Dataset: Wave Glider - Holographic Images

Name: 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)
Published: 2018-01-05
Keywords: oceans

Cite This Dataset

Spatial Extent: N:29.46362 E:-144.84739 S:19.99956 W:-156.0326

Temporal Extent: 2015-06-01 - 2015-10-30

Project:

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

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)

Version:

Version Date:

2018-01-05

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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)

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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

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

BCO-DMO Processing

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.

Data Files

File
holo.csv (Comma Separated Values (.csv), 3.37 MB) MD5:b77f695d31ede318b8f224a5e5766ff9 Primary data file for dataset ID 718403
RAW Holographic Images filename: RAW.zip (ZIP Archive (ZIP), 11.41 GB) MD5:40ae1c9f17cac2d41f9afb5a4125b91c 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.

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
HoneyBadger2015		2015-10-31	AUV Honey Badger		data info

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

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

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

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Dataset: Wave Glider - Holographic Images