Dataset: ZooSCAN images of zooplankton collected during BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study from 2016 to 2018

Name: ZooSCAN images of zooplankton collected during BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study from 2016 to 2018
Published: 2021-10-07
Keywords: oceans

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.853440.1Version 1 (2021-10-07)Dataset Type:Cruise Results

Principal Investigator: Leocadio Blanco-Bercial (Bermuda Institute of Ocean Sciences)

Co-Principal Investigator: Amy Maas (Bermuda Institute of Ocean Sciences)

Technician: Hannah Gossner (Bermuda Institute of Ocean Sciences)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

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

Abstract

ZooSCAN images from BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study (BATS) in July of 2016, 2017, and 2018 as well as October 2018 (eight casts in total, 63 discrete nets). These data were published in Maas et al. (2021).

Cite Dataset

Spatial Extent: N:32.31 E:-64.06 S:31.67 W:-64.79
Temporal Extent: 2016-07-11 - 2018-10-30

217

Views

443

Downloads

These numbers come from web analytics and reflect real user activity on the site. They reliably show dataset usage and are mostly free of bot traffic.

Data File(s)	Type	Description	Action
ZooSCAN_Images_BATS_AE1614.tar.gz (31.83 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1614 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 80 images in .tif format.	ZooSCAN_Images_BATS_AE1614.tar.gz
ZooSCAN_Images_BATS_AE1712.tar.gz (27.60 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1712 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 68 images in .tif format.	ZooSCAN_Images_BATS_AE1712.tar.gz
ZooSCAN_Images_BATS_AE1819.tar.gz (25.94 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1819 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 65 images in .tif format.	ZooSCAN_Images_BATS_AE1819.tar.gz
ZooSCAN_Images_BATS_AE1830.tar.gz (31.88 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1830 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 81 images in .tif format.	ZooSCAN_Images_BATS_AE1830.tar.gz

Supplemental File(s)	Type	Description	Action
image_sample_information.csv (30.56 KB)	Comma Separated Values (.csv)	Image Sample Metadata for ZooSCAN images collected during R/V Atlantic Explorer cruises AE1614, AE1712, AE1819, AE1830 between 2016-2018. Parameters (column name, description, units): image_name,Image name, unitless cruise_id,Cruise identifier, unitless mocness_id,MOCNESS identifier,unitless net_id,Net identifier,unitless size_fraction,Size fraction (e.g. d3). See methodology,unitless r... Show more	image_sample_information.csv View Table

Files

Filename: ZooSCAN_Images_BATS_AE1614.tar.gz (31.83 GB)
Type: GZIP (.gz)

Description:

Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1614 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 80 images in .tif format.

ZooSCAN_Images_BATS_AE1614.tar.gz

Filename: ZooSCAN_Images_BATS_AE1712.tar.gz (27.60 GB)
Type: GZIP (.gz)

Description:

Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1712 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 68 images in .tif format.

ZooSCAN_Images_BATS_AE1712.tar.gz

Filename: ZooSCAN_Images_BATS_AE1819.tar.gz (25.94 GB)
Type: GZIP (.gz)

Description:

Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1819 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 65 images in .tif format.

ZooSCAN_Images_BATS_AE1819.tar.gz

Filename: ZooSCAN_Images_BATS_AE1830.tar.gz (31.88 GB)
Type: GZIP (.gz)

Description:

Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1830 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 81 images in .tif format.

ZooSCAN_Images_BATS_AE1830.tar.gz

Supplemental Files

Filename: image_sample_information.csv (30.56 KB)
Type: Comma Separated Values (.csv)

Description:

Image Sample Metadata for ZooSCAN images collected during R/V Atlantic Explorer cruises AE1614, AE1712, AE1819, AE1830 between 2016-2018. Parameters (column name, description, units): image_name,Image name, unitless cruise_id,Cruise identifier...

image_sample_information.csv View Table

Methodology: To obtain samples, a 1 m Multiple Opening/Closing Net and Environmental Sensing System (MOCNESS; Wiebe et al., 1985) equipped with 150 µm nets was deployed during the mid-day and mid-night on cruises carried out in the vicinity of the Bermuda Atlantic Time-series Study site (BATS) in July of 2016, 2017, and 2018 as well as October 2018 (eight casts in total, 63 discrete nets). The net sampling plan used adaptive profiling, modifying the depth of closure to capture eight distinct ecological zones from surface to 1000 m depth: e.g. the thermocline, deep chl-a maximum (DCM), above the O2 minimum, within the O2 minimum core, and below the O2 minimum (Maas et al., 2014, Steinberg et al., 2008a). The actual tow depths were set on a cruise-by-cruise basis, using CTD profiles to determine the depths of each ecological zone. Upon retrieval, the catch from each of the eight discrete nets were divided into splits. Half were preserved in 95% undenatured ethanol and the remainder preserved in buffered 4% formalin in seawater.

A representative subsample of the zooplankton community from each net were imaged from the formalin-preserved samples, then measured, using a ZooSCAN ver. 3 at 4,800 dpi (following the methods in: Gorsky et al., 2010, Vandromme et al., 2012). 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. The remainder of the sample was sieved through a 1-mm mesh sieve, and both size fractions were individually scanned. 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.

Image names:

Image names include:
cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _1.tif

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. 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).

Example of image names:

ae1830_m13_n4_d3_a_1.tif [a replicate]

ae1830_m13_n4_d3_b_1.tif [a replicate]

ae1830_m13_n5_d1_1.tif [no replicate]

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 _# at the end. 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

Problem report: During the July 2018 cruise the top net of the night cast failed, and consequently images from this net are absent.

Related Datasets

IsRelatedTo

Dataset: ZooSCAN output MOCNESS BATS: M3 to M13
Relationship Description:

ZooScan output for the images in this dataset.

Blanco-Bercial, L., Maas, A., Gossner, H. (2021) ZooSCAN output from of imaged zooplankton collected during BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study from 2016 to 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-10-05 doi:10.26008/1912/bco-dmo.857891.1

Methods

Dataset: http://ecotaxa.obs-vlfr.fr

Picheral M, Colin S, Irisson J-O (2017). EcoTaxa, a tool for the taxonomic classification of images. http://ecotaxa.obs-vlfr.fr

References

Dataset: ZooSCAN biomass:biovolume BATS
Relationship Description:

Biovolume:biomass conversion provides validation for the analysis of the ZooScan images.

Blanco-Bercial, L., Maas, A., Gossner, H. (2021) 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. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-06-17 doi:10.26008/1912/bco-dmo.854077.1

Related Publications

Results

Maas, A. E., Gossner, H., Smith, M. J., & Blanco-Bercial, L. (2021). Use of optical imaging datasets to assess biogeochemical contributions of the mesozooplankton. Journal of Plankton Research, 43(3), 475–491. doi:10.1093/plankt/fbab037

Methods

Gorsky, G., Ohman, M. D., Picheral, M., Gasparini, S., Stemmann, L., Romagnan, J.-B., … Prejger, F. (2010). Digital zooplankton image analysis using the ZooScan integrated system. Journal of Plankton Research, 32(3), 285–303. doi:10.1093/plankt/fbp124

Methods

Maas, A. E., Frazar, S. L., Outram, D. M., Seibel, B. A., & Wishner, K. F. (2014). Fine-scale vertical distribution of macroplankton and micronekton in the Eastern Tropical North Pacific in association with an oxygen minimum zone. Journal of Plankton Research, 36(6), 1557–1575. doi:10.1093/plankt/fbu077

Methods

Motoda, S. (1959) Devices of simple plankton apparatus. Memoirs of the Faculty of Fisheries Hokkaido University, 7, 73-94. Available from http://hdl.handle.net/2115/21829.

Methods

Steinberg, D. K., Cope, J. S., Wilson, S. E., & Kobari, T. (2008). A comparison of mesopelagic mesozooplankton community structure in the subtropical and subarctic North Pacific Ocean. Deep Sea Research Part II: Topical Studies in Oceanography, 55(14-15), 1615–1635. doi:10.1016/j.dsr2.2008.04.025

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Dataset: ZooSCAN images of zooplankton collected during BATS MOCNESS tows during R/V Atlantic Explorer cruises AE1614, AE1712, AE1830, and AE1819 in the vicinity of the Bermuda Atlantic Time-series Study from 2016 to 2018

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.853440.1Version 1 (2021-10-07)Dataset Type:Cruise Results

Principal Investigator: Leocadio Blanco-Bercial (Bermuda Institute of Ocean Sciences)

Co-Principal Investigator: Amy Maas (Bermuda Institute of Ocean Sciences)

Technician: Hannah Gossner (Bermuda Institute of Ocean Sciences)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

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

Abstract

Cite Dataset

Spatial Extent: N:32.31 E:-64.06 S:31.67 W:-64.79
Temporal Extent: 2016-07-11 - 2018-10-30

217

Views

443

Downloads

These numbers come from web analytics and reflect real user activity on the site. They reliably show dataset usage and are mostly free of bot traffic.

Data File(s)	Type	Description	Action
ZooSCAN_Images_BATS_AE1614.tar.gz (31.83 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1614 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 80 images in .tif format.	ZooSCAN_Images_BATS_AE1614.tar.gz
ZooSCAN_Images_BATS_AE1712.tar.gz (27.60 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1712 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 68 images in .tif format.	ZooSCAN_Images_BATS_AE1712.tar.gz
ZooSCAN_Images_BATS_AE1819.tar.gz (25.94 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1819 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 65 images in .tif format.	ZooSCAN_Images_BATS_AE1819.tar.gz
ZooSCAN_Images_BATS_AE1830.tar.gz (31.88 GB)	GZIP (.gz)	Images acquired using the ZooSCAN imaging system during R/V Atlantic Explorer cruise AE1830 in the vicinity of the Bermuda Atlantic Time-series Study (BATS). The tar.gz bundle of compressed files contains 81 images in .tif format.	ZooSCAN_Images_BATS_AE1830.tar.gz

Supplemental File(s)	Type	Description	Action
image_sample_information.csv (30.56 KB)	Comma Separated Values (.csv)	Image Sample Metadata for ZooSCAN images collected during R/V Atlantic Explorer cruises AE1614, AE1712, AE1819, AE1830 between 2016-2018. Parameters (column name, description, units): image_name,Image name, unitless cruise_id,Cruise identifier, unitless mocness_id,MOCNESS identifier,unitless net_id,Net identifier,unitless size_fraction,Size fraction (e.g. d3). See methodology,unitless r... Show more	image_sample_information.csv View Table

Files

Filename: ZooSCAN_Images_BATS_AE1614.tar.gz (31.83 GB)
Type: GZIP (.gz)

Description:

ZooSCAN_Images_BATS_AE1614.tar.gz

Filename: ZooSCAN_Images_BATS_AE1712.tar.gz (27.60 GB)
Type: GZIP (.gz)

Description:

ZooSCAN_Images_BATS_AE1712.tar.gz

Filename: ZooSCAN_Images_BATS_AE1819.tar.gz (25.94 GB)
Type: GZIP (.gz)

Description:

ZooSCAN_Images_BATS_AE1819.tar.gz

Filename: ZooSCAN_Images_BATS_AE1830.tar.gz (31.88 GB)
Type: GZIP (.gz)

Description:

ZooSCAN_Images_BATS_AE1830.tar.gz

Supplemental Files

Filename: image_sample_information.csv (30.56 KB)
Type: Comma Separated Values (.csv)

Description:

image_sample_information.csv View Table

Image names:

Image names include:
cruise#_mocnessID_net#_sizefraction_ and _a|b if a replicate and end in _1.tif

Example of image names:

ae1830_m13_n4_d3_a_1.tif [a replicate]

ae1830_m13_n4_d3_b_1.tif [a replicate]

ae1830_m13_n5_d1_1.tif [no replicate]

Problem report: During the July 2018 cruise the top net of the night cast failed, and consequently images from this net are absent.

Related Datasets

IsRelatedTo

Dataset: ZooSCAN output MOCNESS BATS: M3 to M13
Relationship Description:

ZooScan output for the images in this dataset.

Methods

Dataset: http://ecotaxa.obs-vlfr.fr

Picheral M, Colin S, Irisson J-O (2017). EcoTaxa, a tool for the taxonomic classification of images. http://ecotaxa.obs-vlfr.fr

References

Dataset: ZooSCAN biomass:biovolume BATS
Relationship Description:

Biovolume:biomass conversion provides validation for the analysis of the ZooScan images.

Related Publications

Results

Methods

Motoda, S. (1959) Devices of simple plankton apparatus. Memoirs of the Faculty of Fisheries Hokkaido University, 7, 73-94. Available from http://hdl.handle.net/2115/21829.

Methods