373Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
Marine habitats map of “Isla del Caño”, Costa Rica,
comparing Quickbird and Hymap images classification results
A.C. Fonseca1,2,4, Héctor M. Guzmán3, Jorge Cortés1,2,4 & Carlomagno Soto5
1. Centro de Investigación en Ciencias del Mar y Limnología (CIMAR), Ciudad de la Investigación, Universidad de
Costa Rica, 11501-2060 San José, Costa Rica; ana.fonsecaescalante@ucr.ac.cr
2. Escuela de Biología, Universidad de Costa Rica, 11501-2060 San José, Costa Rica; jorge.cortes@ucr.ac.cr
3. Smithsonian Tropical Research Institute, P.O. Box 0843-0392 Ancon, Republic of Panama; guzmanh@si.edu
4. The Nature Conservancy, consultant, 230-1225, San José, Costa Rica
5. Centro Nacional de Alta Tecnología, 1174, San José, Costa Rica; csoto@conare.ac.cr
Received 22-v-2009. Corrected 20-Ix-2009. Accepted 20-x-2009.
Abstract: Isla del Caño is a marine protected area on the south Pacific coast of Costa Rica, surrounded by coral
reefs and coral communities. The ecology of these coral reefs has been studied for over 20 years, but they have
not been mapped. Maps are considered a great research, planning, management and monitoring tool. Medium to
high resolution images (HyMap 2005 and Quickbird 2007 respectively) were processed and classified in order
to test and compare their accuracy in producing a marine habitat map. Manta tow surveys were performed in the
field for identification of 7 marine habitats 1. Coral community; 2. Coral reef; 3. Bed rock; 4. Sand; 5. Sand with
boulders; 6. Sand with rodolyths; and 7. Deep water. The overall accuracy was slightly higher using Quickbird
(87%) than using Hymap (60%), however the difference was not significant. The map produced using Quickbird
was selected to represent the marine habitats of Isla del Caño. This map will help to analyze the adequate size
and zoning of the marine protected area. Rev. Biol. Trop. 58 (1): 373-381. Epub 2010 March 01.
Keywords: marine habitat map, coral reef, Costa Rica, Isla del Caño, Hymap, Quickbird.
Maps are considered a great research,
planning, management and monitoring tool
because they can provide the extent and dis-
tribution of benthic habitats and can improve
conservation efforts (Mumby et al. 1997, Guz-
man et al. 2004). The use of different spatial
resolution satellite images and aerial photog-
raphy has proven to be relatively effective in
mapping (Mumby et al. 1997). Hyperspectral
sensors, like Hymap (18 optical bands, 16m
pixel size), increase our capability to detect
narrow spectral bands that can be used for
discriminating benthic communities of low and
moderate mapping complexity (Kutser et al.
2003). However, the high spatial resolution of
sensors like Quickbird (2m pixel size), which
is comparable to IKONOS (4m pixel size),
has proven to be important for high mapping
complexity independently of the spectral reso-
lution (Capolsini et al. 2003). Remote sensing
has been applied already with success in the
tropical eastern Pacific region for medium-high
resolution mapping of coral reefs in Panama
(Guzman et al. 2004, Benfield et al. 2007).
Coral reefs are the most diverse marine
ecosystems (Reaka-Kudla 1997) and they are
being threatened by natural and human impacts
(Coté & Reynolds 2006). Costa Rica has coral
communities and reefs on the Caribbean coast
and on the Pacific side (coast and off-shore
islands) (Cortés & Jiménez 2003a, 2003b).
Corals are in better condition on the protected

374 Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
off-shore islands, like “Isla del Caño”, where
there is less impact from human activities
(Cortés & Jiménez 2003b). However, every-
where corals are also affected by global climate
change (Wilkinson 2008), with little chance
of recovery (Richmond 1993, Nyström et al.
2000, Nyström & Folke 2001), with few excep-
tions in the tropical eastern Pacific, included
“Isla del Caño” (Guzmán & Cortés 2001).
“Isla del Caño” is surrounded by fringing
reefs (Guzman & Cortés 1989), sandy (Cortés
et al. 1996) and rocky bottoms. It is protected
by the category of Biological Reserve since
1976 for terrestrial habitats and since 1984 for
marine habitats, and it is an important step in
for the eastern Pacific marine corridor. Its coral
reefs have been studied for more than 20 years
(Guzman & Cortés 2001). Cortés et al. (1996)
produced deep bottom profiles and sediment
analysis on surrounding waters from 30 to
110m deep. Fonseca et al. (in prep.) completed
the bathymetric model of “Isla del Caño” with
information from shallow waters. Coral reefs
of Costa Rica have not been mapped so far
with high resolution, high accuracy and field
validation.
It is very important for an adequate man-
agement of the marine environments of the
island, that receives daily a large number of
visitors for diving and beach recreation, to have
an accurate marine habitats map. This map will
help analyze the adequate size and zoning of
the marine protected area. The objective of
this study was to compare the performance of
Hymap (16m) and Quickbird (2m) in creating
a marine habitats map around “Isla del Caño”,
and to give recommendations for the manage-
ment of these marine environments, aiming to
increase the size of the protected area.
MATERIAL AND METHODS
Site description:“Isla del Caño” is located
15km west from the Península de Osa, south
Pacific of Costa Rica, eastern tropical Pacific
(ETP), and it is protected as a Biological
Reserve (Figs. 2 and 3). Mean water visibility
is 20m. The island has five coral reef flats,
mainly built by pocilloporid corals covered by
crustose coralline algae, and isolated microat-
olls of Porites lobata. The reef slope and base is
dominated by the massive coral Porites lobata,
which is the predominant species of the island.
The shallow sections of the reef are structured
mainly by physical factors: wave action, tem-
perature and salinity fluctuations, and low
tide exposure. While the deeper sections are
controlled by biological interactions: bioero-
sion, damselfish algal lawns, and corallivores
(Guzman 1986, 1988, Guzman & Cortés 1989,
2001, Fonseca 1999, Fonseca et al. 2006).
Image processing: A Hymap imagery
from the island was obtained from the Costa
Rican Airborne Research and Technology
Application (CARTA) mission, in March 29,
2005, at 15:30 and at altitude of 7820m; a
project of the National Aeronautics and Space
Administration (NASA). This image had a
medium spatial resolution (16m pixel size).
It was georeferenced to ground control points
from the island coastline and had atmospheric
correction performed with the HyCorr soft-
ware that converts the radiance values into
apparent surface reflectance values (level
compatible with ATREM3 processing). An
unsupervised classification (30 classes) was
performed on this image before going to the
field as a guide for collecting the ground con-
trol points. The near infrared band (NIR) was
used to mask out the land. Areas of cloud and
shade were removed from the Hymap image
by using manual digitized areas of interest in
ENvI 4.1. software.
A Quickbird imagery with a resolution of
2m and a radius of 6km around the island was
taken on February 24, 2007, at 16:28, after
the fieldtrip. An atmospheric correction was
performed to this image using the dark pixel
subtraction (Lyzenga 1978, 1981; Armstrong
1993).
The images and the maps were processed
using ENvI 4.1 and ArcGIS 9.1 and enhanced
with a 2% linear stretching. The image process-
ing procedure is summarized in Fig. 1.

375Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
Field work: The scientific expedition to
“Isla del Caño” took place from January 25 to
February 5, 2007, on the M/v Phoenix, as part
of an initiative of The Nature Conservancy to
improve the coastal and marine management
of the Península de Osa. Ground control points
from the coastline and marine environments
of the island were collected during manta tow
surveys (Rogers et al. 1994, Guzman et al.
2004) using a GPS Garmin GPSMAP 76S with
an accuracy of ±10m. visual identification of
marine habitats from the surface was surveyed
at 994 points to a maximum depth of 20m using
pre-identified mapping categories.
Image pre-processing: The level of geo-
metric accuracy of the raw imagery was checked
from the ground control points collected along
the coastline. A Principal Component Analysis
was performed to the 18 bands of the visible
spectral range of Hymap in order to compute a
component that includes the contributing effects
of all these bands, to reduce redundancy in the
datasets and to integrate radiometric variance
associated with the multispectral bands (sensu
Jensen 2004, Mishra et al. 2006). PCA bands
1, 2, 3 were selected since they accounted
for 99% of the variance. The following band
combinations were also processed for accuracy
comparison, and the water column was corrected
for these bands combination with the empirical
method Depth Invariant Index (Lyzenga 1978,
1981): bands 15,7,3 equivalent to the ETM mean
wavelength for each visible band (1,2,3); bands
13,5,1 equivalent to the ETM minimum wave-
length for each visible band (1,2,3); bands 13,9,1
equivalent to the CASI bands 2,4,5; bands 13,6,1
equivalent to the CASI bands 2,3,5; and bands
13,7,1 equivalent to the default bands selected
for the True Color Composition of Hymap.
Quickbird image with
geometric correction
Atmospheric correction
ROI for deep dark waters
+ Dark pixel subtraction
NDVI Land mask +
Clouds and shadows mask
1. Linearisation depth vs. radiance per band (1, 2, 3)
2. ROI for shallow and deep sand
3. Variance and covariance between bands
4. Ratio of attenuation coecients per pair of bands
1. Supervised classication with MLC
2. Filter (3x3 window)
3. Accuracy assessment
1. Supervised classication with MLC
2. Filter (3x3 window)
3. Accuracy assessment
Depth Invariant Index (DII) of
botton type for band pairs
DII=In(bi)+(ki/kj*In(band j))
Training with growing ROI
from ground control points
Training with growing ROI
from ground control points
Global accuracy = 87% Global accuracy = 60%
Comparison of overall
accuracies using Z-test
Training from ground
control points for coral
reefs and communities
PCA - Principal Component Analysis; ROI - Region of Interest; MLC - Maximum Likelihood Classier
Live coral cover map Habitats dimension Layout
QB Marine
Habitats Map
Validation of georeference
with ground control points
PCA
Submap of shallow waters
NDVI Land mask + Clouds
and shadows mask
Hymap image with
atmospheric and geometric
correcction
Fig. 1. Image processing scheme.

376 Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
The water column was corrected in the
Quickbird image using the “Depth Invariant
Index” (Lyzenga 1978, 1981). The band pairs
used for the Depth Invariant Index and final
classification of this image were 3/1, 3/2, 2/1.
Marine Habitats Classification: Half of
the ground control points were chosen ran-
domly for image classification training data
and the other half for accuracy assessment.
From both images, supervised spectral sig-
natures were generated for each habitat class
using each point as a seed pixel for a “growing
region of interest (ROI)”, so the number of
pixels for Hymap grew to 62 and for Quick-
bird to 5870. ROI’s were assessed with photo-
interpretation. The maximum likelihood was
chosen for the supervised classification of
both images and a 3x3 filter was applied to
smooth the borders between categories in the
final map.
The following seven marine habitat cat-
egories were used for a supervised classifica-
tion of both images: 1. Coral community: coral
colonies on sandy or rocky substrate; 2. Coral
reef: corals forming a framework; 3. Bed rock:
bare rocky substrate; 4. Sand: sandy substrate,
soft bottom; 5. Sand with boulders: loose rocks
in sandy bottom; 6. Sand with rodolyths: round
red calcareous algae in sandy bottom; 7. Deep
water: areas deeper than 20m.
Accuracy Assessment: Overall accuracy
and Kappa coefficient were used to compare
the classification results from both images.
Kappa accounts for the amount of agreement
that could be expected due to chance alone:
poor = less than 0.20; fair = 0.20 to 0.40; mod-
erate = 0.40 to 0.60; good = 0.60 to 0.80; and
very good = 0.80 to 1.00 (Juurlink & Detsky
2005). Z tests were performed to test for sig-
nificant differences between the Kappa coef-
ficients. In order to determine the distribution
of live coral cover, the following coral cover
categories were used during the manta tow sur-
vey: 1. High: live coral>40%; 2. Moderate: live
coral 20-40%, 3. Low: live coral <20%.
The overall classification accuracy for the
different band combinations of Hymap is very
similar (Table 1), so the different classifications
were compared visually. The PCA bands 1,2,3,
were selected for final classification of Hymap
because they yielded a marine habitats map
closer to what was found in the field.
TABLE 1
Comparison of overall accuracy using a medium to high resolution classification
Image Band selection criteria Band composition
Overall
accuracy (%)
Kappa
coefficient
Quickbird visible bands DII 3/1, 2/1, 3/2 87.33 0.79
Hymap PCA bands (99%) PCA 1, 2, 3 59.68 0.49
All processed selected band pairs DII 12 pair bands
13/7, 7/1, 13/1, 13/6, 6/1,
13/9, 9/1, 13/5, 5/1, 15/3,
15/7, 7/3
56.45 0.46
Bands 15,7,3 equivalent to the ETM mean
wavelength for each visible band (1,2,3)
DII 15/7, 15/3, 7/3 53.22 0.42
Bands 13,5,1 equivalent to the ETM
minimum wavelength for each visible band
(1,2,3)
DII 13/5, 13/1, 5/1 58.06 0.48
Bands 13,9,1 equivalent to the CASI bands
2,4,5
DII 13/9, 13/1, 9/1 64.52 0.55
Bands 13,6,1 equivalent to the CASI bands
2,3,5
DII 13/6, 13/1, 6/1 66.13 0.57
Bands 13,7,1 equivalent to the default bands
selected for the True Color Composition of
Hymap
DII 13/7, 13/1, 7/1 64.52 0.56

377Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
RESULTS
The overall accuracy for classification (7
classes) was slightly higher using Quickbird
(87%) than using Hymap (60%), but the differ-
ence was not significant (Z=4.33, df=61/5869,
p=0.05); the Kappa coefficient for Quickbird is
good (0.79) and for Hymap is moderate (0.49)
(Table 1); deep water and sand category showed
the best accuracies. Quickbird improved the
user’s accuracy for 4 classes, and it was more
trustable because the image was taken at a date
closer to the time of the field trip, so the map
produced from Quickbird was selected to show
the marine habitats distribution from “Isla del
Caño” (Fig. 2).
Coral reefs and coral communities in “Isla
del Caño” account for 13% (325 pixels) and
14% (353 pixels) from shallow environments
(2537 pixels) of the Quickbird image respec-
tively (this proportion was calculated omitting
the deep water category, > 20m). The result-
ing area was 1412m2 (0.14ha) for coral com-
munities and 1300m2 (0.13ha) for coral reefs
(Table 2).
During classification the sand with
rodolyths was confused mainly with coral
community, coral community was mainly mis-
classified as sand with boulders, all deep water
pixels were classified correctly, bedrock was
misinterpreted mainly as coral reef, sand with
boulders was mostly mistaken as sand with
rodolyths and coral reef as bedrock. The user
and producer accuracies in the classification of
coral reefs and coral communities are relatively
high (Table 2).
Fig. 2. Marine habitats map of the marine protected area of “Reserva Biológica Isla del Caño”, and tourist diving sites.
Results from the Quickbird image classification.
83º56’0” W 83º55’0” W 83º54’0” W 83º53’0” W 83º52’0” W 83º51’0” W 83º50’0” W
8º
46
’0”
N
8º
45
’0”
N
8º
44
’0”
N
8º
43
’0”
N
8º
42
’0”
N
8º
41
’0”
N
8º
40
’0”
N
Isla del
Caño
Pacic
Ocean
Pacic
Ocean
Costa Rica
Legend
Parkrangers house
Tourist divin sites
Marine limit of biological reserve
Sand with houlders
Sand
Bedrock
Coral community
Sand with rodolyths
Coral reef
Deep Water
Paraíso
Barco
Hundido
Jardín
Isla del Caño
AnclaCueva
Bajo
El Diablo
N
E
S
W
0 0.5 1 2 3 4 km
1:75000

378 Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
Live coral cover is higher in the northern
and eastern coral reefs and communities, espe-
cially in the main coral flats of Bajo Glynn,
Platanillo, Bajo Beltrán, Bajo Richmond and
Bajo Cortés (Fig. 3).
DISCUSSION
Green et al. (2000) suggest that 60 to
80% is the recommended overall accuracy for
coastal and marine resources inventory, so both
sensors were considered good for medium to
high resolution mapping and quantification
of these habitats, as an input for coastal and
marine management plans (Table 1). The higher
spectral resolution of Hymap compensates to
some extent for the lack of spatial resolution.
Although the main limitation of Hymap is the
loss of the habitats particular shape, currently
Hymap is more cost effective than Quickbird
in the case of Costa Rica, since 80% of the
country was covered with Hymap in 2005,
and images have a much lower user cost than
Quickbird. This fact justifies the use of Hymap
images to continue mapping shallow marine
habitats from Costa Rica, with a medium to
high resolution. If there will be possibility to
collect airborne data in the future in Costa Rica
we would recommend lower flights to obtain
higher spatial resolutions of less than 1-2m, and
planning the field work at the same time than
the flight to improve the classification accuracy,
although this would be more expensive. Habitat
categories could have been combined in three
broad classes to yield an even higher accuracy,
but the 7 classes map was considered of more
value for management purposes. Other studies
using high resolution sensors like Quickbird or
IKONOS, same classification method and an
average of seven habitat classes report similar
overall accuracies (Maeder et al. 2002, Mumby
& Edwards 2002, Mishra et al. 2006, Benfield
et al. 2007). However Benfield et al. (2007)
improved the classification of Quickbird by
17% with the “Object Oriented Method”, which
was not available for this study.
The user and producer accuracies in the
Quickbird classification of coral reefs and coral
communities, which are the habitats of more
interest in this study, are relatively high (Table
2), however, as pointed by Mishra et al. (2006),
there is still a significant amount of intermix-
ing between marine habitats even at a spatial
resolution of 2m.
Coral reefs and communities in “Isla del
Caño” were impacted by the 1982-83 and the
TABLE 2
Confusion matrix for the marine habitats map classified using Quickbird (n=5870 pixelsa)
Class/ Ground
truthing (%)
Sand with
rodolyths
Coral
community
Deep
water
Bedrock
Sand with
boulders
Sand
Coral
reef
Total nº
pixels
Commission
(%)
User Acc.
(%)
Unclassified 0 0 0 0 0 0 0 0 0
Sand with rodolyths 36.81 19.41 0 1.23 0 4.32 2.76 190 68.42 31.58
Coral community 5.52 53.85 0 27.16 56.52 1.37 21.87 353 58.36 41.64
Deep water 0 0 100 0 0 0 0 3333 0 100
Bedrock 0 3.3 0 24.69 0 0 34.18 190 89.47 10.53
Sand with boulders 12.88 0 0 0 0 0 0.42 23 100 0
Sand 44.79 0 0 0 9.78 94.30 0 1456 5.63 94.37
Coral reef 0 23.44 0 46.91 33.70 0 40.76 325 40.92 59.08
Total nº pixels 163 273 3333 81 92 1457 471
Omission (%) 63.19 46.15 0 75.31 100 5.7 59.24
Prod. Acc. (%) 36.81 53.85 100 24.69 0 94.3 40.76
a. Overall Accuracy (%)=(5126/5870)*100=87.33; Kappa coefficient =0.79.

379Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
1997-1998 El Niño, with loses of up to 50% of
the live coral coverage (Guzman et al. 1987,
Guzman & Cortés 1989, 2001), and by phy-
toplankton blooms in 1985, maybe associated
with La Niña, with loss of some coral species
from shallow reef zones (Guzman et al. 1990).
Currently they are recovering (Guzman & Cor-
tés 2001, Guzman et al. in prep.).
MANAGEMENT RECOMMENDATIONS
“Isla del Caño” holds a great diversity
of marine habitats and should be considered
an important area within the Eastern Tropical
Marine Corridor. Close to the island (4km to
the northeast) there is a carbonated bank that is
being used as a diving site called “Paraíso”, but
it is not within the Biological Reserve border
which is 3km offshore. We recommend that this
carbonate bank be considered as an important
feature that should be represented by expand-
ing the marine protected area to 4km offshore.
There is some illegal commercial fishing that
should be regulated to improve current protec-
tion. Many fish and shrimp fishing vessels are
anchoring inside the Biological Reserve where
83º54’0” W 83º53’0” W 83º52’0” W
8º
44
’0”
N
8º
43
’0”
N
8º
43
’0”
N
8º
42
’0”
N
N
E
S
W
Isla del
Caño
Pacic
Ocean
Pacic
Ocean
Costa Rica
0 0.25 0.5 1 1.5 2 km
1:30000
Osa
Isla del Caño
Bajo
Beto
Bajo
Glynn
Bajo
Beltrán
Punta
Ballena
Bajo
Richmond
Bajo
Cortés
Platanillo
Legend
Live coral cover
Parkrangers house
Trails
Low
Moderate
High
Fig. 3. Live coral cover around “Isla del Caño”.

380 Rev. Biol. Trop. (Int. J. Trop. Biol. ISSN-0034-7744) Vol. 58 (1): 373-381, March 2010
they pollute the water with solid and liquid
wastes. Patrolling is done mostly on the north
side of the island and in day time. We strongly
recommend reinforcing the vigilance all around
the island and all day and night long. For this
purpose the reserve needs more staff and navi-
gation equipment. The protected area zoning,
carrying capacity and behavior of vessels and
visitors and other regulations according to the
management plan should be respected in order
to secure the long term protection of the island.
Mainly, the number of diving sites should not
be increased, the number of tourist vessels per
buoy and visitors per day should be reduced,
and fishing and fishing vessels should not be
allowed at all within the reserve.
ACKNOWLEDGMENTS
Thanks to O. Breedy, J.J. Alvarado, C.
Fernández, A. Segura, E. Ruiz, C. Sevilla, M.
Montero, C. Benavídez, D. Torres and the crew
of the Phoenix for their help. We also thank L.
Handley, from USGS, for the meticulous revi-
sion of the English language and content of
this manuscript. This study was elaborated by
CIMAR and the Smithsonian Tropical Research
Institute, under contract #CR-OSA0038S from
TNC, as part of their conservation activities in
ACOSA.
RESUMEN
Isla del Caño es un área marina protegida en la costa
del Pacífico de Costa Rica y está rodeada de arrecifes
coralinos. La ecología de estos arrecifes coralinos ha sido
estudiada a lo largo de 20 años pero todavía no habían sido
mapeados. Los mapas son considerados una buena herra-
mienta de investigación, planificación, manejo y monito-
reo. Imágenes de mediana y alta resolución (Hymap 2005
y Quickbird 2007 respectivamente) fueron procesadas y
clasificadas con el fin de evaluar y comparar su desempeño
en la elaboración de un mapa de hábitats marinos. En el
campo se realizaron sondeos tipo Manta para la identifica-
ción de siete hábitats marinos: 1. Comunidad coralina; 2.
Arrecife coralino; 3. Roca; 4. Arena; 5. Arena con cantos;
6. Arena con rodolitos; y 7. Agua profunda. La exactitud
de la clasificación resultó un poco mayor usando Quickbird
(87%) que Hymap (60%), sin embargo la diferencia no
era significativa. Se seleccionó el mapa resultante de la
clasificación con Quickbird para representar los hábitats
marinos de Isla del Caño. Este mapa puede ayudar a ana-
lizar el tamaño adecuado y la zonificación del área marina
protegida.
Palabras clave: mapa de hábitats marinos, arrecifes de
coral, Costa Rica, Isla del Caño, Hymap, Quickbird.
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