Dataset: Wave Glider - Holographic Images
Deployment: HoneyBadger2015

Holographic Images from LISST-Holo system

Principal Investigator:

Tracy A. Villareal (University of Texas at Austin, UT Austin)

Co-Principal Investigator:

Dr Cara Wilson (National Oceanic and Atmospheric Administration - Southwest Fisheries Science Center, NOAA SWFSC ERD)

Contact:

Tracy A. Villareal (University of Texas at Austin, UT Austin)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Long Duration AUVs as tools to explore Mesoscale feature aggregate interactions (MAGI) (MAGI)

Data URL:

https://www.bco-dmo.org/dataset-deployment/718410/data

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Description

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 Image metadata, cell counts (e.g. number of Hemiaulus cells in aggregate form), and all raw holographic images are in the RAW.zip (12GB) file.

Software for further processing the raw holographic images provided here is available at the Sequoia Scientific, Inc. LISST-Holo page The following montage and depth images can be created for every raw image using the LISST-Holo software.

holographic images

Methods & Sampling

Dataset acquisition description

The LISST-Holo Submersible Digital Holographic Camera from 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. Holographic images were acquired in bursts every 6 hours. During each burst, 15 images were taken in 5 seconds.

The software "Batch-Holo" was used to generate the biovolume from particles with an equivalent spherical diameter of 11.094-58.1 microns. See "Parameters" section for more details.

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.

The manual and specifications for the LISST-Holo system, and software used in this dataset are available on the instrument page. The software can be obtained from the Sequoia Scientific, Inc. LISST-Holo page.

The calculation of cells per liter was done using the following the following formula:

formula

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-1430048	NSF Division of Ocean Sciences

Instruments

Sea-Bird Glider Payload CTD

Supplied Name: GPCTD

Supplied Description:

Instrument Type

Generic Name: Sea-Bird Glider Payload CTD

Acronym: GPCTD

Generic Description:

The GPCTD is a modular instrument for autonomous gliders. For more information see: http://www.seabird.com/glider-payload-ctd

Sequoia LISST Digital Holographic Particle Imaging System

Supplied Name: LISST-Holo

Supplied 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 Type

Generic Name: Sequoia LISST Digital Holographic Particle Imaging System

Acronym: LISST-Holo

Generic 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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Raw_thumbnail	Reduced size image thumbnail (.jpg) of the raw holographic image for display purposes. Formatted as html with a link to larger size thumbnail.	unitless	file_link
Imagename_raw	Image name of the holographic raw .pgm image	unitless	file_name
CTDTime	Timestamp from data recorded from the CTD (UTC) in format yyyy-mm-dd HH:MM	unitless	DateTime
CTDTime_ISO	Timestamp from data recorded in the CTD based on the ISO 8601:2004(E) standard in format YYYY-mm-ddTHH:MMZ (UTC)	unitless	ISO_DateTime_UTC
latitude	Degrees North as recorded from the CTD	decimal degrees	lat
longitude	Degrees East as recorded from the CTD	decimal degrees	lon
timeStamp	Timestamp for data recorded from the LISST-Holo in UTC. Format yyyy-mm-dd HH:MM	unitless	DateTime
Date	Date in format yyyy-mm-dd	unitless	date
holoNum	Number assigned to images taken by the LISST-Holo by the LISST-Holo	unitless	sample_descrip
holoNum_difs	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	unitless	sample_descrip
hemiCells	Number of Hemiaulus cells identified in the holo image	individuals per image	abundance
hemiChains	Number of chains of Hemiaulus cells identified in the holo image	individuals per image	abundance
hemiAggs	Number of Hemiaulus Aggregates identified in the holo image	individuals per image	abundance
hemiCellsINAggs	Number of Hemiaulus cells in Aggregate form identified in the holo image	individuals per image	abundance
RhizoCells	Number of Rhizosolenia cells identified in the holo image	individuals per image	abundance
smBV	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)	microliters per liter (um/L)	biovolume
qtrTimeStamp	Average Timestamp for the 15 holos (burst) taken 4 times a day. Format yyyy-mm-dd HH:MM	unitless	DateTime
qtrDate	The average Date for the 15 holos (burst) taken 4 times a day. Format yyyy-mm-dd	unitless	date
qtrHCells	The sum of the Hemiaulus cells in each burst	individuals per burst	abundance
qtrHCellsPL	The calculated Hemiaulus cells per Liter in each burst. Calculation: (Average Hemiaulus cells in a burst) * 538	cells per Liter	abundance
qtrHChains	Sum of Hemiaulus chains in each burst	individuals per burst	abundance
qtrHAggs	Sum of Hemiaulus Aggregates in each burst	individuals per burst	abundance
qtrHAggPL	Calculated number of Hemiaulus Aggregates per Liter in each burst	individuals per burst	abundance
qtrHAggCells	Sum of Hemiaulus cells in aggregated form in each burst.	individuals per burst	abundance
qtrHAggCellsPL	Calculated number of Hemiaulus cells in aggregate form per Liter in each burst	individuals per burst	abundance
PercHAgg	Percent of Hemiaulus cells in Aggregate form for each burst. (Total Hemiaulus cells in Aggregate form per Liter) / (Total Hemiaulus cells per Liter)	percent	DateTime
qtrRCells	Sum of Rhizosolenia cells in each burst	individuals per burst	abundance
qtrRCellsPL	Calculated number of Rhizosolenia cells per Liter in each burst. Calculation: (Average Rhizonsolenia cells in a burst) * 538	cells per Liter	sample_descrip
qtrsmBV_SUM_ulL	The sum of the smBV biovolume in each burst	microliters per liter (um/L)	biovolume
qtrsmBV_MEAN_ulL	The average smBV biovolume in each burst	microliters per liter (um/L)	biovolume
QtrLat	Average Latitude of the Honey Badger's position for each burst	decimal degrees	lat
QtrLong	Average Longitude of the Honey Badger's position for each burst	decimal degrees	lon

Database

Contribute Data

Dataset: Wave Glider - Holographic Images
Deployment: HoneyBadger2015

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Wave Glider - Holographic ImagesDeployment: HoneyBadger2015

Dataset acquisition description

Dataset Processing Description

Dataset: Wave Glider - Holographic Images
Deployment: HoneyBadger2015