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

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

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.892258.1Version 1 (2023-03-21)Dataset Type:Other Field Results

Principal Investigator: Peter J. Edmunds (California State University Northridge)

Student: John Girard (California State University Northridge)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

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 Re...

Cite Dataset

Spatial Extent: N:18.31 E:-64.72 S:18.31 W:-64.73
Temporal Extent: 2019-07-26 - 2020-01-27

19

Views

591

Downloads

These numbers come from web analytics and reflect real user activity on the site. They reliably show dataset usage and are mostly free of bot traffic.

Data File(s)	Type	Description	Action
closure_image_analysis.csv (27.93 KB)	Comma Separated Values (.csv)	Primary data file for dataset 892258.	closure_image_analysis.csv View Table

Supplemental File(s)	Type	Description	Action
photo_inventory.csv (148.68 KB)	Comma Separated Values (.csv)	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 i... Show more	photo_inventory.csv View Table
site_list.csv (192.00 B)	Comma Separated Values (.csv)	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	site_list.csv View Table
Girard_and_Edmunds_2023_supporting_photos.zip (3.77 GB)	ZIP Archive (ZIP)	See "photo_inventory.csv" for a full file listing within this photo zip file. Photo inventory also includes site and quadrat information.	Girard_and_Edmunds_2023_supporting_photos.zip

Files

Filename: closure_image_analysis.csv (27.93 KB)
Type: Comma Separated Values (.csv)

Description:

Primary data file for dataset 892258.

closure_image_analysis.csv View Table

Supplemental Files

Filename: photo_inventory.csv (148.68 KB)
Type: Comma Separated Values (.csv)

Description:

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 S...

photo_inventory.csv View Table

Filename: site_list.csv (192.00 B)
Type: Comma Separated Values (.csv)

Description:

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 d...

site_list.csv View Table

Filename: Girard_and_Edmunds_2023_supporting_photos.zip (3.77 GB)
Type: ZIP Archive (ZIP)

Description:

See "photo_inventory.csv" for a full file listing within this photo zip file. Photo inventory also includes site and quadrat information.

Girard_and_Edmunds_2023_supporting_photos.zip

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

Related Datasets

IsRelatedTo

Dataset: Benthic Invertebrate Abundances associated with Octocoral Forests of St. John, US Virgin Islands
Relationship Description:

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Girard, J., Edmunds, P. J. (2023) Benthic invertebrate abundances associated with octocoral forests in St. John, US Virgin Islands from July 2019 to Jan 2020. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 doi:10.26008/1912/bco-dmo.892248.1

IsRelatedTo

Dataset: Canopy Closure Data of the Octocoral Forests sampled for Light Intensity, St. John U.S. Virgin Islands
Relationship Description:

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Girard, J., Edmunds, P. J. (2023) Canopy closure values from photographs taken within octocoral forestsalong the south shore of St. John, U.S. Virgin Islands in March of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 doi:10.26008/1912/bco-dmo.892323.1

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Girard, J., Edmunds, P. J. (2023) Light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation in East Cabritte, in Grootpan Bay, St. John U.S. Virgin Islands in March of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 doi:10.26008/1912/bco-dmo.892300.1

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Girard, J., Edmunds, P. J. (2023) Light intensity (lux) of downwelling light upon the benthos along differing conditions of octocoral canopy formation in Lameshur Bay St. John, U.S. Virgin Islands in March of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 doi:10.26008/1912/bco-dmo.892272.1

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Girard, J., Edmunds, P. J. (2023) Octocoral canopy metrics (mean height, density, and closure) in St. John, US Virgin Islands in March of 2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-03-21 doi:10.26008/1912/bco-dmo.892293.1

Related Publications

Results

Girard, J. F., & Edmunds, P. J. (2023). Effects of arborescent octocoral assemblages on the understory benthic communities of shallow Caribbean reefs. Journal of Experimental Marine Biology and Ecology, 561, 151870. https://doi.org/10.1016/j.jembe.2023.151870

Methods

GoPro (2013). Hero 3 silver edition: user manual. 1–62. https://gopro.com/content/dam/help/hero3-silver-edition/manuals/HERO3_Silver_UM_ENG_RevC_web.pdf. Accessed: 21/Dec/2022

Methods

Jennings, S. (1999). Assessing forest canopies and understorey illumination: canopy closure, canopy cover and other measures. Forestry, 72(1), 59–74. https://doi.org/10.1093/forestry/72.1.59

Software

Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. https://doi.org/10.1038/nmeth.2089

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

ValidatedFinal no updates expectedDOI: 10.26008/1912/bco-dmo.892258.1Version 1 (2023-03-21)Dataset Type:Other Field Results

Principal Investigator: Peter J. Edmunds (California State University Northridge)

Student: John Girard (California State University Northridge)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

Abstract

Cite Dataset

Spatial Extent: N:18.31 E:-64.72 S:18.31 W:-64.73
Temporal Extent: 2019-07-26 - 2020-01-27

19

Views

591

Downloads

These numbers come from web analytics and reflect real user activity on the site. They reliably show dataset usage and are mostly free of bot traffic.

Data File(s)	Type	Description	Action
closure_image_analysis.csv (27.93 KB)	Comma Separated Values (.csv)	Primary data file for dataset 892258.	closure_image_analysis.csv View Table

Supplemental File(s)	Type	Description	Action
photo_inventory.csv (148.68 KB)	Comma Separated Values (.csv)	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 i... Show more	photo_inventory.csv View Table
site_list.csv (192.00 B)	Comma Separated Values (.csv)	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	site_list.csv View Table
Girard_and_Edmunds_2023_supporting_photos.zip (3.77 GB)	ZIP Archive (ZIP)	See "photo_inventory.csv" for a full file listing within this photo zip file. Photo inventory also includes site and quadrat information.	Girard_and_Edmunds_2023_supporting_photos.zip

Files

Filename: closure_image_analysis.csv (27.93 KB)
Type: Comma Separated Values (.csv)

Description:

Primary data file for dataset 892258.

closure_image_analysis.csv View Table

Supplemental Files

Filename: photo_inventory.csv (148.68 KB)
Type: Comma Separated Values (.csv)

Description:

photo_inventory.csv View Table

Filename: site_list.csv (192.00 B)
Type: Comma Separated Values (.csv)

Description:

site_list.csv View Table

Filename: Girard_and_Edmunds_2023_supporting_photos.zip (3.77 GB)
Type: ZIP Archive (ZIP)

Description:

See "photo_inventory.csv" for a full file listing within this photo zip file. Photo inventory also includes site and quadrat information.

Girard_and_Edmunds_2023_supporting_photos.zip

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

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

Related Datasets

IsRelatedTo

Dataset: Benthic Invertebrate Abundances associated with Octocoral Forests of St. John, US Virgin Islands
Relationship Description:

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

IsRelatedTo

Dataset: Canopy Closure Data of the Octocoral Forests sampled for Light Intensity, St. John U.S. Virgin Islands
Relationship Description:

Octocoral measurements and invertebrate counts were done in the same quadrats. Therefore, the quadrat IDs correspond to each other across community & canopy data sets.

Related Publications

Results

Methods

GoPro (2013). Hero 3 silver edition: user manual. 1–62. https://gopro.com/content/dam/help/hero3-silver-edition/manuals/HERO3_Silver_UM_ENG_RevC_web.pdf. Accessed: 21/Dec/2022

Methods

Jennings, S. (1999). Assessing forest canopies and understorey illumination: canopy closure, canopy cover and other measures. Forestry, 72(1), 59–74. https://doi.org/10.1093/forestry/72.1.59

Software

Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. https://doi.org/10.1038/nmeth.2089

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

Principal Investigator: Peter J. Edmunds (California State University Northridge)

Student: John Girard (California State University Northridge)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

Abstract

Metadata

19

591

Files

Supplemental Files

Related Datasets

Related Publications

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

Principal Investigator: Peter J. Edmunds (California State University Northridge)

Student: John Girard (California State University Northridge)

BCO-DMO Data Manager: Amber D. York (Woods Hole Oceanographic Institution)

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

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

Abstract

Metadata

19

591

Files

Supplemental Files

Related Datasets

Related Publications