:2004(E) standard in format YYYY-mm-ddTHH:MMZ (UTC)</p>
http://lod.bco-dmo.org/id/dataset-parameter/719093.rdf
Name: latitude
Units: decimal degrees
Description: <p>Degrees North as recorded from the CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/719094.rdf
Name: longitude
Units: decimal degrees
Description: <p>Degrees East as recorded from the CTD</p>
http://lod.bco-dmo.org/id/dataset-parameter/719095.rdf
Name: timeStamp
Units: unitless
Description: <p>Timestamp for data recorded from the LISST-Holo in UTC. Format yyyy-mm-dd HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/719096.rdf
Name: Date
Units: unitless
Description: <p>Date in format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/719097.rdf
Name: holoNum
Units: unitless
Description: <p>Number assigned to images taken by the LISST-Holo by the LISST-Holo</p>
http://lod.bco-dmo.org/id/dataset-parameter/719098.rdf
Name: holoNum_difs
Units: unitless
Description: <p>To track the numbering of the images. Values greater than 1 indicates a skip in numbering. Dispite the missed number there are still 15 holos/burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719099.rdf
Name: hemiCells
Units: individuals per image
Description: <p>Number of Hemiaulus cells identified in the holo image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719100.rdf
Name: hemiChains
Units: individuals per image
Description: <p>Number of chains of Hemiaulus cells identified in the holo image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719101.rdf
Name: hemiAggs
Units: individuals per image
Description: <p>Number of Hemiaulus Aggregates identified in the holo image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719102.rdf
Name: hemiCellsINAggs
Units: individuals per image
Description: <p>Number of Hemiaulus cells in Aggregate form identified in the holo image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719103.rdf
Name: RhizoCells
Units: individuals per image
Description: <p>Number of Rhizosolenia cells identified in the holo image</p>
http://lod.bco-dmo.org/id/dataset-parameter/719104.rdf
Name: smBV
Units: microliters per liter (um/L)
Description: <p>The biovolume from particles with an equvalent spherical diameter between 11.094-58.1 microns as calculated by the Holo_Batch software. "na" means the BV was due to non-phytoplankton particles (bubbles; large zooplankton; hologram errors)</p>
http://lod.bco-dmo.org/id/dataset-parameter/719105.rdf
Name: qtrTimeStamp
Units: unitless
Description: <p>Average Timestamp for the 15 holos (burst) taken 4 times a day. Format yyyy-mm-dd HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/719106.rdf
Name: qtrDate
Units: unitless
Description: <p>The average Date for the 15 holos (burst) taken 4 times a day. Format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/719107.rdf
Name: qtrHCells
Units: individuals per burst
Description: <p>The sum of the Hemiaulus cells in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719108.rdf
Name: qtrHCellsPL
Units: cells per Liter
Description: <p>The calculated Hemiaulus cells per Liter in each burst. Calculation: (Average Hemiaulus cells in a burst) * 538</p>
http://lod.bco-dmo.org/id/dataset-parameter/719109.rdf
Name: qtrHChains
Units: individuals per burst
Description: <p>Sum of Hemiaulus chains in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719110.rdf
Name: qtrHAggs
Units: individuals per burst
Description: <p>Sum of Hemiaulus Aggregates in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719111.rdf
Name: qtrHAggPL
Units: individuals per burst
Description: <p>Calculated number of Hemiaulus Aggregates per Liter in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719112.rdf
Name: qtrHAggCells
Units: individuals per burst
Description: <p>Sum of Hemiaulus cells in aggregated form in each burst.</p>
http://lod.bco-dmo.org/id/dataset-parameter/719113.rdf
Name: qtrHAggCellsPL
Units: individuals per burst
Description: <p>Calculated number of Hemiaulus cells in aggregate form per Liter in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719114.rdf
Name: PercHAgg
Units: percent
Description: <p>Percent of Hemiaulus cells in Aggregate form for each burst. (Total Hemiaulus cells in Aggregate form per Liter) / (Total Hemiaulus cells per Liter)</p>
http://lod.bco-dmo.org/id/dataset-parameter/719115.rdf
Name: qtrRCells
Units: individuals per burst
Description: <p>Sum of Rhizosolenia cells in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719116.rdf
Name: qtrRCellsPL
Units: cells per Liter
Description: <p>Calculated number of Rhizosolenia cells per Liter in each burst. Calculation: (Average Rhizonsolenia cells in a burst) * 538</p>
http://lod.bco-dmo.org/id/dataset-parameter/719117.rdf
Name: qtrsmBV_SUM_ulL
Units: microliters per liter (um/L)
Description: <p>The sum of the smBV biovolume in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719118.rdf
Name: qtrsmBV_MEAN_ulL
Units: microliters per liter (um/L)
Description: <p>The average smBV biovolume in each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719119.rdf
Name: QtrLat
Units: decimal degrees
Description: <p>Average Latitude of the Honey Badger's position for each burst</p>
http://lod.bco-dmo.org/id/dataset-parameter/719120.rdf
Name: QtrLong
Units: decimal degrees
Description: <p>Average Longitude of the Honey Badger's position for each burst</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
3529136
https://datadocs.bco-dmo.org/file/LAAGO7Vtm4rZ0p/holo.csv
holo.csv
Primary data file for dataset ID 718403
download
12256385706
https://datadocs.bco-dmo.org/file/8XB0xvMuYp2MM4/RAW.zip
RAW Holographic Images
Raw holograms stored in .pgm format, which is a lossless compression format (see Methodology).
OpenSeeIt (http://openseeit.sourceforge.net/) is a free viewer for pgm files.
download
https://osprey.bco-dmo.org/dataset/718403/data/download
download
onLine
dataset
<p>The LISST-Holo Submersible Digital Holographic Camera from&nbsp;Sequoia Scientific, Inc. was mounted on in a tow fish deployed on a 10 m tether behind the sub-body of the AUV Honey Badger.&nbsp;Holographic images were acquired in bursts every 6 hours.&nbsp; During each burst, 15 images&nbsp;were taken in 5 seconds.</p>
<p>The software "Batch-Holo" was used to generate the biovolume from particles with an equivalent spherical diameter of 11.094-58.1 microns.&nbsp; See "Parameters" section for more details.</p>
<p>Hemiaulus and Rhizosolenia cells were identified by hand. Each image was viewed using the "Holo_Detail" software and any Hemiaulus or Rhizosolenia cells were counted.</p>
<p>The manual and specifications for the LISST-Holo system, and software used in this dataset are available on the instrument page.&nbsp; The software can be obtained from the&nbsp;Sequoia Scientific, Inc.&nbsp;<a href="https://www.sequoiasci.com/product/lisst-holo/" target="_blank">LISST-Holo&nbsp;page</a>.</p>
<p>The calculation of cells per liter was done using the following the following formula:</p>
<p><img alt="formula" src="https://datadocs.bco-dmo.org/d3/data_docs/MAGI/LISST_Holo/formula.png" style="height:154px; width:505px" /></p>
Specified by the Principal Investigator(s)
Data version 2018-01-05 replaces version 2017-10-31. The new version includes updated calculations of cells per liter. The previous version used a multiplication factor of 602 while the new version uses 538 (see Methods & Sampling section).
BCO-DMO Data Manager Processing Notes for version 2017-10-31:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* 406 values of #DIV/0! caused by zero division removed. They empty cells display as "nd" for "no data" in the served dataset.
* added CTDTime_ISO from CTD timestamp column. The CTDTime_ISO is in format yyyy-mm-ddTHH:MMZ.
* latitude,longitude,QtrLat,QtrLon rounded to 5 decimal places
* added imagename column based on the deployment number "004" and the holo image number (with 4 place 0 padding)
* added embedded <img> with link to a thumbnail .jpg of each holographic image. Note, the thumbnails are not holographic images themselves, and are only useful for display purposes.
BCO-DMO Data Manager Processing Notes for version 2018-01-05:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* 406 values of #DIV/0! caused by zero division removed. They empty cells display as "nd" for "no data" in the served dataset.
* added CTDTime_ISO from CTD timestamp column. The CTDTime_ISO is in format yyyy-mm-ddTHH:MMZ.
* latitude,longitude,QtrLat,QtrLon rounded to 5 decimal places
* added imagename column based on the deployment number "004" and the holo image number (with 4 place 0 padding)
* added embedded <img> with link to a thumbnail .jpg of each holographic image. Note, the thumbnails are not holographic images themselves, and are only useful for display purposes.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
GPCTD
GPCTD
PI Supplied Instrument Name: GPCTD Instrument Name: Sea-Bird Glider Payload CTD Instrument Short Name:GPCTD Instrument Description: The GPCTD is a modular instrument for autonomous gliders. For more information see: http://www.seabird.com/glider-payload-ctd
LISST-Holo
LISST-Holo
PI Supplied Instrument Name: LISST-Holo PI Supplied Instrument Description:LISST-Holo Submersible Digital Holographic Camera from Sequoia Scientific, Inc.
Specs and manual for the LISST-Holo used in this dataset:
LISST-Holo specs (PDF)
LISST-HOLO-manual-v3.0 (PDF) Instrument Name: Sequoia LISST Digital Holographic Particle Imaging System Instrument Short Name:LISST-Holo Instrument Description: Submersible Digital Holographic Particle Imaging System for measurement of large, complex flocs and biological particles. Also used for investigation of frazil ice formation and in-situ measurements of falling snow flakes. A laser beam traverses the optical path of the camera, overfilling a CCD array, creating a hologram.
Deployment: HoneyBadger2015
HoneyBadger2015
AUV Honey Badger
AUV Honey Badger
glider
AUV Honey Badger
AUV Honey Badger
glider