Dataset: Thermal Stress Experiment: Color Score Physiology

Name: Physiology color score extracted from pictures taken during a thermal stress experiment using reef building corals collected in Kāne'ohe Bay, O'ahu, Hawai'i.
Published: 2023-01-31
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.884220.1

Project:

NSFOCE-BSF: COLLABORATIVE RESEARCH: Elucidating adaptive potential through coral holobiont functional integration (Holobiont Integration)

Co-Principal Investigator:

Hollie Putnam (University of Rhode Island, URI)

Student:

Emma Strand (University of Rhode Island, URI)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2023-01-31

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Physiology color score extracted from pictures taken during a thermal stress experiment using reef building corals collected in Kāne'ohe Bay, O'ahu, Hawai'i.

Abstract:

Understanding the response of the coral holobiont to environmental change is crucial to inform conservation efforts. The most pressing problem is “coral bleaching,” usually precipitated by prolonged thermal stress. This dataset spans a five week thermal stress experiment in which images were taken of coral individuals and analyzed for a "color score".

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2023-01-31	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.884220.1	2023-02-07

Methods & Sampling

From the waters of Kāne‘ohe Bay, HI, four colonies of each coral species M. capitata and P. acuta were identified and collected under SAP 2019-60. Each of the four colonies for each species was fragmented into 30 pieces at the Hawaiʻi Institute of Marine Biology, located on Moku o Loʻe in Kāne‘ohe Bay, HI, and hot-glued to labeled plugs. (21N 157 W ; depth 1m).

Data Processing Description

Each sample was photographed using a digital camera with a red/blue/green color standard. Red/blue/green values that were extracted in ImageJ, version 1.51 (Schneider et al. 2012) from the coral were standardized to the color standards by dividing the experimental value observed in the coral against the corresponding actual recorded value from the color standards (Edmunds et al. 2003). Using the normalized intensity values from each color channel, a bleaching score was quantified as PC1 from principle components analysis of these data. As stress is prolonged and bleaching becomes more pronounced, the red/blue/green color readings from the coral will equalize around the same number because white is an equal expression of all colors. All nubbins available at each time points were used for color assessment.

Data Files

File
thermal_colorscore.csv (Comma Separated Values (.csv), 178.60 KB) MD5:b59e9683f571a8ddf7c3072834a54222 Primary data file for dataset ID 884220

Supplemental Files

File
Thermal_Stress_Experiment_Color_Score_Images filename: Thermal_Stress_Experiment_Color_Score_Images_Emma_Strand.zip (ZIP Archive (ZIP), 286.59 MB) MD5:9dc5de3f06d3ae13b279e88e528b7fde Pictures of coral during a thermal stress experiment where physiology color score has been extracted from using ImageJ.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1756623

Deployments

None available yet

Instruments

Camera

Supplied Name: Digital Camera

Supplied Description:

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

ruler

Supplied Name: Ruler with three red, blue, and green colored bands

Supplied Description:

Instrument Type

Generic Name: ruler

Generic Description:

A device used for measuring or for drawing straight lines, consisting of an elongated piece of rigid or semi-rigid material marked with units for measurement. Device that allows one or more physical dimensions of a sample or specimen to be determined by visible comparison against marked graduations in units of measurement of dimension length.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Date	Date of measurement (Month-Day-Year) Format: %Y-%m-%d	unitless	date
Timepoint	Categorical timepoint of experiment	unitless	time_sample
PLUG_ID	Plug ID indicating coral ID	unitless	sample
Genotype	Genotype ID	unitless	sample
Species	Coral species	unitless	species
Photo_Number	ID of photograph taken	unitless	file_name
Tank	Tank ID	unitless	tank
Treatment	Temperature treatment	unitless	treatment
Red_Standard	Color value of red standard, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Green_Standard	Color value of green standard, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Blue_Standard	Color value of blue standard, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Red_Coral	Red color in coral measurement, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Green_Coral	Green color in coral measurement, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Blue_Coral	Blue color in coral measurement, raw RGB values extracted from ImageJ.	pixels	no_bcodmo_term
Notes	Notes	units	comment

Database

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Dataset: Thermal Stress Experiment: Color Score Physiology