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
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xlsx, csv, tif, R
Gulf of Mexico Research Initiative
University of Georgia / Skidaway Institute of Oceanography
2016-07-24 to 2016-07-28
larval fishes, fine-scale, hypoxia, imagery, In Situ Ichthyoplankton Imaging System (ISIIS), phytoplankton
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).
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
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.
Data Parameters and Units:
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).
Provenance and Historical References:
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