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Internship Opportunity

Assessing juvenile coral density and size distribution using fluorescence imaging and Structure from Motion (SfM) techniques (HI)

Posted on: 01/09/2018
Research Area(s): Internships / General

Summary / Description

In 2014, Hawaii’s coral experienced record levels of bleaching, this followed by continued thermal stress in 2015 and 2016 creating back-to-back bleaching events. In areas already under stress, the added impact of thermal stress can make recovery even more difficult for coral. In an effort to promote conditions favorable to corals in West Maui, the Kahekili Herbivore Fisheries Management Area (KHFMA) was developed to protect herbivorous fishes and sea urchins in 2009. Continued monitoring of this area has shown an increase in herbivorous fish biomass and crustose coralline algae cover since the KHFMA was established. With slow growing coral, changes are more subtle and can take more time. By 2012, coral cover within the KHFMA was on the rise, until the bleaching event in 2015, which caused some coral mortality. This raises some pressing questions as to how these coral reef ecosystems will recover and how long that recovery might take. By monitoring juvenile and young coral growth and survivorship using fluorescence imaging and Structure from Motion technologies, we can gain a better understanding about the resilience of the coral population and the timescale for recovery. Detecting juvenile and young coral (<10 cm maximum diameter) is difficult in the field and even more difficult from photographs. In an effort to improve our ability to quantify juvenile coral cover and recruitment, as well as changes of colonies over time, we are employing an emerging technology – Fluorescence Imagery. This technology is used to detect the chlorophyll-a fluorescence of coral, which makes coral appear to glow in a photograph. This method has the potential to greatly improve the ability to detect very small coral in photographs and make automated delineation and sizing in ArcGIS much more effective. In addition, the use of Structure from Motion (SfM) techniques provides a highly accurate, scaled image, which allows colony size to be recorded along with coral species and substrate type over a large area. Structure from Motion is a photogrammetric method used to create two-dimensional mosaic images and three-dimensional surfaces from a series of photographs. The resulting photomosaic is analyzed to compare changes in coral colonies and seafloor structure over time.As a team member of this project, your activities could include post-processing of seafloor imagery, classification of sessile organisms and benthic habitats, creating 3D surface models from image series, spatial analysis and map production using ArcGIS, creating product documentation (metadata), creating imagery and maps for presentations and outreach, and more. Your activities will be varied and your ability to follow precise instructions, work independently as well as with a team while producing high quality work are crucial.

Skills Required

Interns are not required to have previous experience with Fluorescence Imaging or Structure from Motion techniques. A working knowledge of ArcGIS Desktop and experience with Microsoft Excel is needed. Experience working with digital imagery and knowledge of Hawaiian benthic flora and fauna are not required but preferred. Interns must pay close attention to detail, have strong organizational skills, the ability to focus on repetitive tasks, work with a variety of data and work well independently under the guidance and supervision of a mentor within the ESD team.


The intern position is located at NOAA Fisheries, Pacific Islands Fisheries Science Center (PIFSC), Ecosystem Sciences Division (ESD), located at the NOAA Inouye Regional Center (IRC), 1845 Wasp Blvd, Building 176 in Honolulu, Hawaii. Note: The IRC is located on a military base. Selected applicants will need to meet several requirements in advance of the internship to gain base access.

Other Information

Intern Supervisor:
Rhonda Suka
Number of Slots Available:
Is free housing available:
Can international students be placed:

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NCCOS delivers ecosystem science solutions for stewardship of the nation’s ocean and coastal resources, in direct support of NOS priorities, offices, and customers, and to sustain thriving coastal communities and economies.

National Centers for Coastal Ocean Science
1305 East West Highway, Rm 8110
Silver Spring, MD 20910
Phone: (240) 533-0300 / Fax: (301) 713-4353
Email: nccos.webcontent@noaa.gov