Dataset: 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

Release Date:2025-04-01Final no updates expectedDOI: 10.26008/1912/bco-dmo.932236.1Version 1 (2024-07-11)Dataset Type:Cruise Results

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

Co-Principal Investigator: Leocadio Blanco-Bercial (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: Zooplankton mediation of particle formation in the Sargasso Sea (Zooplankton Mediation)


Abstract

This dataset consists of the raw ZooSCAN images taken of zooplankton caught in the upper 600m using Multiple Opening-Closing Net and Environmental Sensing System (MOCNESS) tows during day- and night-time. These samples were collected over two years, with three cruises a year to capture distinct seasons. The goal of this data was to assess high-resolution vertical distribution of zooplankton in order to distinguish diel vertical migrators from resident populations and to quantify contributions to...

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One pair of 1m2 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).  Once onboard, samples were split in two using a Motoda splitter (Motoda, 1959)  with half preserved with sodium tetraborate buffered 4% formalin in seawater to be scanned with a ZooSCAN (Gorsky et al, 2010) and half placed in 95% undenatured ethanol for metabarcoding. 

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" >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.

Image names:

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

ae2112_m22_n4_d3_a_raw_1.tif  [a replicate]
ae2112_m22_n4_d3_b_raw_1.tif  [b replicate]
ae2204_m27_n5_d1_raw_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


Related Datasets

IsRelatedTo

Dataset: ZooProcess and Ecotaxa Output for Zooplankton Mediated Aggregates
Relationship Description: Data derived from analyzing these Zooscan images.
Blanco-Bercial, L., Maas, A., Gossner, H. (2024) ZooProcess and Ecotaxa output from ZooSCANs of zooplankton collected with MOCNESS tows during six R/V Atlantic Explorer cruises from 2021 to 2023. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2024-07-08 doi:10.26008/1912/bco-dmo.931883.1

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