http://lod.bco-dmo.org/id/dataset/932236
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
2024-07-11
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
ZooSCAN images of zooplankton collected with MOCNESS tows during six R/V Atlantic Explorer cruises in the northwest Atlantic (Sargasso Sea) from 2021 to 2023
2024-07-11
publication
2024-07-11
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-09-27
publication
https://doi.org/10.26008/1912/bco-dmo.932236.1
Amy Elizabeth Maas
Bermuda Institute of Ocean Sciences
principalInvestigator
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
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: Maas, A., Blanco-Bercial, L. (2024) ZooSCAN images of zooplankton collected with MOCNESS tows during six R/V Atlantic Explorer cruises in the northwest Atlantic (Sargasso Sea) from 2021 to 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-11 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.932236.1 [access date]
Methods and Sampling: <p>One pair of 1m<sup>2</sup> MOCNESS (Multiple Open Closing Nets with Environmental Sensor System) tows were performed during each cruise- one during the day, and one at night (MOCNESS, Wiebe et al, 1985). Nets with 150um mesh were used to better capture the smaller midwater zooplankton community in the region. Eight nets were fired in sequence along the upcast to capture spatially discrete zooplankton samples between 600m and the surface. While nets one, two, and three consistently targeted depths of 600-500m, 500m-400m, and 400-300m, depths for nets four through eight varied based on hydrographic features including the thermocline, deep chlorophyll maximum, and oxygen minimum zone (Maas et al, 2014, Steinberg et al, 2008).&nbsp; Once onboard, samples were split in two using a Motoda splitter (Motoda, 1959)&nbsp; with half preserved with sodium tetraborate buffered 4% formalin in seawater to be scanned with a ZooSCAN&nbsp;(Gorsky et al, 2010) and half placed in 95% undenatured ethanol for metabarcoding.&nbsp;</p>
<p>A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at either 4,800 dpi or 2,400 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012 as detailed in Maas et al. 2021). The change in resolution partway through the project was a result of recommendations from Hydroptic and loss of software support for 4800dpi imaging. In order to better represent all size classes in the images, the original sample was divided into three size categories. All individuals larger than 2 cm were selected by eye and scanned separately from all the others (fraction "d1"). The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions were individually scanned ("d2" &gt;1000um, "d3" 153-1000um). From these smaller size fractions, at least 1500 particles were scanned after subsampling using a Motoda splitter (Motoda, 1959), requiring generation of two separate scans for both size classes. This resulted in a total of five images per net.</p>
<p><strong>Image names:</strong></p>
<p>Image names include:<br />
cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _raw_1.tif</p>
<p>Multiple images of the same size fraction were sometimes taken to obtain a sufficient number of particles. These replicates are named a or b. If there is no replicate they don’t have a letter in the image name. An a and b scan were always done for size classes d2 and d3.&nbsp; This was important because the split size is for the sum of a+b (e.g. if a is ¼ and b is ¼, the acq_sub_part will be 0.5).</p>
<p><strong>Example of image names:</strong></p>
<p>ae2112_m22_n4_d3_a_raw_1.tif&nbsp; [a replicate]<br />
ae2112_m22_n4_d3_b_raw_1.tif&nbsp;&nbsp;[b replicate]<br />
ae2204_m27_n5_d1_raw_1.tif&nbsp; &nbsp; &nbsp;&nbsp;[no&nbsp;replicate]</p>
<p>Related Datasets may contain the "object_id" (the particle/organism id) which is constructed the same way as the image name except it as an additional _#&nbsp;at the end.&nbsp; This additional number in the object_id is added by the ZooProcess software (Hydroptic, 2016).<br />
e.g.<br />
object_id:&nbsp; &nbsp; &nbsp; &nbsp;ae1614_m3_n1_d2_a_1_100<br />
image_name: ae1614_m3_n1_d2_a_1.tif</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023621 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023621
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-2023372 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=2023372
completed
Amy Elizabeth Maas
Bermuda Institute of Ocean Sciences
508-289-2462
17 Biological Station Ferry Reach
St.George's GE 01
Bermuda
amaas4@asu.edu
pointOfContact
Leocadio Blanco-Bercial
Bermuda Institute of Ocean Sciences
leocadio@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
MOCNESS (1m2 mouth size)
ZooSCAN ver. 4
theme
None, User defined
MOCNESS1
ZooSCAN
instrument
BCO-DMO Standard Instruments
AE2112
AE2124
AE2204
AE2214
AE2224
AE2306
service
Deployment Activity
Bermuda
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.
Collaborative Research: Zooplankton mediation of particle formation in the Sargasso Sea
https://osprey.bco-dmo.org/project/816744
Collaborative Research: Zooplankton mediation of particle formation in the Sargasso Sea
<p><em>NSF Award Abstract:</em><br />
The purpose of this collaborative project is to advance understanding of the role of marine planktonic animals (or zooplankton) in the biological pump, or transport of carbon from surface to deeper ocean waters. This movement of carbon from surface to deep ocean water can ultimately affect carbon dioxide in the atmosphere, with implications for global climate. Many marine zooplankton, including species of copepods and krill, play a direct role in the biological pump both because they are abundant and because they can migrate from surface waters at night, where they feed, to depths of more than 500 m at night. At the same time, some organisms called flux feeders will remain at depth and do not migrate. Instead, they rely on particles produced by other zooplankton feeding in surface waters. In this project, the investigators are focusing on populations of flux feeders in the deeper ocean waters of the Sargasso Sea. They are leveraging an ongoing long-term research program, conducting field collections using specialized nets and particle traps, as well lab experiments, as a way to understand how these organisms modify the particles around them. This project is supporting a postdoctoral scientist and providing research experiences for undergraduates at two institutions. An education specialist is creating lesson plans for an award-winning Ask-A-Biologist website, designed for public and K-12 audiences. Images of zooplankton will be disseminated to the public and scientific community via EcoTaxa (a web platform devoted to plankton biodiversity, with images and taxonomic annotation) and physical samples will be archived as part of a teaching library.</p>
<p>The oceanic biological carbon pump refers to the export of dissolved and particulate organic carbon to the deep ocean, and it is a significant driver of atmospheric carbon uptake by the oceans. Evidence from long-term research carried out at the Bermuda Atlantic Time-series Study (BATS) site suggests that the spectrum of particles collected by gel-traps below the euphotic zone changes drastically below 150 m, which is attributed to resident populations of zooplankton that feed on vertically migrating zooplankton as well as sinking particles. The goals of this study are to investigate the role of different zooplankton taxa on both particle aggregate formation and in particle transformation, and to compare and characterize the particles generated by the zooplankton communities with those collected by particle traps. The investigators are combining field collections with experiments onboard ship and in environmental chambers. They are collecting samples over two years, with three cruises a year to capture distinct seasons. They are assessing high-resolution vertical distribution of zooplankton in the upper 600 m using Multiple Opening-Closing Net and Environmental Sensing System (MOCNESS) tows during day- and night-time, to distinguish diel vertical migrators from resident populations and to quantify contributions to particulate organic carbon flux via fecal pellet production. On each cruise, sinking particles are being collected using gel trap tubes attached to the particle traps deployed monthly at BATS. In addition, roller tank experiments are determining how individual zooplankton mediate aggregate formation. Particle types and fecal pellets are being characterized using image analysis and DNA-based analysis of microbial communities. Finally, ongoing data collection from the long-term BATS program is providing invaluable environmental context and will ensure results from this study contribute to ongoing community efforts to observe and predict the fate of carbon in our global system.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Zooplankton Mediation
largerWorkCitation
project
eng; USA
oceans
Bermuda
-64.342467
-64.148983
31.509833
31.679467
2021-07-14
2023-03-24
Sargasso Sea/BATS area
0
BCO-DMO catalogue of parameters from ZooSCAN images of zooplankton collected with MOCNESS tows during six R/V Atlantic Explorer cruises in the northwest Atlantic (Sargasso Sea) from 2021 to 2023
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
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
25781053316
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/5c98ceeb-03c1-4ced-acb1-ce254e2f998c/content
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25814364125
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8a8ca147-c9d7-4e61-980e-344722e1782a/content
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25850105271
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fa32f8f2-0629-42b7-a782-d1df19205e43/content
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25839119292
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/3bc1a9d7-4cfb-43f8-9623-1a4652e83696/content
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25841570105
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/f99cfe75-5555-4325-91a0-df6924e11092/content
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25815493988
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/285a9c7b-2297-4e5b-88bd-111c13dc6c55/content
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https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/93e28875-3fdd-45a3-8d54-d352f51c9747/content
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25850504632
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/116e5cc5-2813-479f-a051-fb1d0fd081ed/content
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25726240150
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/afe8b3cd-3b32-42dc-a735-609d625e7095/content
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25755789411
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/57556831-57bf-4661-a6ce-aca0b1355f93/content
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68572320204
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/fd18f84f-a8a5-4bdc-902d-f1c4ea3076ce/content
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69562269295
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/a74cd7f1-5d3c-4db2-bf11-87a5dba2e148/content
download
https://doi.org/10.26008/1912/bco-dmo.932236.1
download
onLine
dataset
<p>One pair of 1m<sup>2</sup> MOCNESS (Multiple Open Closing Nets with Environmental Sensor System) tows were performed during each cruise- one during the day, and one at night (MOCNESS, Wiebe et al, 1985). Nets with 150um mesh were used to better capture the smaller midwater zooplankton community in the region. Eight nets were fired in sequence along the upcast to capture spatially discrete zooplankton samples between 600m and the surface. While nets one, two, and three consistently targeted depths of 600-500m, 500m-400m, and 400-300m, depths for nets four through eight varied based on hydrographic features including the thermocline, deep chlorophyll maximum, and oxygen minimum zone (Maas et al, 2014, Steinberg et al, 2008).&nbsp; Once onboard, samples were split in two using a Motoda splitter (Motoda, 1959)&nbsp; with half preserved with sodium tetraborate buffered 4% formalin in seawater to be scanned with a ZooSCAN&nbsp;(Gorsky et al, 2010) and half placed in 95% undenatured ethanol for metabarcoding.&nbsp;</p>
<p>A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at either 4,800 dpi or 2,400 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012 as detailed in Maas et al. 2021). The change in resolution partway through the project was a result of recommendations from Hydroptic and loss of software support for 4800dpi imaging. In order to better represent all size classes in the images, the original sample was divided into three size categories. All individuals larger than 2 cm were selected by eye and scanned separately from all the others (fraction "d1"). The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions were individually scanned ("d2" &gt;1000um, "d3" 153-1000um). From these smaller size fractions, at least 1500 particles were scanned after subsampling using a Motoda splitter (Motoda, 1959), requiring generation of two separate scans for both size classes. This resulted in a total of five images per net.</p>
<p><strong>Image names:</strong></p>
<p>Image names include:<br />
cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _raw_1.tif</p>
<p>Multiple images of the same size fraction were sometimes taken to obtain a sufficient number of particles. These replicates are named a or b. If there is no replicate they don’t have a letter in the image name. An a and b scan were always done for size classes d2 and d3.&nbsp; This was important because the split size is for the sum of a+b (e.g. if a is ¼ and b is ¼, the acq_sub_part will be 0.5).</p>
<p><strong>Example of image names:</strong></p>
<p>ae2112_m22_n4_d3_a_raw_1.tif&nbsp; [a replicate]<br />
ae2112_m22_n4_d3_b_raw_1.tif&nbsp;&nbsp;[b replicate]<br />
ae2204_m27_n5_d1_raw_1.tif&nbsp; &nbsp; &nbsp;&nbsp;[no&nbsp;replicate]</p>
<p>Related Datasets may contain the "object_id" (the particle/organism id) which is constructed the same way as the image name except it as an additional _#&nbsp;at the end.&nbsp; This additional number in the object_id is added by the ZooProcess software (Hydroptic, 2016).<br />
e.g.<br />
object_id:&nbsp; &nbsp; &nbsp; &nbsp;ae1614_m3_n1_d2_a_1_100<br />
image_name: ae1614_m3_n1_d2_a_1.tif</p>
Specified by the Principal Investigator(s)
<p>Scans were processed using&nbsp;ZooProcess&nbsp;(version 8.22, ImageJ macro suite). The "Convert and process from RAW" function was used to separate particles into individual vignettes and generate a suite of measurements for each particle. "Doubles" (vignettes containing more than one particle) were manually separated in the software and reprocessed.&nbsp;</p>
<p>Processed scans and their corresponding metadata were then uploaded to Ecotaxa (Picheral et al,&nbsp;https://ecotaxa.obs-vlfr.fr/), where a training set was created using manually classified images from this project as well as existing validated images from other projects in the Sargasso Sea. Classification categories were chosen based on taxon of interest, identification level in previous projects, and known limitations of the software. Generally, broader level taxonomic groups are used. Identification of all particles was predicted, then manually validated.&nbsp;</p>
Specified by the Principal Investigator(s)
Version 1:
* All raw scan images were bundled into zip files named by <cruise_id>_<mocness_id>.zip
* The filesize and md5 checksum was added to the image metadata table.
** After images were transferred to BCO-DMO, a file inventory was made containing the filename, filesize in bytes, and checksum (md5sum). This file inventory table was joined with the provided metadata table to verify the file collection is complete without any missing files.
* an additional supplemental file was added containing metadata for each file (including zips) which includes file access links to aid in programmatic download of all image bundles in the dataset once the dataset is released.
* two imagenames in the metadata table were changed to match the actual filenames. The data submitter was consulted and advised this was the correct course of action. The 3 was omitted in d3 of the imagename.
image_name ae2124_m24_n1_d_a_raw_1.tif -> ae2124_m24_n1_d3_a_raw_1.tif
image_name ae2124_m24_n1_d_b_raw_1.tif -> ae2124_m24_n1_d3_b_raw_1.tif
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
MOCNESS (1m2 mouth size)
MOCNESS (1m2 mouth size)
PI Supplied Instrument Name: MOCNESS (1m2 mouth size) PI Supplied Instrument 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). The MOCNESS used in this experiment is a 1m2 (mouth size) rigged with nine 150um mesh nets. One is flown open on the downcast to balance the net (Net 0- contents preserved but not analyzed), and the other eight (Net 1-8) are triggered on the upcast at desired depths. This particular MOCNESS was originally manufactured by Biological Environmental Sensor Systems (BESS), but was refit with new electronics from SIO/STS in 2017 (Net Interface Unit, Net Angle Sensor) to allow it to interface with Seabird instruments (SBE9Plus CTD, SBE3S Temperature, SBE4C Conductivity, SBE11 Deck Box). Instrument Name: MOCNESS1 Instrument Short Name:MOC1 Instrument Description: The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/
ZooSCAN ver. 4
ZooSCAN ver. 4
PI Supplied Instrument Name: ZooSCAN ver. 4 PI Supplied Instrument Description:A representative subsample of the formalin-preserved zooplankton community from each net were imaged using a ZooSCAN ver. 4 at either 4,800 dpi or 2,400 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012 as detailed in Maas et al. 2021). Instrument Name: ZooSCAN Instrument Short Name: Instrument 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.
Cruise: AE2112
AE2112
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2112
Rodney J. Johnson
Cruise: AE2124
AE2124
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2124
Paul J. Lethaby
Cruise: AE2204
AE2204
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2204
Zachary Anderson
Cruise: AE2214
AE2214
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2214
Zachary Anderson
Cruise: AE2224
AE2224
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2224
Rodney J. Johnson
Cruise: AE2306
AE2306
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE2306
Claire Medley
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel