Dataset: St. John Octocoral Forest Closure Photo Analysis for Community Quadrats

Name: Canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020
Published: 2023-03-21
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.892258.1

Spatial Extent: N:18.3147 E:-64.7218 S:18.3074 W:-64.7314

Temporal Extent: 2019-07-26 - 2020-01-27

Project:

Collaborative Research: Pattern and process in the abundance and recruitment of Caribbean octocorals (Octocoral Community Dynamics)

RUI: Pattern and process in four decades of change on Caribbean reefs (St John Coral Reefs)

Principal Investigator:

Peter J. Edmunds (California State University Northridge, CSUN)

Student:

John Girard (California State University Northridge, CSUN)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-03-21

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands from July 2019 to Jan 2020

Abstract:

These data represent the determination of canopy closure values from photographs taken within octocoral forests in Lameshur Bay St. John, U.S. Virgin Islands. Sampling was performed July – August 2019, and January 2020 in quadrats (1m2) placed at ≤ 13-m depth. These data were recorded in conjunction with invertebrate species abundances and used to test for an association between octocoral canopy metrics and benthic invertebrate communities. These data were collected as part of an NSF Coral Reef Time Series, Virgin Islands: Long-term coral reef community dynamics in the Virgin Islands National Park and were published in Girard and Edmunds (2023).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2023-03-21	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.892258.1	2023-05-24

Methods & Sampling

Research was conducted from the University of the Virgin Islands Marine Station in Lameshure Bay during July – August 2019 and January 2020.

Methods & Sampling
Quadrats were randomly placed along 20 m, non-overlapping transects that were positioned haphazardly along fringing reefs. Canopy closure was quantified using a modified method from (Jennings et. al. 1999) whereby a GoPro Hero 3+ camera with a 130° field of view (manufacturer’s specification, Go-Pro., Inc. San Mateo, CA) was used to record still images in the center, and at each of the four corners, of quadrats, with all five images quadrat-1 recorded within < 5 minutes. To avoid biases in estimating canopy closure caused by adjacent non-living substrata (e.g., boulders and rock walls), images were excluded when they included these features. Images were analyzed using ImageJ software (v1.52a, Schneider et al., 2012), in which 300 randomly located dots (~ 0.5 pixel in diameter) were superimposed on each image. The number of dots on the octocoral canopy were counted and expressed as a percentage of the dot population. This metric was used to quantify canopy closure, and the results from the five images quadrat-1 were averaged to characterize each quadrat.

Instruments
PVC Quadrats (1 m2)
Transect tapes
GoPro Hero 3+ camera

Data Processing Description

Data processing
To calculate canopy closure images were analyzed using ImageJ software (v1.52a, Schneider et al., 2012), in which 300 randomly located dots (~ 0.5 pixel in diameter) were superimposed on each image. The number of dots on the octocoral canopy were counted and expressed as a proportion of the dot population. To aid in the quantification of dots a grid of twenty squares was superimposed on the image. Each "box" was scored for the number of points in it that fell on the octocoral canopy. All twenty boxes for each image were summed for the total points out of 300 falling on the octocoral canopy.

BCO-DMO Data Manager Processing Notes:
* File "St.John_Octocoral Forest Closure Photo Analysis for Community Quadrats.csv" imported as the primary table for this dataset.
* Supplemental files shared with other related datasets also added here (site list, photo inventory, photos).
* Photo ID transformed to be uppercase in this data table to match the actual file names.
* lat lon values added into the table by joining with the site list.
* Proportion_Closed rounded to three decimal places.
* Column names adjusted to conform to BCO-DMO naming conventions designed to support broad re-use by a variety of research tools and scripting languages. [Only numbers, letters, and underscores. Can not start with a number]

Data Files

File
closure_image_analysis.csv (Comma Separated Values (.csv), 27.93 KB) MD5:106f15972bffca32a8959ec584fb36b3 Primary data file for dataset 892258.

Supplemental Files

File
Photo inventory filename: photo_inventory.csv (Comma Separated Values (.csv), 148.68 KB) MD5:2bdcfdff1945b4e75048f03870524b7b Photo inventory table for files within Girard_and_Edmunds_2023_supporting_photos.zip This table has columns: filename, file name relative_filepath, relative path inside the zip file filesize_bytes, filesize in bytes md5sum, checksum of image file Site, site name Quadrat_Num, quadrat number Transect_Num, transect number Year, year (YYYY) lat, site latitude in decimal degrees lon, site longitude in decimal degrees Category, description of survey type (Closure, Community, etc). The site, transect number and quadrat number correspond to the values in the main data table "Benthic Invertebrate Abundance."
Site List filename: site_list.csv (Comma Separated Values (.csv), 192 bytes) MD5:4415feb2d663fc251a671a2a7c5cac04 Site list for all dataset related to the results publication Girard and Edmunds (2023). Parameters (column names, descriptions, and units): Site, Site name used in dataset related to Girard and Edmunds (2023),unitless lat, Site latitude,decimal degrees lon,Site longitude,decimal degrees Alternate_name, Alternate name for the site,unitless
Supporting Photos for Girard and Edmunds (2023) filename: Girard_and_Edmunds_2023_supporting_photos.zip (ZIP Archive (ZIP), 3.77 GB) MD5:55008bec5933c4c2eefb45f7a7824d39 See "photo_inventory.csv" for a full file listing within this photo zip file. Photo inventory also includes site and quadrat information.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756678
NSF Division of Ocean Sciences	OCE-2019992

Deployments

None available yet

Instruments

Underwater Camera

Supplied Name: GoPro Hero 3+ camera

Supplied Description:

Instrument Type

Generic Name: Underwater Camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/180/

Generic Description:

All types of photographic equipment that may be deployed underwater including stills, video, film and digital systems.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
Closure_Photo_ID	ID of photograph analyzed (Filename without .JPG extension)	unitless	sample_descrip
Site	Name of Site	unitless	site
lat	Site latitude	decimal degrees	lat
lon	Site longitude	decimal degrees	lon
Transect_Num	Transect number	unitless	transect
Quadrat_Number	Quadrat number	unitless	sample_descrip
Proportion_Closed	Closure measurment calculated from the sum of all the points scored in each of the twenty boxes divided by 300	unitless	sample_descrip
Box_1	Number of points in Box 1 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_2	Number of points in Box 2 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_3	Number of points in Box 3 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_4	Number of points in Box 4 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_5	Number of points in Box 5 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_6	Number of points in Box 6 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_7	Number of points in Box 7 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_8	Number of points in Box 8 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_9	Number of points in Box 9 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_10	Number of points in Box 10 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_11	Number of points in Box 11 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_12	Number of points in Box 12 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_13	Number of points in Box 13 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_14	Number of points in Box 14 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_15	Number of points in Box 15 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_16	Number of points in Box 16 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_17	Number of points in Box 17 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_18	Number of points in Box 18 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_19	Number of points in Box 19 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count
Box_20	Number of points in Box 20 of the grid superimposed on the closure photograph that fell on octocoral branches	points	count

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Database

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Dataset: St. John Octocoral Forest Closure Photo Analysis for Community Quadrats