Assessing reef health using a low-altitude remote

sensing platform

Joshua LevyUH Biology10/15/15

Coral Reefs

• Biodiversity hotspots• Economically important: Fisheries, tourism,

coastal protection, ecosystem services– Global

• $29.8 billion/year (Cesar et al .2003)

– Hawaii• $360 million/year (Cesar et al. 2002)

The Problem

• Coral reefs are in global decline– 27% already substantially

degraded– Loss of additional 31% by

2030 (Wilkinson, 2000)

• 3rd global coral bleaching event – “Bleachapalooza”

NOAA CRCP

Causes of Coral Bleaching

– High temperature• Thermal anomalies

– El Niño– PDO– Anthropogenic climate change…?

– Coastal runoff• Sedimentation• Freshwater • Nutrients

Clark Little

Effects of coral bleaching• Reduced reef resilience • Ecosystem resilience

“The capacity of an ecosystem to absorb disturbances or shocks, and adapt to change while retaining function and structure”. McClanahan et al. 2012

Reduced resilience

Jen Smith

Phase Shifts

Reduced recovery

Disease

Competition

Hawaiian Reefs

• 85% of US coral reefs• Huge economic

importance• Decrease in reef

resilience after bleaching could impact Hawaiian economy

Hawaii coral bleaching events• 2014

– First recorded mass bleaching event on Hawaiian Islands

– Extensive bleaching in MHI’s, NWHI’s• Moderate-high recovery • Lisianksi mortality

– 1.5 miles

• 2015– Recorded throughout MHI’s,

NWHI’s• Kahe (first recorded bleaching)• Kaneohe Bay*• 22 other Oahu sites

How can corals recover?

• “Normal” SST• Good water quality• High herbivore biomass

How can we help corals recover?

• Good water quality– Reduce pollutants/ coastal

runoff• High herbivore biomass– Reduce fishing

Protect affected areas– Where are they?

Reef Survey Methodologies

• Small scale– In situ (cm-mm)• Snorkel/scuba

• Large scale (km-m)– High Altitude

Remote Sensing• Satellite /Airplane

• Incomplete spatial assessments

Goals• Develop cheap, fast,

spatially accurate, survey technique – High resolution data– Entire large reef area

(16,000m2)– Coral species – Coral bleaching– Coral health at various

spatial scales

UAV’s• Unmanned Aerial Vehicles – Cheap (~$2000)– Portable (4kg)– Low altitude flight (1-400m)• Large resolution range (m-mm’s)

– 15-20min flights– Programmable autonomy

Study Site: Kaneohe Bay • 50+ patch reefs

• History of pollutants/coastal runoff– Cultivation and

agriculture– Stream modification – Dredging– Sewage outfalls

Bleaching in KBay

• 2014– Extensive bleaching– Reports of high recovery

• 2015– Bleaching extent?– Recovery?– Management?

Low Altitude Aerial Surveys

• Ground station• Datalink package• iPad mini• External battery

• DJI P2• H3-3D Gimbal• GoPro 3

Raw Results

Post Processing

• Orthomosaics– Agisoft Photoscan

~1500m2

Structure from Motion

• Estimate 3-D structures from multiple overlapping 2-D image sequences– Identify POI’s using SIFT

• Edges, gradients• Insensitive to varying

orientation/ illumination• # depends on image

quality, resolution, heterogeneity of scene

Post Processing

• Image Classification– Texture + color models – Distinguish • Coral species• Coral vs. sand vs. algae

• Quantify color change • Spatial analysis using ArcGIS

• Geo-reference • Spatial measurements

Caras & Karnieli. Ground-Level Classification of a Coral Reef Using a Hyperspectral Camera. Remote Sens. 7, 7521–7544 (2015).

Workflow

Data collection

Image corrections/Ort

homosaic

Classification

Spatial analysis

Predicted Outcomes

• K-Bay patch reef atlas– Highlight severe

bleaching– Monitor recovery

• Inform Kaneohe Bay reef management groups

Management tool

• Long term monitoring of reef condition– Predict mortality events

• Locate and better manage reefs impacted by local anthropogenic stress

• Increase reef resilience to coral stressors

Future Projects

• Expand to other shallow water coastal habitats

• Automated workflow – Cloud processing– Machine-learning image

classification models• Neural network

Citizen science

• Affordable, user-friendly, low altitude remote sensing package for coastal communities– Hawaii• Coastal communities

depend on healthy reefs• Near real-time reef

assessment• Local (self) enforcement of

dynamic, situational management policies

Scientific advancement

• Citizen science data collection– Generates large quantity of accurate,

unbiased data from various locations – Global reef database – Various temporal and spatial scales

Increase overall understanding of coastal reef system dynamics

Acknowledgments C. Hunter, UHM BiologyE. Hochberg, BIOSE. Franklin, UHM/HIMBR. Bidigare, UHM SOESTR. O’Connor, NOAA/UHM WRRCDARUH MOPNOAA #NA10NM4520163