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J.A. Goodman 1 , L. Guild 2 , R. Armstrong 1 , B. Lobitz 3 , F. Gilbes 1 , R. Berthold 2 , J. Kerr 4 , Y. Detres 1 1 University of Puerto Rico at Mayagüez 2 NASA Ames Research Center 3 University Corporation at Monterey Bay 4 California State University Monterey Bay HyspIRI Workshop 2009 HyspIRI Workshop 2009 Assessing Change in Assessing Change in Coral Reef Ecosystems using Coral Reef Ecosystems using Hyperspectral Remote Sensing Hyperspectral Remote Sensing Imaging Spectroscopy Imaging Spectroscopy
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Page 1: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

J.A. Goodman 1, L. Guild 2, R. Armstrong 1, B. Lobitz 3, F. Gilbes 1, R. Berthold 2, J. Kerr 4, Y. Detres 1

1 University of Puerto Rico at Mayagüez2 NASA Ames Research Center3 University Corporation at Monterey Bay4 California State University Monterey Bay

HyspIRI Workshop 2009HyspIRI Workshop 2009

Assessing Change in Assessing Change in Coral Reef Ecosystems using Coral Reef Ecosystems using Hyperspectral Remote SensingHyperspectral Remote Sensing

Imaging SpectroscopyImaging Spectroscopy

Page 2: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Science ObjectivesScience ObjectivesAssess the capacity for monitoring change in coral reef ecosysteAssess the capacity for monitoring change in coral reef ecosystems ms using remote sensing.using remote sensing.

Explore spatial scaling relationships related to benthic habitatExplore spatial scaling relationships related to benthic habitatclassification, from the field level to airborne and satellite aclassification, from the field level to airborne and satellite analysis.nalysis.

Use Use NASANASA’’s 2004 and 2005 AVIRIS imagery over La Parguera, PR s 2004 and 2005 AVIRIS imagery over La Parguera, PR to map coral reef benthic types and to map coral reef benthic types and change.change.

Use Use AVIRIS data and field measurements to assess the ecological AVIRIS data and field measurements to assess the ecological impact of the 2005 coral bleaching event in Southwestern Puerto impact of the 2005 coral bleaching event in Southwestern Puerto Rico.Rico.

Improve the interpretation of reef habitat variability and biodiImprove the interpretation of reef habitat variability and biodiversity versity from remote sensing from remote sensing data.data.

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 3: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Study AreaStudy Area

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

EnriqueEnriqueSan CristobalSan Cristobal

LaurelLaurel

Media LunaMedia Luna

Isla MagueyesIsla Magueyes

CorralCorral

TurrumoteTurrumote

Page 4: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Assessment Across Spatial ScalesAssessment Across Spatial Scales

FieldworkFieldwork•• Benthic ReflectanceBenthic Reflectance•• Habitat CompositionHabitat Composition

Airborne ImageryAirborne Imagery•• 2005 AVIRIS2005 AVIRIS•• 3m Spatial Resolution3m Spatial Resolution

Airborne ImageryAirborne Imagery•• 2004 AVIRIS2004 AVIRIS•• 16m Spatial Resolution16m Spatial Resolution

Satellite ImagerySatellite Imagery•• Hyperion (30m spatial)Hyperion (30m spatial)•• HyspIRI (60m spatial)HyspIRI (60m spatial)

Page 5: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

CONCEPT : Assemble a multi-level array of field observations and remote sensing imagery describing a natural reef system

OBJECTIVE: Provide researchers with data from a fully-characterized test environment for the development and validation of subsurface aquatic remote sensing algorithms

LEGACY: Utilize scientific publications and web-based distribution to establish Enrique Reef and its associated data as a lasting standard for algorithm assessment

SeaB

ED:

Enriq

ue R

eef

SeaB

ED:

Enriq

ue R

eef

Benthic MeasurementsWater Column MeasurementsSurface MeasurementsHyperspectral Image Data

Page 6: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Field MeasurementsField Measurements

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

•• Reef benthic spectra Reef benthic spectra –– species, substratespecies, substrate

•• Photogrids Photogrids -- photographsphotographs

•• GPS locationsGPS locations

•• Spectra of calibration targetsSpectra of calibration targets

•• Aeronet station Aeronet station –– atmospheric correctionatmospheric correction

•• Water optical Water optical profiler profiler –– water correctionwater correction

Page 7: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

In Situ ReflectanceIn Situ Reflectance

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

A. palmata

M. annularis

Dead A. cervicornis w/ Algae

Dead M. annularis

Page 8: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Habitat ComponentsHabitat Components

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Coral Rubble

M. annularis S. siderea Porites spp.

A. cervicornis

T. testudinumDictyota spp.

A. palmata

Gorgonians

Page 9: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

PrePre--Processing OverviewProcessing Overview

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Raw Raw imageimage StrayStray--Light CorrectionLight Correction Sun Sun Glint Glint RRemovalemoval

Stray-Light CorrectionStray-Light Correction Sun Glint RemovalSun Glint Removal Atmospheric CorrectionAtmospheric Correction

Example: AVIRIS 2005Example: AVIRIS 2005

Page 10: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Sunglint CorrectionSunglint Correction

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Significant CrossSignificant Cross--Track Sun GlintTrack Sun Glint

No Sun Glint CorrectionNo Sun Glint Correction Incomplete CorrectionIncomplete Correction Full CorrectionFull Correction

CrossCross--Track DirectionTrack Direction

0.00.0 0.0

* Cross-track reflectance at 750nm; 10 line average. (Goodman et al. 2008, Applied Optics)(Goodman et al. 2008, Applied Optics)

Page 11: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Inversion

Model

Inversion

Model

Spectral Input ParametersAquatic Absorption Properties

Generic Bottom Reflectance

Spectral Input ParametersAquatic Absorption Properties

Generic Bottom Reflectance

Image Pre-ProcessingCorrect Stray Light Anomaly

Hedley Glint Removal

Tafkaa Atmospheric Correction

Image Pre-ProcessingCorrect Stray Light Anomaly

Hedley Glint Removal

Tafkaa Atmospheric Correction

Raw AVIRIS Imagery

Image GeometryExplicit pixel by pixel subsurface angles

View Illumination

Inversion OutputWater Properties

Bathymetry

Bottom Albedo (550 nm)

Page 12: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Pre-ProcessedAVIRIS Imagery

Spectral Input ParametersAquatic Absorption PropertiesGeneric Bottom Reflectance

Image GeometryExplicit pixel by pixel subsurface angles

View Illumination

Inversion OutputWater Properties

Bathymetry

Unmixing Output

Benthic Composition

Sand

SAVCoral

Forward

Model

Forward

ModelUnmixing

Model

Unmixing

Model

Spectral Endmembers

0

0.1

0.2

0.3

0.4

0.5

400 500 600 700Wavelength, nm

Ref

lect

ance Sand

AlgaeCoral

0

0.1

0.2

0.3

0.4

0.5

400 500 600 700Wavelength, nm

Ref

lect

ance Sand

AlgaeCoralSAV

Page 13: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

AquaCor v1.5cAquaCor v1.5c

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

View and Illumination AnglesView and Illumination Angles

PixelPixel--byby--Pixel vs. Kernel ProcessingPixel vs. Kernel ProcessingOptional Bathymetry InputOptional Bathymetry Input

Spectral Unmixing OptionsSpectral Unmixing Options

Page 14: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Habitat ChangeHabitat Change

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

2004 2005 2006

2007 2008

Page 15: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Coral Point Count (CPCe)Coral Point Count (CPCe)

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 16: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Habitat ChangeHabitat Change

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 17: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Field SpectraField Spectra

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Sand Components SAV Components Coral Components

Page 18: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Spectral Separability @ 0mSpectral Separability @ 0m

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 19: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Spectral Separability @ 1mSpectral Separability @ 1m

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 20: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Spectral Separability @ 10mSpectral Separability @ 10m

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Page 21: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

LADSLADS

Der

ived

Der

ived

Estimated BathymetryEstimated Bathymetry

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

San CristobalSan CristobalRegression (0Regression (0--10m)10m)r = 0.97r = 0.97mm = 1.08= 1.08aavg. diff. = 0.68mvg. diff. = 0.68mnn = 32,600 pixels= 32,600 pixels

0 meters0 meters10102020

Model Derived BathymetryModel Derived Bathymetry LADS BathymetryLADS Bathymetry

Bathymetry 0Bathymetry 0--20m20m

0 meters0 meters10102020

Page 22: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Habitat ClassificationHabitat Classification

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Sand

SAVCoral

Media LunaMedia Luna

EnriqueEnriqueSan CristobalSan Cristobal

Page 23: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

ObservationsObservations

Introduction Fieldwork Pre-Processing Habitat Classification Results

HyspIRI Workshop 2009HyspIRI Workshop 2009

Difficult to achieve spectral separability at the species level,Difficult to achieve spectral separability at the species level, and and even at the level of general reef classes, particularly when youeven at the level of general reef classes, particularly when youadd the overlying water column.add the overlying water column.

General reef classes are composed of a variety of actual habitatGeneral reef classes are composed of a variety of actual habitatcomponents.components.

Image spectral classification techniques can effectively Image spectral classification techniques can effectively differentiate general reef classes.differentiate general reef classes.

Image classification is correlated with field observations.Image classification is correlated with field observations.

Accurate preAccurate pre--processing is essential for effective classification.processing is essential for effective classification.

The strength of these classification maps, particularly at the sThe strength of these classification maps, particularly at the scale cale of satellite observations, is the capacity to identify and trackof satellite observations, is the capacity to identify and tracklargelarge--scale ecosystem change.scale ecosystem change.

Page 24: Assessing Change in Coral Reef Ecosystems using ... · J.A. Goodman1, L. Guild2, R. Armstrong1, B. Lobitz 3, F. Gilbes1, R. Berthold2, J. Kerr4, Y. Detres1 1 University of Puerto

Project ContactsProject Contacts

James Goodman James Goodman [email protected]@upr.edu

Liane GuildLiane Guild [email protected]@nasa.gov

Roy Armstrong Roy Armstrong [email protected]@upr.edu

Brad Lobitz Brad Lobitz [email protected]@nasa.gov

HyspIRI Workshop 2009HyspIRI Workshop 2009


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