57610
Benthic Cover from Automated Annotation of Benthic Images Collected at Coral Reef Sites in the Pacific Remote Island Areas and American Samoa in 2018
Benthic Cover - Robot
Data Set
Published / External
28844
National Coral Reef Monitoring Program
Project
On Going
2019-09
2019
The coral reef benthic community data described here result from the automated annotation (classification) of benthic images collected during photoquadrat surveys conducted by the NOAA Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (ESD, formerly the Coral Reef Ecosystem Division) as part of NOAA's ongoing National Coral Reef Monitoring Program (NCRMP). SCUBA divers conducted benthic photoquadrat surveys in coral reef habitats according to protocols established by ESD and NCRMP during the ESD-led NCRMP mission to the islands and atolls of the Pacific Remote Island Areas (PRIA) and American Samoa from June 8 to August 11, 2018. Still photographs were collected with a high-resolution digital camera mounted on a pole to document the benthic community composition at predetermined points along transects at stratified random sites surveyed only once as part of Rapid Ecological Assessment (REA) surveys for corals and fish and permanent sites established by ESD and resurveyed every ~3 years for climate change monitoring. Overall, 30 photoquadrat images were collected at each survey site.
The benthic habitat images were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015). Ten points were randomly overlaid on each image and the machine-learning algorithm "robot" identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to functional group (Tier 1: hard coral, soft coral, sessile invertebrate, macroalgae, crustose coralline algae, and turf algae) for coral, algae, invertebrates, and other taxa following Lozada-Misa et al. (2017). These benthic data can ultimately be used to produce estimates of community composition, relative abundance (percentage of benthic cover), and frequency of occurrence.
The use of the CoralNet machine-learning, image annotation tool is essential to the timely and cost-effective analysis of benthic imagery collected Pacific-wide under the auspices of the NOAA National Coral Reef Monitoring Program (NCRMP). Timely analysis and reporting of cover estimates are fundamental to understanding status and change of coral reef benthic communities, particularly in a fast-changing climate.
The NOAA National Coral Reef Monitoring Program (NCRMP) details a long term approach to provide an ecosystem perspective via monitoring climate, fish, benthic, and socioeconomic variables in a consistent and integrated manner. The NCRMP coordinates various NOAA Coral Reef Conservation Program (CRCP) biological, physical, and human dimensions activities into a cohesive NOAA-wide effort. Through the implementation of the NCRMP, NOAA is able to clearly and concisely communicate results of national-scale monitoring to national, state, and territorial policy makers, resource managers, and the public on a periodic basis.
NCRMP is a framework for conducting sustained observations of biological, climate, and socioeconomic indicators at some ~40 priority coral reefs systems across the U.S. and its territories. This integrated approach consolidates monitoring of coral reefs under a uniform method in the Pacific, Atlantic, Caribbean, and the Gulf of Mexico for the first time. NCRMP is funded by the CRCP and supported by NOAA Fisheries, NOAA National Centers for Coastal Ocean Science (NCCOS), and many other partners. The Ecosystem Sciences Division at NOAA Fisheries is leading biological and climate monitoring in the U.S. Pacific Islands Region.
The biological component of NCRMP in the Pacific provides a triennial ecological characterization at a broad spatial scale of general reef condition for reef fishes, corals and benthic habitat (i.e., fish species composition/density/size, benthic cover, and coral density/size/condition). The climate component of NCRMP in the Pacific provides a comprehensive view of climate change impacts on coral reef ecosystems and helps identify areas of resilience and vulnerability. The key indicators used to identify and monitor climate-driven trends include 1) thermal stress caused by changes in sea temperature, 2) ocean acidification resulting from changes in carbonate chemistry, and 3) ecological impacts by collecting data on coral growth rates, erosion, and community structure to understand the impacts of thermal stress and ocean acidification on the ecosystem. Each year, ESD scientists work closely with CRCP and partners during Pacific RAMP missions to collect data using moored oceanographic (subsurface temperature recorders) and ecological (calcification accretion units [CAUs] and autonomous reef monitoring structures [ARMS]) instruments stationed at fixed sites in the Pacific Ocean, and water samples collected by divers. The in-situ data (along with satellite-based observations) are also used in modeling efforts. Innovative analysis techniques are used to develop products that give fellow scientists, managers, decision makers and the public a better understanding of a region's resources and how they are changing over time.
Theme
ISO 19115 Topic Category
biota
Theme
CRCP Project
743
Theme
CRCP Project
National Coral Reef Monitoring Program
Theme
CoRIS Discovery Thesaurus
Numeric Data Sets > Benthic
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Aquatic Habitat > Benthic Habitat
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Aquatic Habitat > Reef Habitat
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Microbiota > Blue-green Algae
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Vegetation > Algae > Crustose Coralline Algae
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Vegetation > Algae > Encrusting Macroalgae
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Vegetation > Algae > Turf Algae
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Benthos Analysis
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Photographic Analysis
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Biosphere > Zoology > Corals > Reef Monitoring and Assessment > Rapid Assessment Studies
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Coastal Processes > Coral Reefs > Coral Reef Ecology > Benthic biology
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Marine Biology > Coral
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Marine Biology > Coral Communities
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Marine Biology > Marine Invertebrates > Macroinvertebrates
Theme
CoRIS Theme Thesaurus
EARTH SCIENCE > Oceans > Ocean Chemistry > Climate Change
Theme
NODC DATA TYPES THESAURUS
BENTHIC COMMUNITIES
Theme
NODC DATA TYPES THESAURUS
BENTHIC SPECIES
Theme
NODC DATA TYPES THESAURUS
BENTHIC SPECIES - TAXA IDENTITIES
Theme
NODC INSTRUMENT TYPES THESAURUS
machine-learning algorithm
Theme
NODC INSTRUMENT TYPES THESAURUS
photograph
Theme
NODC OBSERVATION TYPES THESAURUS
benthic
Theme
NODC OBSERVATION TYPES THESAURUS
other
Theme
NODC PLATFORM NAMES THESAURUS
HI'IALAKAI
Theme
NODC PROJECT NAMES THESAURUS
CORAL REEF STUDIES
Theme
NODC PROJECT NAMES THESAURUS
Coral Reef Conservation Program
Theme
NODC PROJECT NAMES THESAURUS
National Coral Reef Monitoring Program
Theme
NODC PROJECT NAMES THESAURUS
Pacific Reef and Assessment Monitoring Program
Theme
NODC SUBMITTING INSTITUTION NAMES THESAURUS
US DOC; NOAA; NMFS; Pacific Islands Fisheries Science Center; Ecosystem Sciences Division
Theme
CRED
Theme
CREP
Theme
Coral Reef Ecosystem Division
Theme
Coral Reef Ecosystem Program
Theme
ESD
Theme
Ecosystem Sciences Division
Theme
PIFSC
Theme
Pacific Islands Fisheries Science Center
Theme
RAMP
Theme
Reef Assessment and Monitoring Program
Theme
StRS
Theme
automated annotation
Theme
image analysis
Theme
stratified random
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > American Samoa (14S170W0000)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ofu Island (14S169W0013)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Olosega Island (14S169W0014)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Rose Atoll (14S168W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Swains Atoll (11S171W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Ta'u Island (14S169W0012)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > American Samoa > Tutuila Island (14S170W0016)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > Ofu Island > Ofu (14S169W0002)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > American Samoa > Olosega Island > Olosega (14S169W0016)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Baker Island (00N176W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Howland Island (00S176W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Jarvis Island (00S160W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Kingman Reef (06N162W0001)
Spatial
CoRIS Place Thesaurus
COUNTRY/TERRITORY > United States of America > USA Minor Outlying Islands > Palmyra Atoll (05N162W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > American Samoa > American Samoa (14S170W0000)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > American Samoa > Rose Atoll (14S168W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > American Samoa > Swains Atoll (11S171W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > American Samoa > Tutuila Island (14S170W0016)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Baker Island > Baker Island (00N176W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Howland Island > Howland Island (00S176W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Jarvis Island (00S160W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Kingman Reef (06N162W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Central Pacific Ocean > Line Islands > Palmyra Atoll (05N162W0001)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu (14S169W0002)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Manu'a Group > Ofu Island (14S169W0013)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega (14S169W0016)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Manu'a Group > Olosega Island (14S169W0014)
Spatial
CoRIS Place Thesaurus
OCEAN BASIN > Pacific Ocean > Manu'a Group > Ta'u Island (14S169W0012)
Spatial
NODC Sea Area Names Thesaurus
Equatorial Pacific Ocean
Spatial
NODC Sea Area Names Thesaurus
Pacific Remote Islands Marine National Monument
Spatial
NODC Sea Area Names Thesaurus
Rose Atoll Marine National Monument
Spatial
NODC Sea Area Names Thesaurus
South Pacific Ocean
Spatial
PRIA
Spatial
PRIMNM
Spatial
Pacific Remote Island Areas
Pacific Islands Fisheries Science Center
Honolulu
HI
USA
Data Set
CSV Files
As Needed
Created September 2019 for benthic data generated by robot from images collected in 2018.
Table (digital)
Raw benthic community data include metadata for each survey (where, when, who); site characteristics (depth, reef zone); unique image name, and individual point observations of benthic elements identified to benthic taxa group, referred to as "Tier 1", which includes hard coral, soft coral, macroalgae, turf algae, crustose coralline algae, invertebrates, mobile fauna, and sediment.
https://www.fisheries.noaa.gov/inport/item/57660
While every effort has been made to ensure that these data are accurate and reliable within the limits of the current state of the art, NOAA cannot assume liability for any damages caused by errors or omissions in the data, nor as a result of the failure of the data to function on a particular system. NOAA makes no warranty, expressed or implied, nor does the fact of distribution constitute such a warranty.
PIFSC Ecosystem Sciences Division and funded by the NOAA Coral Reef Conservation Program
57660
Entities: MV_BIA_CNET_ANALYSIS_DATA_ROB
MV_BIA_CNET_ANALYSIS_DATA_ROB
Published / External
Completed
Benthic image analysis results generated by robot.
Data Table
Yes
GISDAT
Benthic image analysis results generated by robot.
1
ROUNDID
NUMBER
22
Yes
No
28
0
Active
Unique Identifier for MISSIONID.
2
MISSIONID
VARCHAR2
30
Yes
No
Active
Mission identifier.
3
REGION_NAME
VARCHAR2
30
No
No
Active
The name of the region surveyed in the Pacific Islands region: American Samoa, Pacific Remote Island Areas, Mariana Archipelago, main Hawaiian Islands, Northwestern Hawaiian Islands.
4
ISLAND
NVARCHAR2
150
No
No
Active
Name of island or atoll surveyed in the Pacific Islands region (REGION_NAME).
5
SITE
NVARCHAR2
150
No
No
Active
The code for the site surveyed at the island or atoll (ISLAND). Combines a 3-letter island code with a 2-5 digit site number.
6
LATITUDE
NUMBER
22
No
No
38
8
Active
Latitude in decimal degrees, WGS84, for the given SITE.
7
LONGITUDE
NUMBER
22
No
No
28
8
Active
Longitude in decimal degrees, WGS84 for the given SITE.
8
REEF_ZONE
NVARCHAR2
150
No
No
Active
The reef zone for the given SITE (Forereef, Backreef, Lagoon, Protected Slope).
8
SURVEY_TYPE
TEXT
No
No
Active
They type of survey conducted. Random sites selected using a stratified random sampling design surveyed for reef fish and coral demographics are type FISH or BENTHIC, respectively. Permanent sites surveyed for climate monitoring are type OCEANOGRAPHY. OCEANOGRAPHY sites are usually flagged as PERM_SITE or CLIMATE_STATION, and may be flagged as both.
TEXT
9
DEPTH_BIN
NVARCHAR2
60
No
No
Active
Classification of depth (shallow, mid, deep) based on midpoint between minimum and maximum depths of transect(s) of a given SITE. Shallow: >0-6 m, Mid: >6-18 m, Deep: >18-30 m.
10
PERM_SITE
NUMBER
22
No
No
5
0
Active
Flag for permanent site (-1), many of which were established in the early years of the Pacific Reef Assessment and Monitoring Program. Applicable only to 'oceanography' SURVEY_TYPE. Only a subset of activities conducted at CLIMATE STATIONS are conducted at permanent sites. OCEANOGRAPHY sites are usually flagged as PERM_SITE or CLIMATE_STATION, and in some cases may be flagged as both.
11
CLIMATE_STATION_YN
NUMBER
22
No
No
Active
Flag for NCRMP climate station (-1). Applicable only to 'oceanography' SURVEY_TYPE. Climate stations are permanent sites (regardless of PERM_SITE flag). OCEANOGRAPHY sites are usually flagged as PERM_SITE or CLIMATE_STATION, and may be flagged as both.
Typically, 3-4 climate stations were selected to be roughly equally spaced around the island/atoll, along the 15-m contour, on hard bottom, and at least 1-km away from a river mouth or embayment (if relevant to the island/atoll). Multiple features of the coral reef environment are assessed at climate stations, including in-situ water temperature using subsurface temperature recorders (STRs), seawater carbonate chemistry from water samples, net carbonate accretion using calcification accretion units (CAUs), bioerosion using bioerosion monitoring units (BMUs), and cryptobiota diversity using autonomous reef monitoring structures (ARMS).
12
MIN_DEPTH
NUMBER
22
No
No
38
8
Active
Minimum depth (measured in feet). Only recorded for coral demographic surveys ('benthic' SURVEY_TYPE).
13
MAX_DEPTH
NUMBER
22
No
No
28
8
Active
Maximum depth (measured in feet). Only recorded for coral demographic surveys ('benthic' SURVEY_TYPE).
14
DATE_
DATE
7
Yes
No
Active
Date the survey was conducted (DD-MMM-YY).
15
IMAGE_NAME
VARCHAR2
4000
No
No
Active
Image name (SITE_YEAR_REP_PHOTOID).
16
OBS_YEAR
VARCHAR2
16
No
No
Active
4-digit year the survey was conducted (DATE_).
17
REP
VARCHAR2
4
No
No
Active
Letter associated to replicate for the survey. For 'benthic' and 'fish' SURVEY_TYPE, Rep is A for reef fish surveys, and A or B for benthic coral demographic surveys. For 'oceanography' SURVEY_TYPE, Rep is A.
18
PHOTOID
VARCHAR2
4000
No
No
Active
Sequential image number along transect, usually 1-30, though some sites may exceed 30.
19
ANALYST
VARCHAR2
20
No
No
Active
Initials of the person that annotated the images. The analyst for automated annotations (as opposed to annotations generated by humans) is ROBOT.
20
TIER_1
VARCHAR2
5
No
No
Active
Code for CATEGORY NAME.
21
CATEGORY_NAME
VARCHAR2
20
No
No
Active
Category classification for the point on the analyzed image. Taxa/functional group includes: coral, coralline alga, macroalga, mobile fauna, sediment, sessile invertebrate, soft coral, tape and wand, turf alga, and unclassified.
26
X_POS
NUMBER
22
No
No
38
Active
X position of the analyzed point on the image.
27
Y_POS
NUMBER
22
No
No
Active
Y position of the analyzed point on the image.
57828
Benthic Image analysis classification scheme - TIER1
Published / External
Completed
Description of Tier 1 categories
Data Table
Yes
GISDAT
Description of Tier 1 categories
Crustose Coralline Red Alga (CCA)
VARCHAR2
No
No
Active
For the purpose of these image analyses, CCA is defined as any calcified, hard, non-segmented, encrusting or branched, red (or pink) alga.
CCA growing on rubble substrate (CCAR), CCA growing on hard[bottom] substrate (CCAH)
Hard Coral
VARCHAR2
No
No
Active
For the purposes of this image analysis, hard corals are defined as those that are responsible for the persistent, hard, three-dimensional structure of a coral reef. In general, this classification will include all members of Order Scleractinia, as well as some other small groups of non-scleractinian corals with hard skeletons, including fire corals (Family Milleporidea), blue coral (Order Helioporacea), and Stylasterid hydrocorals (Family Stylasteridae).
Massive (MASS), Tabulate (TAB), Encrusting (ENC), Branching (BR), Columnar (COL), Free-living (FREE), Foliose (FOL), Non-scleractinian hard coral (NS)
Macroalga and Seagrass
VARCHAR2
No
No
Active
Any alga whose structure can be seen in the photograph should be labeled as a macroalga rather than turf. Macroalgae possess numerous different types of morphologies that resemble leaves, blades, umbrellas, ferns, grapes, balls, feathers, branched shrubs, etc. Some macroalgae do possess calcification; however, for the purpose of image analyses here, calcified and fleshy representatives (with the exception of Halimeda sp., below) will be lumped together.
Upright macroalga (UPMA), Encrusting macroalga (EMA), Blue-green macroalga (a.k.a. cyanobacteria) (BGMA), Halimeda sp. (HAL), Seagrass
Mobile Fauna
VARCHAR2
No
No
Active
Photographs capture a solitary instant in time. As a result, creatures that are not permanently affixed to a single location on the sea floor (e.g. sea cucumbers, sea stars, sea urchins, fish) sometimes also appear in photographs intended for benthic analysis. While every effort should be made to discern what the benthic classification is underneath the mobile fauna, if that is not possible, this classification category should be used. This is both a Tier 1 and Tier 2 classification category.
Mobile fauna (MOBF)
Sediment
VARCHAR2
No
No
Active
Sediment describes a "soft" benthos smaller than rubble (i.e. < 5 mm) which due to it's unsettled nature generally, but not always, is devoid of organisms growing on the individual gains comprising the sediment. However, sea grasses, macroalgae including Halimeda spp., and blue-green algae (a.k.a. cyanobacteria) can be found in soft sediment areas. If a classification point falls on an identifiable organism growing in sediment, that's what should be used for the point classification. The sediment classification should only be used if point falls on the sediment itself.
Sand (SAND), Fine sediment (FINE)
Sessile Invertebrate
VARCHAR2
No
No
Active
Many organisms besides corals and algae are found in coral reef ecosystems. This Tier 1 classification is to be used for animals that are permanently affixed to the substrate. Animals with ability to move about the substrate or swim are classified as Mobile Fauna.
Giant clam (GC), Bivalve (BI), Sponge (SP), Tunicate (TUN), Bryozoan (BRY), Corallimorph (CMOR), Anemone (AMNE), Zoanthid (ZO), Unclassified (UI)
Soft Coral
VARCHAR2
No
No
Active
For the purposes of this image analysis, this category groups a collection of fairly related organisms that do not produce a substantial, rigid calcium carbonate skeleton and therefore are neither reef-builders nor do they lay new foundations for future corals. This classification will include members of Subclass Alcyonaria (octocorals), except blue coral and the organ pipe coral, which includes true soft corals, sea fans, sea whips, sea pens, and also members of the Order Antipatheria (black corals).
Octocoral (OCT), Unclassified (USC)
Turf Alga
VARCHAR2
No
No
Active
Turf algae is a category that includes numerous species from multiple evolutionary groups (red algae, green algae, brown algae, and cyanobacteria). These types of mixed algal assemblages are typically short in stature (< 2 cm in height), and often contain filamentous algae (hair-like morphologies) as opposed to fleshy algae (thick branched or sheet-like morphologies).
Visible turf on rubble substrate (TURFR), Visible turf on hard[bottom] substrate (TURFH), [Invisible turf on] Rubble substrate (RUB), [Invisible turf on] Hard[bottom] substrate (HARD)
Unclassified
VARCHAR2
No
No
Active
A particular analysis point may be unclassified because image quality was poor, because not enough of the surrounding area is visible to definitively classify the organism underneath the point, because the benthos is obstructed by something other than mobile fauna, tape, wand, or shadow (e.g. bubble or smear on the camera lens, high turbidity in the water column).
Tape, Wand, or Shadow (TAPE, WAND, SHAD), Unclassified (UNK)
Data Set Credit
2018
Organization
NOAA Coral Reef Conservation Program
CRCP
1305 East West Highway 10th Floor
Silver Spring
MD
20910-3281
(301) 713-3155
https://coralreef.noaa.gov
Link to the NOAA Coral Reef Conservation Program website
Online Resource
Data Steward
2018
Person
Couch, Courtney S
courtney.s.couch@noaa.gov
Distributor
2019
Organization
National Centers for Environmental Information - Silver Spring, Maryland
NCEI-MD
NOAA/NESDIS E/OC SSMC3, 4th Floor, 1351 East-West Highway
Silver Spring
MD
20910-3282
(301) 713-3277
Distributor
2018
2019
Person
Trick, Kevin L
kevin.trick@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
808-725-5421
Metadata Contact
2018
Person
DesRochers, Annette M
annette.desrochers@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
(808)725-5461
8 am - 5 pm
Originator
2018
Organization
Pacific Islands Fisheries Science Center
PIFSC
pifsc.info@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
808-725-5360
https://www.pifsc.noaa.gov
Pacific Island Fisheries Science Center homepage
Online Resource
8:00 a.m. - 4:30 p.m.
Point of Contact
2018
Person
Vargas-Angel, Bernardo
bernardo.vargasangel@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
(808)725-5423
Ground Condition
Pacific Remote Island Areas (PRIA) including Baker, Howland, and Jarvis islands, Kingman Reef, and Palmyra atoll, and the islands and atolls of American Samoa.
-176.626077
-159.971695
6.451465
-0.382607
Phoenix (Baker and Howland) and Line Islands (Jarvis, Kingman, and Palmyra) of the Pacific Remote Island Areas.
-171.092425
-168.141129
-11.045273
-14.558022
American Samoa, including Tutuila, Ta`u, Ofu and Ologega, and Swains islands, and Rose Atoll.
Range
2018-06-08
2018-06-15
HA1801
Time frame of benthic images collected during ASRAMP 2018, Leg 1 to Howland and Baker islands of the PRIA that were analyzed for benthic community data.
Range
2018-06-19
2018-07-18
HA1801
Time frame of benthic images collected during ASRAMP 2018, Leg 2 to the islands of American Samoa that were analyzed for benthic community data.
Range
2018-07-28
2018-08-11
HA1801
Time frame of benthic images collected during ASRAMP 2018, Leg 3 to Jarvis, Palmyra and Kingman of the PRIA that were analyzed for benthic community data.
Unclassified
Not applicable
Not applicable
NOAA Coral Reef Ecosystem Program (CREP) Data Sharing Recommendations, version 9.0 updated August 12, 2015:
CREP welcomes the opportunity to collaborate on research issues contributing to the scientific basis for better management of marine ecosystems. CREP has a very diverse set of field activities that generates large volumes of data using an array of data collection protocols.
The following recommendations are for your consideration as you use this data:
1) Data analyses should take all field exigencies into account. The most effective way to do this would be active collaboration with CREP principal investigators.
2) In all presentations, product releases, or publications using data generated by CREP, proper acknowledgement of both CREP and the individuals responsible for data collection is expected. Citing the DOI (if available) is preferred, a non-DOI example is listed below.
3) If you collect or generate data for the same study areas, CREP requests that you share relevant information on complimentary data collections.
4) Those receiving data are strongly urged to inform the CREP Data Management Team of any errors and discrepancies that are discovered during the course of using these data. They are further urged to bring to the attention of the Team all problems and difficulties encountered in using these data. This information is necessary in order to improve the collections and to facilitate more efficient and economical data processing and retrieval. The users are asked to supply copies of any missing data that may be located, and to provide information as to significant subsets and special aggregations of data that are developed in using the material provided.
Example citation:
"This publication makes use of data products provided by the Ecosystem Sciences Division (ESD), Pacific Islands Fisheries Science Center (PIFSC), National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA), with funding support from the NOAA Coral Reef Conservation Program (CRCP). The analysis and interpretations presented here are solely that of the current authors.”
Data can be accessed online via the NOAA National Centers for Environmental Information (NCEI) Ocean Archive.
None
Please cite PIFSC Ecosystem Sciences Division (ESD) when using the data.
Example:
Ecosystem Sciences Division; Pacific Islands Fisheries Science Center, 2019: Benthic Cover from Automated Annotation of Benthic Images Collected at Coral Reef Sites in the Pacific Remote Island Areas and American Samoa in 2018, https://www.fisheries.noaa.gov/inport/item/57610.
None
None
https://accession.nodc.noaa.gov/0157633
2019
Organization
National Centers for Environmental Information - Silver Spring, Maryland
PIFSC_H-17-02_2017_SOP_ImageAnalysis_CN.pdf
PIFSC Administrative Report, January 2017: Analysis of benthic survey images via CoralNet : a summary of standard operating procedures and guidelines
2017-01-31T00:00:00
PDF
PDF - Adobe Portable Document Format
https://accession.nodc.noaa.gov/0204646
2019
Organization
National Centers for Environmental Information - Silver Spring, Maryland
BIA_CNET_ROBOT_2018.csv
Benthic community data generated from automated annotation of benthic photoquadrat images by a trained robot in CoralNet that were collected at random and permanent survey sites across the Pacific Remote Island Areas and American Samoa in 2018 by the Pacific Islands Fisheries Science Center Ecosystem Sciences Division as part of the National Coral Reef Monitoring Program.
2019-10-02T00:00:00
csv (comma-separated values)
CSV - Comma Separated Values (Text)
https://coralnet.ucsd.edu/
CoralNet
Online Resource
HTML
CoralNet Home Page
https://origin-apps-pifsc.fisheries.noaa.gov/ecosystem_sciences/
Ecosystem Sciences Division
Online Resource
NOAA Fisheries, Pacific Islands Fisheries Science Center website
https://www.coris.noaa.gov/monitoring/
NOAA National Coral Reef Monitoring Program
Online Resource
PHP
NOAA National Coral Reef Monitoring Program (NCRMP) website.
PIFSC Oracle database view: CoralNet: MV_BIA_CNET_ANALYSIS_DATA_ROB
Data sets derived from the machine-learning, image annotation tool, CoralNet, are highly reliable within the stipulated taxonomic context (Tier 1). Substantial effort is required to manually annotate benthic images, which is expensive and leads to lags before data are available.
Human, expert-analyzed imagery from NOAA’s Pacific Reef Assessment and Monitoring Program is used to train the machine-learning image analysis tool, CoralNet (Beijbon et al 2015), to generate fully-automated Tier 1 benthic estimates of site-level coral cover that are highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less; Williams et al. 2019). CoralNet was generally effective at estimating coral cover (Pearson’s r > 0.92 and with bias of 2% or less in 6 of 7 cases), but performance was mixed for other groups including algal categories.
As image acquisition is relatively straightforward, the capacity of fully-automated image analysis tools to minimize the need for resource-intensive human analysts creates the opportunity to dramatically increase the quantity and consistency of coral reef benthic data available to researchers and managers.
Handheld GPS units were used to locate and mark site locations.
Permanent transects/plots were marked to allow direct, site-level temporal comparisons.
The data set derived from the annotated images is as good as the images themselves; poor images with low contrast, inappropriate white balance, or out of focus may have been discarded. Therefore, total annotations for some sites may have differing number of points between sites (300 annotations are expected per site if there were 30 photographs for the site and 10 points analyzed per photograph). Although the analysis process is statistically robust to allow for differing n (points) between sites, users should be aware of this limitation.
Only shallow water (0 to 30 meter depth range) hard-bottom habitats are surveyed.
Classification is complete to the functional/taxa group level (Tier 1).
Survey sites in which less than 15 images were collected are discarded from the analysis.
The same method of image analysis was used at each surveyed site.
Machine-generated fully-automated benthic estimates of site-level coral cover (Tier 1) are highly comparable to those generated by human analysts (Pearson’s r > 0.97, and with bias of 1% or less; Williams et al. 2019).
Pre- and post-automated benthic image analysis quality control procedures include spot checks for:
1- Image quality integrity: focus, white balance, distance from bottom (too high or too low)
2- image inventory completeness (all images acquired for each island are included in the analysis)
3- Duplicate sites
4- Complete and coherent upload of imagery to CoralNet
5- Integrity and completeness of robot-generated image annotations
Yes
Unknown
Yes
No
Unknown
NCEI-MD
Unknown
The image analysis data is captured in two different locations: exported files from CoralNet that reside on a file server, which are ingested into a table in the PIFSC Oracle database. Both the file server and PIFSC Oracle database are maintained and regularly backed up by PIFSC ITS.
Protocol describing the automated annotation of benthic images to generate benthic community data. Still photographs (30 per survey site) collected during photoquadrat surveys at random and permanent sites in coral reef habitats by the PIFSC Ecosystem Sciences Division were later annotated by a human-trained robot in CoralNet.
Ayotte, P., K. McCoy, A. Heenan, I. Williams, and J. Zamzow. 2015. Coral Reef Ecosystem Division standard operating procedures: data collection for Rapid Ecological Assessment fish surveys. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-15-07, 33 p. doi: 10.7289/V5SN06ZT.
Organization
Pacific Islands Fisheries Science Center, PIFSC
Originator
2015-12-21
https://dx.doi.org/10.7289/V5SN06ZT
NOAA Institutional Repository
Survey protocol for reef fish surveys.
Beijbom, Oscar, Peter J. Edmunds, Chris Roelfsema, Jennifer Smith, David I. Kline, Benjamin P. Neal, Matthew J. Dunlap, et al. 2015. “Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation.” Edited by Chaolun Allen Chen. PLOS ONE 10 (7): e0130312.
Organization
PLOS ONE
Publisher
2015-07-08
https://doi.org/10.1371/journal.pone.0130312
PLOS ONE
Research article, RE: CoralNet
Lozada-Misa P., B. D. Schumacher, and B. Vargas-Ángel. 2017. Analysis of benthic survey images via CoralNet: a summary of standard operating procedures and guidelines. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-17-02, 175 p. doi:10.7289/V5/AR-PIFSC-H-17-02.
Organization
Pacific Islands Fisheries Science Center, PIFSC
Originator
2017-01-31
https://doi.org/10.7289/V5/AR-PIFSC-H-17-02
NOAA Institutional Repository
Protocol to annotate benthic images using CoralNet.
Swanson D, Bailey H, Schumacher B, Ferguson M, Vargas-Angel B. 2018. Ecosystem Sciences Division standard operating procedures: data collection for rapid ecological assessment benthic surveys. U.S. Dept. of Commerce, NOAA Technical Memorandum NOAA-TM-NMFS-PIFSC-71, 63 p. doi:10.25923/39jh-8993.
Organization
Pacific Islands Fisheries Science Center, PIFSC
Originator
2018-08-01
https://doi.org/10.25923/39jh-8993
NOAA Institutional Repository
Survey protocol for coral demographic surveys
Williams ID, Couch CS, Beijbom O, Oliver TA, Vargas-Angel B, Schumacher BD and Brainard RE (2019) Leveraging Automated Image Analysis Tools to Transform Our Capacity to Assess Status and Trends of Coral Reefs. Front. Mar. Sci. 6:222. doi:10.3389/fmars.2019.00222.
Organization
NOAA Pacific Islands Fisheries Science Center
Originator
2019-04-30
https://doi.org/10.3389/fmars.2019.00222
Frontiers in Marine Science: Ocean Observation
Ocean Observation, a specialty section of Frontiers in Marine Sciences, aims to progress our understanding of the ocean and of its role in a changing environment. Frontiers provides online free and open access to all of its research publications.
Research study to assess the feasibility/capacity of machine-learning to generate benthic data from photographs for coral reef ecosystems.
1
RANDOM SURVEY SITES:
A stratified random sampling (StRS) design was employed to select the random sites surveyed for reef fish and corals. The survey domain encompassed the majority of the mapped area of reef and hard bottom habitats in the 0-30 m depth range. The stratification scheme included island, reef zone, and depth. Sampling effort was allocated based on strata area and sites were randomly located within strata. The StRS design effectively reduces estimate variance through stratification using environmental covariates and by sampling more sites rather than sampling more transects at a site. Therefore, site-level estimates and site-to-site comparisons should be used with caution.
Photoquadrat surveys conducted during surveys for reef fish (Ayotte et al. 2015) occur along one 30-m transect that spans the length of two stationary point count (SPC) cylinders used to assess fish abundance (30 images total, Rep A). Benthic photos are taken at 1-m intervals along the right hand side of the 30-m transect line.
Photoquadrat surveys conducted during coral demographic surveys (Swanson et al. 2018) occur along two, independent 18-m transects. Photos of the benthic substrate are taken at 1-m intervals starting at meter one, along the left hand side of each 18-m transect (15 images/transect, 30 images total, Rep A and B).
Person
Williams, Ivor D
ivor.williams@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
(808)725-5427
2
PERMANENT SURVEY SITES:
Permanent sites were chosen in hard-bottom habitat at ~15-m depths, and a subset of the permanent sites called climate stations were established at north, south, east, and west points around each of the islands and atolls. A minimal suite of climate monitoring activities are conducted at permanent sites, whereas a full complement of activities are conducted at climate stations.
Divers estimated and delineated each site’s rectangular perimeter by temporarily placing measuring tapes with 1-m markers starting from a permanently installed reference stake on the reef. Along the nearshore 10-m side of the survey site and the downslope 5-m side, the measuring tapes marked every meter of the L-shaped 15-m transect used for photoquadrat documentation. The divers photographed the reef at 1-m intervals on both sides of the 15-m transect, generating 30 photographs per survey site.
Person
Barkley, Hannah C
hannah.barkley@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
3
IMAGE PROCESSING:
Photoquadrat images are organized by site, color-corrected (if necessary), and quality controlled to remove non-photoquadrat/poor quality images. An optical validation script is used to guarantee that all photoquadrat sites have the respective correct metadata.
Post image analysis quality control steps include spot checks of the machine-generated output data for completeness and adequate analysis of optical data.
Person
Vargas-Angel, Bernardo
bernardo.vargasangel@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
(808)725-5423
4
AUTOMATED ANNOTATION OF BENTHIC IMAGES:
Benthic habitat images were quantitatively analyzed using the web-based, machine-learning, image annotation tool, CoralNet (https://coralnet.ucsd.edu; Beijbom et al. 2015). Ten points were randomly overlaid on each image and the machine-learning algorithm "robot" identified the organism or type of substrate beneath, with 300 annotations (points) generated per site. Benthic elements falling under each point were identified to functional group (Tier 1: hard coral, soft coral, sessile invertebrate, macroalgae, crustose coralline algae, and turf algae) for coral, algae, invertebrates, and other taxa following Lozada-Misa et al. (2017).
The description of each functional group is included in the benthic image analysis classification scheme.
Person
Vargas-Angel, Bernardo
bernardo.vargasangel@noaa.gov
1845 Wasp Blvd.
Honolulu
HI
96818
USA
(808)725-5423
Lozada-Misa P., B. D. Schumacher, and B. Vargas-Ángel. 2017. Analysis of benthic survey images via CoralNet: a summary of standard operating procedures and guidelines. Pacific Islands Fish. Sci. Cent., Natl. Mar. Fish. Serv., NOAA, Honolulu, HI 96818-5007. Pacific Islands Fish. Sci. Cent. Admin. Rep. H-17-02, 175 p. doi:10.7289/V5/AR-PIFSC-H-17-02.
Not Applicable
Not Applicable
57828
Entity
Benthic Image analysis classification scheme - TIER1
57660
Entity
Entities: MV_BIA_CNET_ANALYSIS_DATA_ROB
25274
Data Set
National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected during Stratified Random Surveys (StRS) across American Samoa in 2015, 2018, and 2023.
Cross Reference
Human-annotated benthic cover for stratified random sites, American Samoa
36157
Data Set
National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected during Stratified Random Surveys (StRS) across the Pacific Remote Island Areas since 2014
Cross Reference
Human-annotated benthic cover for stratified random sites, Pacific Remote Island Areas
25383
Data Set
National Coral Reef Monitoring Program: Benthic Cover Derived from Analysis of Benthic Images Collected for Climate Stations across American Samoa since 2015
Cross Reference
Human-annotated benthic cover for permanent sites, American Samoa
36148
Data Set
National Coral Reef Monitoring Program: Benthic Cover from Annotated Benthic Images Collected During Photoquadrat Surveys at Climate Stations across the Pacific Remote Island Areas since 2014
Cross Reference
Human-annotated benthic cover for permanent sites, PRIA
36145
Data Set
National Coral Reef Monitoring Program: Benthic Images Collected During Photoquadrat Surveys at Climate Stations across the Pacific Remote Island Areas since 2014
Cross Reference
Source images
25380
Data Set
National Coral Reef Monitoring Program: Benthic Images Collected from Climate Stations across American Samoa since 2015
Cross Reference
Source images
25247
Data Set
National Coral Reef Monitoring Program: Benthic Images Collected from Stratified Random Sites (StRS) across American Samoa since 2015
Cross Reference
Source images
36154
Data Set
National Coral Reef Monitoring Program: Benthic Images Collected from Stratified Random Sites (StRS) across the Pacific Remote Island Areas since 2014
Cross Reference
Source images
gov.noaa.nmfs.inport:57610
Annette DesRochers
2019-09-17T23:03:10
SysAdmin InPortAdmin
2023-10-17T16:12:19
2019-11-25
Pacific Islands Fisheries Science Center
PIFSC
1845 Wasp Blvd.
Honolulu
HI
96818
USA
808-725-5300
http://www.pifsc.noaa.gov
8:00 a.m. - 4:30 p.m.
1001
Public
No
2019-11-25
1 Year
2020-11-25