Dataset: ZooSCAN biomass:biovolume BATS

Name: ZooSCAN biovolume to biomass from imaged zooplankton collected during MOCNESS tows during various R/V Atlantic Explorer cruises and small boat deployments in the Sargasso Sea betwen 2016 to 2019
Published: 2021-06-17
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.854077.1

Spatial Extent: N:32.3065 E:-64.05553 S:31.37146333 W:-64.7935

Temporal Extent: 2016-07-11 - 2019-11-28

Project:

Bermuda Institute of Ocean Sciences Simons Collaboration on Ocean Processes and Ecology (BIOSSCOPE)

Collaborative Research: Diel physiological rhythms in a tropical oceanic copepod (Zooplankton Diel Rhythm)

Quantifying the drivers of midwater zooplankton community structure (Zooplankton Gradients)

Principal Investigator:

Leocadio Blanco-Bercial (Bermuda Institute of Ocean Sciences, BIOS)

Co-Principal Investigator:

Amy Maas (Bermuda Institute of Ocean Sciences, BIOS)

Technician:

Hannah Gossner (Bermuda Institute of Ocean Sciences, BIOS)

BCO-DMO Data Manager:

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

Version:

Version Date:

2021-06-17

Restricted:

Validated:

Yes

Current State:

Final no updates expected

ZooSCAN biovolume to biomass from imaged zooplankton collected during MOCNESS tows during various R/V Atlantic Explorer cruises and small boat deployments in the Sargasso Sea betwen 2016 to 2019

Abstract:

ZooSCAN biovolume to biomass from the Sargasso Sea including locations in the vicinity of the Bermuda Atlantic Time-series Study (BATS). Samples were collected during MOCNESS tows during R/V Atlantic Explorer cruises between 2016 to 2019 (AE1614, AE1712, AE1830, AE1917, AE1918, AE1931) and a few small boat deployments. These data were published in Maas et al. (2021) as Supplementary Table 1.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-06-17	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.854077.1	2021-11-05

Methods & Sampling

Methodology: Individual zooplankton of a variety of taxa were individually selected from multiple MOCNESS and Reeve net tows. Organisms were picked from both surface and deep nets and across a range of sizes to represent the full range of potential morphologies. They were imaged on a ZooSCAN ver. 3 at 4,800 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012). Raw images were then processed in ZooProcess (Gorsky et al., 2010, Vandromme et al., 2012), resulting in a measurement and metadata file. After imaging each individual organism was weighed wet on a Mettler-Toledo XPR microbalance, dried for 3 days in a drying oven at 60 C, and reweighed.

Sampling and analytical procedures: Most samples (all from the MOCNESS) had been preserved in formalin for between 1 and 4 years. Individuals from the Reeve net had been preserved in ethanol or stored at -80C for 1-2 years. All individuals were imaged in DI water at room temperature.

Object_id and imagenames:

Related Datasets may contain the image name which is constructed the same way as the object_id in this dataset except it does not have the additional _# at the end, and the imagename ends in the .tif extension. This additional number in the object_id is added by the Zooprocess software (Hydroptic, 2016).
e.g.
object_id: ae1614_m3_n1_d2_a_1_100
image_name: ae1614_m3_n1_d2_a_1.tif

Data Processing Description

Zooscan pixel measurements come directly from the ZooProcess pipeline. These were converted to mm based on the dpi conversion factor of mm= 0.005291667(dpi). Biovolume was calculated assuming an ellipsoidal shape where mm^3=4/3pi(minor0.5)^2(major0.5)

BCO-DMO data manager processing notes:
* File BATS_biomass_biovolume.xlsx sheet "Data" imported into the BCO-DMO data system.
* Fields renamed to comply with BCO-DMO naming conventions. See https://www.bco-dmo.org/page/bco-dmo-data-processing-conventions

Data Files

File
zooscan_bats_biovolume.csv (Comma Separated Values (.csv), 107.01 KB) MD5:ee93027778334027043c6c565e2953a8 Primary data file for dataset ID 854077

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1948162
NSF Division of Ocean Sciences	OCE-1829318
Simons Foundation	unknown SCOPE Simons

Deployments

Deployment	Start Date	Platform	Investigator
AE1614	2016-07-09	R/V Atlantic Explorer	Craig A. Carlson (Chief Scientist)	data info
AE1712	2017-07-08	R/V Atlantic Explorer	Craig A. Carlson (Chief Scientist)	data info
AE1830	2018-10-27	R/V Atlantic Explorer	Maureen H. Conte (Chief Scientist)	data info
AE1917	2019-07-14	R/V Atlantic Explorer	Paul J. Lethaby (Chief Scientist)	data info
AE1918	2019-07-25	R/V Atlantic Explorer	Leocadio Blanco-Bercial (Chief Scientist)	data info

Instruments

MOCNESS

Supplied Name: 1m MOCNESS

Supplied Description:

Instrument Type

Generic Name: MOCNESS

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974).(from MOCNESS manual) This designation is used when the specific type of MOCNESS (number and size of nets) was not specified by the contributing investigator.

scale

Supplied Name: Mettler-Toledo XPR microbalance

Supplied Description:

Instrument Type

Generic Name: scale

Acronym: balance

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB13/

Generic Description:

An instrument used to measure weight or mass.

ZooSCAN

Supplied Name: ZooSCAN ver. 3

Supplied Description:

http://www.hydroptic.com/index.php/public/Page/product_item/ZOOSCAN

Instrument Type

Generic Name: ZooSCAN

Generic Description:

Description excerpt from Hydroptic website
http://www.hydroptic.com/index.php/public/Page/product_item/ZOOSCAN

The ZooSCAN (CNRS patent) system makes use of scanner technology with custom lighting and a watertight scanning chamber into which liquid zooplankton samples can be placed. The scanner recovers a high-resolution, digitial image and the sample can be recovered without damage. These digital images can then be investigated by computer processing. While the resolution of the digitized zooplankton images is lower than the image obtained using a binocular microscope this technique has proved to be more than adequate for large sample sets. Identification of species is done by automatic comparison of the image (vignette) of each individual animal in the scanned image with a library data set which may be built by the investigator for each individual survey or imported from a previous survey. The latest machine learning algorithm allows high recognition levels even if we recommend complementary manual sorting to achieve a high number of taxonomic groups.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
object_id	Organismal identification number. Typically cruiseID_mocnessID_net#_taxonomy_image# unless from a Reeve tow	unitless	individual
taxa	broad taxonomic classification	unitless	taxon
object_major	Zooscan pixel measurement of major axis	dpi	image_analysis
object_minor	Zooscan pixel measurement of minor axis	dpi	image_analysis
object_feret	Zooscan pixel measurement of feret diameter. Object maximum feret diameter, i.e., the longest distance between any two points along the object boundary in pixels.	dpi	image_analysis
object_esd	Zooscan pixel measurement of estimated spherical diameter (Object Equivalent Spherical Diameter).	dpi	ESD
object_area_exc	Zooscan pixel measurement of area (Zooscan "Area_exc"). Surface of the object excluding holes in square pixel (=Area*(1-(%area/100)).	dpi^2	image_analysis
object_major_mm	particle major axis	mm	image_analysis
object_minor_mm	particle major axis	mm	image_analysis
object_feret_mm	particle feret length	mm	image_analysis
object_esd_mm	particle estimated spherical diameter	mm	ESD
object_area_mm2	particle area	mm^2	image_analysis
BioVolume	particle biovolume assuming an ellipsoidal shape	mm^3	biovolume
wet_wt	measured wet weight	mg	dry_wgt_globec
dry_wt	measured dry weight	mg	weight

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Database

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Dataset: ZooSCAN biomass:biovolume BATS