Larval fish distributions in relation to diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28

Consortium for Oil Spill Exposure Pathways in Coastal River-Dominated Ecosystems (CONCORDE)

DOI:
10.7266/B9735RKQ
 
UDI:
R4.x260.000:0129
Last Update:
Oct 15 2020 16:06 UTC
 
Dataset Author(s):
Greer, Adam T., Valerie J. Cruz, Carla Culpepper, and Frank J. Hernandez
Point of Contact:
Greer, Adam
University of Georgia / Skidaway Institute of Oceanography
10 Ocean Science Circle
Savannah, GA  31411
USA
atgreer@uga.edu
Funding Source:
RFP-IV
Data Collection Period:
2016-07-24 to 2016-07-28

Identified Submitted In-Review Available
3 3 3 3

Suggested Citation:

Greer, Adam T., Valerie J. Cruz, Carla Culpepper, and Frank J. Hernandez. 2021. Larval fish distributions in relation to diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/B9735RKQ

Abstract:

This dataset contains larval fish distributions in relation to the diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard the R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28. As part of the CONCORDE field sampling campaign, we sampled with an In Situ Ichthyoplankton Imaging System (ISIIS) along one transect spanning about 10 km three times during the day and three times during the night. This dataset examines the western-most corridor for abundances of different larval fishes during day and night in summer 2016. Particles above a 2000 pixel size threshold (~3.3 mm equivalent spherical diameter) were automatically extracted and manually identified with the highest taxonomic resolution possible (in many cases, to genus or species level). The ISIIS collected images of plankton along with high-resolution physical oceanographic data, which were merged using the nearest time stamp. Larval fishes were also extracted from a dataset sampling a thin layer in the same location three days prior (July 24, 2016). Larval fishes were identified, the standard length was measured in pixels, which is then converted to mm in the R code (2048 pixels is equal to 120 mm). The dataset also contains dates, longitude and latitudes of sample collection. In addition, measurements of temperature, oxygen content, and salinity were recorded. The goal of the study was to understand the distribution of different larval fish families in relation to the diel cycle, low oxygen conditions, and fine-scale aggregation of plankton, all of which are likely common in the Mississippi Bight during the summer. Other related zooplankton, ichthyoplankton, BIONESS (Bedford Institute of Oceanography Net Environmental Sampling System) profile, and zooplankton net samples data collected during this cruise are available under GRIIDC Unique Dataset Identifiers (UDIs) R4.x260.000:0009 (DOI: 10.7266/n7-0txv-z733) and R4.x260.000.0003 (DOI: 10.7266/N74T6GQD).

Purpose:

The purpose of the In Situ Ichthyoplankton Imaging System (ISIIS) deployment was to map the fine-scale spatial distribution of fish larvae, measure their sizes, and understand how they respond to bottom water hypoxia.

Theme Keywords:

larval fishes, fine-scale, hypoxia, imagery, In Situ Ichthyoplankton Imaging System (ISIIS), phytoplankton

File Format:

xlsx, csv, tif, R

Filename:

R4.x260.000.0129.zip (157.81 MB)

Dataset Downloads:

0

Larval fish distributions in relation to diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28



Identification Information
Distribution Information
Metadata Maintenance Information

Metadata: 
  File identifier: 
      R4.x260.000-0129-metadata.xml
  Language: 
      eng; USA
  Character set: 
    Character set code: 
      utf8
  Hierarchy level: 
    Scope code: 
      dataset
  Metadata author: 
    Responsible party: 
      Individual name: 
          Adam Greer
      Organisation name: 
          University of Georgia / Skidaway Institute of Oceanography
      Position name: 
          Assistant Professor
      Contact info: 
        Contact: 
          Phone: 
            Telephone: 
              Voice: 
                  912-598-2334
              Facsimile: 
          Address: 
            Address: 
              Delivery point: 
                  10 Ocean Science Circle
              City: 
                  Savannah
              Administrative area: 
                  GA
              Postal code: 
                  31411
              Country: 
                  USA
              Electronic mail address: 
                  atgreer@uga.edu
      Role: 
        Role code: 
          pointOfContact
  Date stamp: 
      2021-09-30T19:49:11+00:00
  Metadata standard name: 
      ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
  Metadata standard version: 
      ISO 19115-2:2009(E)
  Dataset URI: 
      https://data.gulfresearchinitiative.org/metadata/R4.x260.000:0129
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Identification info: Data identification: Citation: Citation: Title: Larval fish distributions in relation to diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28 Alternate title: Distribution of larval fishes in relation to hypoxia Date: Date: Date: 2021-06-30 Date type: Date type code: publication Identifier: Identifier: Code: Anchor: xlink: https://dx.doi.org/10.7266/B9735RKQ title: DOI doi:10.7266/B9735RKQ Abstract: This dataset contains larval fish distributions in relation to the diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard the R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28. As part of the CONCORDE field sampling campaign, we sampled with an In Situ Ichthyoplankton Imaging System (ISIIS) along one transect spanning about 10 km three times during the day and three times during the night. This dataset examines the western-most corridor for abundances of different larval fishes during day and night in summer 2016. Particles above a 2000 pixel size threshold (~3.3 mm equivalent spherical diameter) were automatically extracted and manually identified with the highest taxonomic resolution possible (in many cases, to genus or species level). The ISIIS collected images of plankton along with high-resolution physical oceanographic data, which were merged using the nearest time stamp. Larval fishes were also extracted from a dataset sampling a thin layer in the same location three days prior (July 24, 2016). Larval fishes were identified, the standard length was measured in pixels, which is then converted to mm in the R code (2048 pixels is equal to 120 mm). The dataset also contains dates, longitude and latitudes of sample collection. In addition, measurements of temperature, oxygen content, and salinity were recorded. The goal of the study was to understand the distribution of different larval fish families in relation to the diel cycle, low oxygen conditions, and fine-scale aggregation of plankton, all of which are likely common in the Mississippi Bight during the summer. Other related zooplankton, ichthyoplankton, BIONESS (Bedford Institute of Oceanography Net Environmental Sampling System) profile, and zooplankton net samples data collected during this cruise are available under GRIIDC Unique Dataset Identifiers (UDIs) R4.x260.000:0009 (DOI: 10.7266/n7-0txv-z733) and R4.x260.000.0003 (DOI: 10.7266/N74T6GQD). Purpose: The purpose of the In Situ Ichthyoplankton Imaging System (ISIIS) deployment was to map the fine-scale spatial distribution of fish larvae, measure their sizes, and understand how they respond to bottom water hypoxia. Status: Progress code: completed Point of contact: Responsible party: Individual name: Adam Greer Organisation name: University of Georgia / Skidaway Institute of Oceanography Position name: Assistant Professor Contact info: Contact: Phone: Telephone: Voice: 912-598-2334 Facsimile: Address: Address: Delivery point: 10 Ocean Science Circle City: Savannah Administrative area: GA Postal code: 31411 Country: USA Electronic mail address: atgreer@uga.edu Role: Role code: pointOfContact Point of contact: Responsible party: Individual name: Frank Hernandez Organisation name: University of Southern Mississippi / Department of Coastal Sciences Position name: Assistant Professor Contact info: Contact: Phone: Telephone: Voice: 2288188800 Facsimile: Address: Address: Delivery point: Gulf Coast Research Laboratory 703 East Beach Drive City: Ocean Springs Administrative area: Mississippi Postal code: 39564 Country: USA Electronic mail address: frank.hernandez@usm.edu Role: Role code: pointOfContact Descriptive keywords: Keywords: Keyword: larval fishes Keyword: fine-scale Keyword: hypoxia Keyword: imagery Keyword: In Situ Ichthyoplankton Imaging System (ISIIS) Keyword: phytoplankton Type: Keyword type code: theme Descriptive keywords: Keywords: Keyword: Mississippi Bight Keyword: Gulf of Mexico Type: Keyword type code: place Resource constraints: title: Cite As Constraints: Use limitation: Greer, Adam T., Valerie J. Cruz, Carla Culpepper, and Frank J. Hernandez. 2021. Larval fish distributions in relation to diel cycle, bottom water hypoxia, and a thin layer of phytoplankton collected aboard R/V Point Sur cruise PS17_02 (PTS03) in the northern Gulf of Mexico from 2016-07-24 to 2016-07-28. Distributed by: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC), Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/B9735RKQ Resource constraints: title: CC0 License Legal constraints: Use constraints: Restriction code: licenceUnrestricted Other constraints: This information is released under the Creative Commons license - No Rights Reserved - CC0 1.0 Universal (https://creativecommons.org/publicdomain/zero/1.0/). The person who associated a work with this deed has dedicated the work to the public domain by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law. You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission. Resource constraints: title: Liability and Warranty Legal constraints: Other constraints: All materials on this website are made available to GRIIDC and in turn to you "as-is." Content may only be submitted by an individual who represents and warrants that s/he has sufficient rights to be able to make the content available under a CC0 waiver. There is no warranty (expressed or implied) to these materials, their title, accuracy, non-infringement of third party rights, or fitness for any particular purpose, including the performance or results you may obtain from their use. Use these materials at your own risk. Under no circumstances shall GRIIDC be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use or the inability to use either this website or the materials available via this website. If you are dissatisfied with any website feature, content, or terms of use, your sole and exclusive remedy is to discontinue use. Language: eng; USA Topic category: Topic category code: oceans Topic category: Topic category code: biota Extent: Extent: Geographic element: Geographic bounding box: West bound longitude: -88.702134 East bound longitude: -88.498887 South bound latitude: 29.454189 North bound latitude: 29.764617 Geographic element: BoundingPolygon: Polygon: Polygon: Outer boundary: Linear ring: gml:posList: 29.454189 -88.702134 29.764617 -88.702134 29.764617 -88.498887 29.454189 -88.498887 29.454189 -88.702134 Temporal element: Temporal extent: Extent: Time period: Description: ground condition Begin date: 2016-07-24 End date: 2016-07-28 Supplemental Information: The main parameters included are: Julian time (percentage of a day, local time), central (local time, central daylight savings time), salinity (ppt), temperature (degrees C), PAR (microE per cm cubed), chlorophyll-a fluorescence (voltage), depth of vehicle (meters), altitude of vehicle above bottom (meters), Forward velocity of vehicle (meters per second), heading (degrees out of 360), dissolved oxygen (voltage and mg per L conversion), pitch of vehicle (degrees), roll of vehicle (degrees), latitude and longitude (decimal degrees), vertical velocity (meters per second), altitude (1 if altitude value is valid, 0 if no bottom detected).
          
The data are organized into 3 folders corresponding to the biological data from the ISIIS (plankton imagery analysis in "ISIIS biological data"), the oceanographic data obtained from the ISIIS instrument package ("ISIIS physical data"), and the code that transforms, merges, and plots the data for the ISIIS ("R code").
          
Within the “ISIIS biological data” folder, the folder "072416thinlayerfish-fishonly" contains the classified image segments that were identified as fish (.tif). The name of each file follows the same pattern. ID_Plankton_YYYYMMDDHHMMSS.SSS.tif_Slice_BX_BY_Width_Height, where ID = identification of the plankton in the image, YYYYMMDDHHMMSS.SSS = time stamp of the image stack Year, Month, Day, Hour, Minute, and seconds to the thousandth of the first frame in the stack (e.g., fish_Plankton_20160724140046.183.tif_1060_132_200_93_98). The fish are organized into folders, with the name of the folder corresponding to the ID. The ISIIS has two camera systems, and the fish were classified from each one. The folder “BC-classes” contains the classes from the large camera system (“Big Camera” = BC, 12 cm field of view and 50 cm depth of field). The folder “SC-classes” contains the classes from the small camera (SC, 4.3 cm field of view and 8.9 cm depth of field). The fish larvae from the “process study” on July 27-28, 2016 are contained in the folder “072716-072816-fish-classified-final.” This folder contains 2 folders corresponding to fishes collected during the day (“dayfish”) and fishes collected at night (“nightfish”). Some fish could not be identified at first (i.e., Fish_B) but were later determined to belong to a particular family. The last word of the folder name should be considered to be the correct identification of the folder contents. There are 3 other files in the “ISIIS biological data” folder. “072416thinlayerfish-env.csv” contains the exact position and physical data associated with each larval fish. In addition to the physical data units listed above, the dataset contains the nearest Julian time in the physical data (nearjul), the Julian time of when the fish was detected (Julian), the larval fish ID (fam), the broad ID (almost all are “fish”, ID), file name (label), the image number within the stack where the fish was found (slice), the x location of the bounding box surrounding the fish (xloc), the y location of the bounding box (yloc), the width of the bounding box (in pixels, width) and the height of the bounding box in pixels (height, with .tif added on to the end accidentally). The parameters for the file “072716DVMfish-env.csv” are the exact same but contain a few new parameters: “slength” is the standard length in pixels, “angle” is the angle of orientation of the head of the larva, “width” is the width of the fish at its widest point in pixels, and “mm” is the length of the fish converted to mm. “Fish727-728-Measurement-all-FINAL.xlsx” contains all of the measurements made on the fishes from the process study.
          
The folder “ISIIS physical data” contains all of the files from the non-imaging sensors on the ISIIS vehicle. The data are in the raw format or interpolated across the transect (corresponding to the folders). The file “20160724physical.csv” contains the raw physical dataset from the thin layer study. The other 6 files in this folder correspond to the 3 passes over the 10-km area during the night (July 27) and day (July 28) for the process study. The column names for the physical data are changed in the R script for ease of typing the column names (see the folder “R code”). The columns in the raw dataset are as follows (with explanations where required): Julian = Julian time (percentage of a day), utc = UTC time, UNIX_timestamp, ALTITUDE_M = altitude of the ISIIS vehicle above the bottom in meters, CTD_TEMPERATURE_DEG_C, DEPTH_M, FLOR = chlorophyll-a fluorescence in volts, FORWARD_VELOCITY_M_PER_S = forward velocity of the vehicle in meters per second, HEADING_DEG = heading of the vehicle in degrees, O2_MG_PER_L = erroneous conversion of the dissolved oxygen concentration that is corrected in the R script, O2_VDC = voltage on the oxygen sensor, PAR_UE_PER_M2 = PAR in micro Eintsteins per cm squared, PAR_VDC = voltage on the PAR sensor, PITCH_DEG = pitch of the vehicle, ROLL_DEG = roll of the vehicle, SALINITY_PPT, TS_LATITUDE_DEG, TS_LONGITUDE_DEG (if zero the GPS is not valid), VERTICAL_VELOCITY_M_PER_S2 = vertical velocity of the ISIIS vehicle, ALTITUDE_OK = binary variable indicating that the altitude data is valid. The files “724FluorInterp.csv”, “724OxyInterp.csv”, “724SalInterp.csv”, “724SigmaInterp.csv”, and “724TempInterp.csv” contain the interpolated physical data for the thin layer. All of the interpolated data for the process study is contained in the file “727daynight-interp.csv,” column names are self-explanatory and have the same units as the raw physical data, with the one exception of the oxygen data, which has correctly been converted to mg/L.
          
The dataset also includes the cruise documentation for the R/V Point Sur cruise PS17_02 (PTS03), led by chief scientist Dr. Christian Briseño-Avena.|The In Situ Ichthyoplankton Imaging System (ISIIS) was towed through a thin layer on July 24, 2016. For further information about the thin layer, please refer to Greer et al., 2020. This dataset only contains the larval fishes. A "process study" was performed on July 27 and July 28 where the ISIIS was towed over the same 10-km area three times during the night (July 27), and that same transect was repeated during the following day (July 28) - also 3 times.|In Situ Ichthyoplankton Imaging System (ISIIS) and Mininess (multiple opening and closing plankton net sampling system).|||Greer, A. T., Boyette, A. D., Cruz, V. J., Cambazoglu, M. K., Dzwonkowski, B., Chiaverano, L. M., … Wiggert, J. D. (2020). Contrasting fine‐scale distributional patterns of zooplankton driven by the formation of a diatom‐dominated thin layer. Limnology and Oceanography. doi:10.1002/lno.11450
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Distribution info: Distribution: Distributor: Distributor: Distributor contact: Responsible party: Organisation name: Gulf of Mexico Research Initiative Information and Data Cooperative (GRIIDC) Contact info: Contact: Phone: Telephone: Voice: 3618253604 Address: Address: Delivery point: 6300 Ocean Drive City: Corpus Christi Administrative area: TX Postal code: 78412 Country: USA Electronic mail address: griidc@gomri.org Online Resource: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org Role: Role code: distributor Distributor format: Format: Name: xlsx, csv, tif, R Version: inapplicable File decompression technique: zip Distributor transfer options: Digital transfer options: Transfer size: 157.8115 Online: Online Resource: Linkage: URL: https://data.gulfresearchinitiative.org/data/R4.x260.000:0129 Protocol: https Name: Data Landing Page Description: GRIIDC dataset landing page Function: Online function code: information
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Metadata maintenance: Maintenance information: Maintenance and update frequency: unknown Maintenance note: This ISO metadata record was automatically generated from information provided to GRIIDC for dataset: R4.x260.000:0129 on 2021-11-29T14:39:19-06:00
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