Imaging and oceanographic data from a thin layer of phytoplankton and surrounding zooplankton abundances on July 24, 2016
No. of Downloads: 4
No. of Files: 70
File Size: 2.18 GB
File Format(s):
tif, csv, txt, png, xlsx, R
Funded By:
Gulf of Mexico Research Initiative
Funding Cycle:
RFP-IV
Research Group:
Consortium for Oil Spill Exposure Pathways in Coastal River-Dominated Ecosystems (CONCORDE)
Adam Greer
University of Georgia / Skidaway Institute of Oceanography
atgreer@uga.edu
zooplankton imaging, plankton ecology, phytoplankton growth and mortality, thin layer
Abstract:
On July 24, 2016, a thin layer of phytoplankton was detected using the In Situ Ichthyoplankton Imaging System (ISIIS). The data were collected to describe the oceanographic influences on plankton distributions. Water samples were taken to describe the phytoplankton community inside and outside of the layer and were imaged with a FlowCAM for identifications. The ISIIS data described the abundance and distribution of zooplankton, while also collecting oceanographic data (e.g., temperature, salinity, dissolved oxygen, PAR, and chlorophyll-a fluorescence). Bottle incubations of water were used to determine rates of primary production and microzooplankton grazing inside and outside of the layer. The dataset also includes a readme file detailing the method used to calculate the rate of grazing by microzooplankton, the chlorophyll-a concentration, and apparently growth rate of phytoplankton. In additional, R code is provided to plot the physical distribution of marine snow, phytoplankton growth rate and community composition, and physical properties/phytoplankton counts.
Suggested Citation:
Adam T. Greer, Adam D. Boyette, Valerie J. Cruz. 2020. Imaging and oceanographic data from a thin layer of phytoplankton and surrounding zooplankton abundances on July 24, 2016. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/CMBVHTD3
Purpose:
These data were collected to characterize multiple plankton trophic levels, their biological responses, and the physical conditions surrounding a thin layer of phytoplankton in the Mississippi Bight (northern Gulf of Mexico). By combining in situ imagery, phytoplankton growth and mortality measurements, and modeling of the physical environment, we wanted to describe how the fine-scale physical environment may influence the abundances and growth rates of different plankton.
Data Parameters and Units:
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, longitude, vertical velocity (meters per second), altitude ok (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 ("R code"). 1) The folder "ISIIS biological data" includes 4 sub-folders. The sub-folder "AllThinLayerSegments-900-infT170" contains the classified image segments (.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., chaeto_Plankton_20160724140046.183.tif_1060_132_200_93_98). The sub-folder "CTD and Bottle sample data" contains the file GrazingRates.csv, which has experiments of microzooplankton grazing inside and outside the layer. Treatment = nutrients added or no nutrients, FracSW = fraction of seawater added, Inside layer and Outside layer = apparent phytoplankton growth inside and outside of the thin layer. The files "GrazingRates_raw_README.txt" and "PTL_uc_README.txt" contain other information about the variables measured in these spreadsheets. PTL-comp2.csv contains the cell concentrations (particles per mL) and biovolumes (microns cubed) measured at the stations within and outside of the thin layer. The sub-folder "ISIIS images for figure" contains example ISIIS images with the corresponding timestamp information. The sub-folder "Processed ISIIS data" contains the files showing the data derived from the ISIIS imagery, and are explained below: The file "724PlanktonCount1-30ofm3.csv" has the binned abundances of different plankton groups (each bin corresponds to 8.71 m horizontal distance, which is 1/30 of 1 cubic meter). The column names are as follows: rdist = rounded distance in meters (to the nearest 8.71 m), ID = plankton identification, mjul = mean julian time (percentage of a day), pco = plankton count for that particular ID within the bin (1/30 of 1 cubic meter), mdepth = mean depth in meters within the bin, msal = mean salinity, mtemp = mean temperature in degrees Celsius, mlat = mean latitude in degrees North. The file "724snowangle2.csv" contains the sizes and orientations information for chaetognaths and marine snow. The column names are as follows: id = label of the image segment followed the same pattern as described previously, area = area of the particle in pixels, perim = perimeter of the particle in pixels, major = length of the major axis of a fitted ellipse to the particle, minor = length of the minor axis of a fitted ellipse to the particle, angle = angle of orientation of the major axis of the fitted ellipse, circ = circularity of the particle, AR = aspect ratio (major axis length / minor axis length), round = roundness of the particle, solidity = solidity of the particle. The details of these measurements can be found on the ImageJ website (https://imagej.nih.gov/ij/docs/menus/analyze.html). The file “CopeAppCounts55555.csv” contains the manual copepod and appendicularian count for a portion of the frames in sequential profiles (up casts). The columns are as follows: Time = timestamp of the image stack of interest following the pattern HHMMSS.SSS, Frame = frame number within the image stack, Profile = profile number corresponding to “fnum” in another physical data file called “724LayerProfs.csv”, Cope# = the count of copepods in that portion of the image, App# = the count of appendicularians in that portion of the image. The file “DoliolidCountInfo.csv” contains a list of the doliolid images with multiple individuals overlapping. This dataset was used to correct for the counts of doliolids, which would be underestimated by overlapping individuals segmented as 1 “particle.” “File Name Info” corresponds to the name of the .tif file segment. Count is the number of individual doliolids that were overlapping in the image. The file “ThinLayer724angles.csv” contains the particle characteristics and physical data for each individual marine snow particle and chaetognath. “Nearjul” is the nearest julian time (percentage of a day) is from the physical dataset used to perform the merger with the information about each particle. The file “ThinLayer724Env-zoop.csv” is the nearest physical environment for each classified image segment. 2) The folder “ISIIS physical data” contains all of the files from the non-imaging sensors on the ISIIS vehicle. The file “20160724physical.csv” contains the raw physical dataset, which has the names changed in the R script for ease of typing the column names. The columns in the raw dataset are as follows: Julian day (decimal fraction of day, local time, most accurate time), Time (UTC, [HH:MM:SS]), Altitude above bottom [m], Unix time stamp (Central timezone, CDT), CTD temperature [degrees Celsius], Depth [m], Chlorophyll-a fluorescence [voltage], Forward velocity of vehicle [m/s], Heading of vehicle [degrees out of 360], Dissolved oxygen [volts], Dissolved oxygen [mg/L], PAR [micro-Einsteins/m^2], PAR [volts], pitch of vehicle [degrees], roll of vehicle [degrees], Salinity [parts per thousand], Latitude [degrees], Longitude [degrees], Vertical velocity [m/s], Altitude OK [1 if altitude is good, 0 if no bottom is detected]. The file “724LayerProfs.csv” contains a subset of the physical data for the “profiles” enumerated for copepods and appendicularians. The column names similar to “20160724physical.csv” with 3 variables added onto the end, including dist = distance along the transect in meters, updown = binary variable indicating whether the ISIIS vehicle is traveling up or down in the water column, fnum = the number of the “profile” along this portion of the transect. The files "724FluorInterp.sv", "724OxyInterp.csv", "724SalInterp.csv", "724SigmaInterp.csv", and "724TempInterp.csv" contain the interpolated physical data used in several of the plots. The format for all is Distance (along-track, [m]), Depth [m], and Measurement. (Note that distance in 724SigmaInterp.csv is too high by a factor of 700.). 3) The folder “R code” contains all of the R scripts used to analyze the data and generate most of the plots. Please note that the Julian date contained in the data files is the most accurate and preferred time estimate.
Instruments:
In Situ Ichthyoplankton Imaging System (ISIIS) - includes CTD (SBE 49), dissolved Oxygen (SBE 43), chlorophyll-a (ECO FL-RT, Wetlabs), and PAR (QCP2300) sensors. Niskin bottles were used to obtain water samples, and chlorophyll-a concentration from these samples was determined using a Turner 10-AU fluorometer.