Khalil

Seasonal and spatial variability of Sea Surface Temperature (SST)
and Chlorophyll-a concentration using MODIS data

in East Kalimantan waters, Indonesia
IDHAM BIN KHALIL

March, 2007
Seasonal and spatial variability of Sea Surface Temperature (SST)
and Chlorophyll-a concentration using MODIS data
in East Kalimantan waters, Indonesia
by
Idham bin Khalil
Thesis submitted to the International Institute for Geo-information Science and

Earth Observation in partial fulfilment of the requirements for the degree of MSc
Geo-information Science and Earth Observation for Environmental Modelling and
Management, Specialisation: Environmental Modelling and Management.
Thesis Assessment Board
Chairman : Dr. Ir. Kees de Bie (ITC, The Netherlands)

External Examiner : Prof. Peter Atkinson (University of Southampton, UK)
First Supervisor : Dr. Ir. Chris Mannaerts (ITC, The Netherlands)
Second Supervisor : Mr. Valentijn Venus (ITC, The Netherlands)
International Institute for Geo-Information Science and

Earth Observation, Enschede, The Netherlands
Disclaimer
This document describes work undertaken as part of a programme of study at

the International Institute for Geo-information Science and Earth Observation.
All views and opinions expressed therein remain the sole responsibility of the
author, and do not necessarily represent those of the institute.
Abstract
Regular monitoring of near shore and open water parameters for marine
management in East Kalimantan waters, Indonesia is still limited. The objective of
this research is to determine and interpret the seasonal and spatial variability of sea
surface temperature (SST) and chlorophyll-a concentration (Chl-a) in East
Kalimantan waters. A standard MODIS SST split window algorithm and empirical
chlorophyll-a OC-3M algorithm were used to generate the Level 2 MODIS SST and
Chl-a images. From March 2005 to August 2006, the SST and Chl-a were retrieved
from the sensor data in East Kalimantan coastal and open sea waters. In situ
measurements from near shore waters were used to validate the MODIS Level 2
data. A comparison of MODIS with in situ values for SST and Chl-a shows
promising result (RMSE=1.21 0C, Bias=-3.42, n=121 and RMSE=1.01mg.m-3,
Bias=+2.45, n=75), although some anomalies were observed in the retrievals in both
datasets. The analysis of seasonal variations indicates that there was low SST
variability between wet and dry season. There was also low variability between SST
values in near shore and open sea waters. However, for both seasons, open sea SST
was paradoxically found to be warmer than the near shore waters. The Chl-a maps
revealed low Chl-a variability between wet and dry season. Different value ranges
in Chl-a were found between near shore waters (1.00-56.00 mg.m-3) and open
waters (1.00-4.00 mg.m-3). The Chl-a values retrieved from MODIS for both
seasons were higher in near shore water. The SST and Chl-a in near shore waters
have a low positive interrelationship in wet season. During dry season, the
relationship between these two variables varies from positive to negative. This
study demonstrated that MODIS Level 2 data from Malaysia Ground Receiving
Station (MGRS) can successfully be used to obtain SST and Chl-a in Southeast
Asian coastal and open waters.
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Acknowledgements
I would like to express my deep and sincere gratitude to a number of people and
organisations who became involved with this thesis, one way or another.
GEM Erasmus Mundus consortium particularly Prof. Andrew Skidmore (ITC, The
Netherlands), Prof. Petter Pilesjo (Lund University, Sweden), Prof. Katarzyna
Dabrowska (University of Warsaw, Poland) and Prof. Peter Atkinson (University of
Southampton, United Kingdom) who have always been very supportive throughout
these 18 months.
My first supervisor, Dr. Chris Mannaerts from Department of Water Resource, ITC
for his understanding, encouraging and personal guidance has been a great value for
me. Mr. Valentijn Venus, my second supervisor from Department of Natural
Resources, ITC who has supported me throughout my thesis with his valuable
comments and suggestions. I would have been lost without both of you.
Malaysian Government particularly Malaysian Centre for Remote Sensing

(MACRES) for providing the satellite imageries and giving me the opportunity to
study in Europe. It was truly an eye-opening and rewarding experience of my life.
I also wish to thank GEM students 2005, the most reliable friends one could have!
Not forgotten, Malaysians in Enschede; Edna, Zaki, Fidah, Fauzi and Prof.
Kamaruzaman Jusoff whose presence helped make the completion of my study
possible.
Ayahanda Khalil bin Yusof, Bonda Siti Rohani bt. Sh. Abdullah serta keluarga di
Kuantan dan Pontian; your love, support, and patience have been a blessing
throughout my study.
I owe my loving thanks to my wife Nor Haslinda, my kids Muhammad Amnan,

Muhrizah Humaira’ and Muhrizah Huda. Pengorbanan mereka tidak dapat
digambarkan. Thesis ini didedikasikan istimewa buat mereka. Alhamdulillah.
Idham Khalil
Enschede
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Table of contents
1. Introduction ..................................................................................................... 1
1.1. Research background .............................................................................. 1
1.2. Research problem .................................................................................... 2
1.3. Research objectives ................................................................................. 4
1.4. Research questions .................................................................................. 4
1.5. Thesis Outline.......................................................................................... 5
2. Literature Review ............................................................................................ 7
2.1. Sea Surface Temperature (SST) .............................................................. 7
2.1.1. SST from space................................................................................... 8
2.1.2. In Situ SST Measurement ................................................................. 10
2.2. Chlorophyll-a concentration (Chl-a)..................................................... 11
2.2.1. Chlorophyll-a from space ................................................................. 11
2.2.2. In situ Chl-a measurement................................................................ 13
3. Study Area...................................................................................................... 15
3.1. Introduction ........................................................................................... 15
3.2. Climate .................................................................................................. 16
3.3. Oceanography........................................................................................ 16
3.3.1. Salinity.............................................................................................. 17
3.3.2. Dissolved Oxygen (DO) ................................................................... 17
3.3.3. Nitrate ............................................................................................... 17
3.3.4. Phospate............................................................................................ 17
4. Materials and Method ................................................................................... 19
4.1. MODIS Datasets.................................................................................... 19
4.1.1. Atmospheric correction .................................................................... 20
4.1.2. Cloud mask ....................................................................................... 20
4.1.3. Geometric correction ........................................................................ 20
4.1.4. Sea Surface Temperature.................................................................. 21
4.1.5. Chlorophyll-a concentration............................................................. 21
4.1.6. Correlation analysis between SST and Chl-a ................................... 22
4.2. Accuracy Assesment ............................................................................. 22
4.3. In situ measurement............................................................................... 23
4.4. Research approach................................................................................. 24
5. Results............................................................................................................. 25
5.1. Sea surface temperature......................................................................... 25
5.2. Chlorophyll-a concentration.................................................................. 29
5.3. Correlation between SST and Chl-a...................................................... 33
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6. Discussion ....................................................................................................... 35
6.1. Cloud cover in the study area ................................................................ 35
6.2. Sea Surface Temperature....................................................................... 37
6.2.1. In situ SST versus MODIS Level 2 SST .......................................... 37
6.2.2. SST in the near shore waters............................................................. 38
6.2.3. SST in the open sea........................................................................... 39
6.3. Chlorophyll-a concentrations ................................................................ 40
6.3.1. In situ Chl-a vs MODIS Level 2 Chl-a............................................. 40
6.3.2. Chl-a in the near shore waters .......................................................... 42
6.3.3. Chl-a in the open sea ........................................................................ 43
6.3.4. Striping lines in Chl-a images .......................................................... 43
6.4. Correlation between SST and Chl-a...................................................... 44
7. Conclusions and Recommendations............................................................. 47
7.1. Conclussions.......................................................................................... 47
7.2. Recommendations ................................................................................. 47
References ............................................................................................................ 49
Appendices........................................................................................................... 57
Appendix-1 : In situ stations, SST and Chl-a concentrations .............................. 57
Appendix-1 : Con’t .............................................................................................. 58
Appendix-1 : Con’t .............................................................................................. 59
Appendix-1 : Con’t .............................................................................................. 60
Appendix-2 : Bivarite Fit of IDWA SST by in situ SST...................................... 61
Appendix-3 : Bivarite Fit of Kriging SST by in situ SST .................................... 62
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List of figures
Figure 1-1: Berau Marine Protected Area (WWF, 2006)........................................... 3

Figure 2-1: NOAA AVHRR SST Global Map 6 – 8 May 2006 (NOAA, 2006) ....... 7
Figure 2-2: Plot of radiance from a blackbody against wavelength, with temperature
as a variable (Lillesand, T. M., and R. W. Kiefer, 2004). .......................................... 8
Figure 2-3: Absorption coefficient and penetration depths of infrared waves
(Wieliczka et al., 1989). ............................................................................................. 9
Figure 2-4: Idealized temperature profiles of the near-surface layer (10-m depth).. 10
Figure 3-1: Study area, East Kalimantan waters, Indonesia ..................................... 15
Figure 3-2: Map of Indonesian Throughflow (ITF) (Susanto et. al, 2006) .............. 16
Figure 4-1: SeaBass data points 2006 (SeaBass, 2006)............................................ 22
Figure 4-2: In situ sample stations............................................................................ 23
Figure 4-3: Simplified schema of the research approach ......................................... 24
Figure 5-1: Daily SST derived from MODIS; Wet Season...................................... 26
Figure 5-2: Daily SST derived from MODIS; Dry Season April – August 2005 .... 27
Figure 5-3: Daily SST derived from MODIS; Dry Season August 05–August 06 .. 28
Figure 5-4: Daily Chlorophyll-a concentration derived from MODIS; Wet Season 30
Figure 5-5: Daily Chl-a derived from MODIS; Dry Season, April – August 2005 . 31
Figure 5-6: Daily Chl-a derived from MODIS; Dry Season August 05–August 06 32
Figure 6-1: Percentage of SST pixels compared to cloud and land pixels ............... 35
Figure 6-2: Percentage of Chl-a pixels compared to cloud and land pixels ............ 36
Figure 6-3: Atmospheric Transmission Window (CRISP, 2006)............................. 36
Figure 6-4: In situ SST vs MODIS IDWA vs MODIS Kriging ............................... 37
Figure 6-5: Bivarate Fit of IDWA and Kriging SST ................................................ 37
Figure 6-6: Minimum and maximum SST in near shore area .................................. 38
Figure 6-7: Minimum and maximum SST in open waters ....................................... 39
Figure 6-8: In situ Chl-a vs. MODIS IDWA vs. MODIS Kriging........................... 40
Figure 6-9: Bivarate Fit of IDWA and Kriging Chl-a.............................................. 41
Figure 6-10: Minimum and maximum Chl-a in near shore waters .......................... 42
Figure 6-11: Minimum and maximum Chl-a in open waters ................................... 43
Figure 6-12: SST and Chl-a correlation in East Kalimantan near shore waters...... 44
Figure 6-13: MODIS cloud mask for SST and Chl-a Level 2.................................. 45
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List of tables
Table 2-1: MODIS specifications (NASA, 2006) .................................................... 11

Table 2-2: Detailed MODIS band specification (NASA, 2006)............................... 12
Table 4-1: MODIS Level 2 data structure ................................................................ 19
Table 4-2: WGS_1984_UTM_Zone_50N parameters ............................................. 20
Table 4-3: Coefficients for the MODIS Band 31 and 32 SST retrieval ................... 21
Table 5-1: SST of East Kalimantan Water from March 2005 to August 2006......... 25
Table 5-2: Chl-a of East Kalimantan Water from March 2005 to August 2006 ...... 29
Table 5-3: SST and Chl-a relationship .................................................................... 33
Table 6-1: Cold pixels percentage in near shore waters ........................................... 39
Table 6-2: Cold pixels percentage in open waters.................................................... 40
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List of Abbreviations
ASEAN The Association of Southeast Asian Nations

ATBD Algorithm Theoretical Basis Documents
Chl-a Chlorophyll-a concentration
CO2 Carbon dioxide
CH4 Methane
GeoTIFF Geographic Tagged Image File Format
HDF Hierarchical Data Format
ICMM Integrated coastal and marine management
IDWA Inverse distance weighted average
ITF Indonesian Throughflow
IUCN International Union for the Conservation of Nature & Natural Resources
K Kelvin
LWIR long-wave Infrared
mg.m-3 milligram per cubic meter
mg/l milligram per liter
MODIS Moderate Resolution Imaging Spectroradiometer
MPA Marine protected area
NO2 Nitrogen dioxide
ppt part per thousand
RMSE Root Mean Square Error
SeaBass SeaWiFS Bio Optical Archive and Storage System
SeaWIFS Sea-viewing Wide Field-of-view Sensor
SST Sea Surface Temperature
SWIR short-wave Infrared
UNESCO United Nations Educational, Scientific and Cultural Organization
UTM Universal Transverse Mercator System
WGS84 World Geodetic System 1984
WWF World Wildlife Federation
0
C degree Celcius
µm micrometer
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SEASONAL AND SPATIAL VARIABILITY OF SEA SURFACE TEMPERATURE (SST)
AND CHLOROPHYLL-a CONCENTRATION USING MODIS DATA
IN EAST KALIMANTAN WATERS, INDONESIA
1. Introduction
1.1. Research background
The Association of Southeast Asian Nations (ASEAN) consist of 10 countries,

Brunei Darussalam, Cambodia, Indonesia, Lao PDR, Malaysia, Myanmar, the
Philippines, Singapore, Thailand and Vietnam. For the past few decades, ASEAN
has been successfully been a leader in economic development among developing
countries. However in a development and environmental study, McDowell (1989)
described that apart from the most promising economic growth in this region, it is
suffering with the depletion of natural resources. Deforestation, erosion and over
fishing mainly because of the rapid population growth have been exhibited as an
indicator to an unbalanced development in ASEAN. As there is a close relationship
between people and the environment, economic development and environmental
issues should not be approached separately in this region. McDowell (1989) further
described that in order for ASEAN to maintain its position as a new growing
economic power, management of natural resource in this region is very crucial.
In reaction to the above suggestion and parallel to The 1992 UN Rio de

Janeiro – the ‘Earth Summit’, the ASEAN Summit 1997 formed a sustainable
development framework for ASEAN countries. Known as ASEAN Vision 2020, the
main aim was described as : “… a clean and green ASEAN with fully established
mechanisms for sustainable development to ensure the protection of the region’s
environment, the sustainability of its natural resources and the high quality of life of
its peoples” (UP-MSI et al., 2002).
In terms of the marine environment, ASEAN contributed to about 14% of

the world’s marine fish production and has 30% of the world’s coral reefs: the most
species diversity in the world (UP-MSI et al., 2002). In order to achieve sustainable
fisheries, The ASEAN Vision 2002 has translated into 2001 Plan of Action on
Sustainable Fisheries for Food Security for the ASEAN Region. One major step in
this plan is to establish marine protected areas (MPAs). The International Union for
the Conservation of Nature and Natural Resources (IUCN) defines marine protected
areas (MPA) as “an area of sea especially dedicated to the protection and
maintenance of biological diversity, and of natural and associated cultural resources,
1
and managed through legal or other effective means” (IUCN, 1994). In lay man
terms, marine protected areas could be described as an alternative way to protect
marine fauna and flora.
As more marine protected areas have been established in the ASEAN region, the
challenge to continuously provide decision makers with sufficient and reliable data
is consider as a major constraint in MPAs management. With limited budget, a cost
estimated at USD 1,584.00 per km2 per year for collecting data and maintaining
MPAs (Balmford et al. 2004) is consider very high for developing countries. The
rapid development in remote sensing technology and its capability to provide two-
dimensional synoptic view offers an alternative to help in these issues. While there
are always arguments on the ‘surface’ monitoring of ocean, there are positive
tendencies in ecosystem–based precautionary management to rely on surrogate’s
data (Vanderklift and Ward, 2000) e.g geophysical features (Ray, 1997) because of
the complexity of ecosystems and lack of data. The reliability of the ocean surface
‘skin’ information has also been proven by Macintyre (1977) who stated that the
first millimetres below the surface represents the top half of the ocean.
In this study, the capability of geophysical product from Moderate Resolution

Imaging Spectroradiometer (MODIS) which is Level 2 sea surface temperature
(SST) and chlorophyll-a concentration (Chl-a) were assessed in providing ocean
parameters for Indonesian waters from May 2005 – August 2006 for a better marine
protected areas management.
1.2. Research problem
This study focuses on marine resources depletion in Indonesian marine

environment. The study area, East Kalimantan waters which consist of Berau
Marine Protected Area as shown in Figure 1-1 is well known as one of the most
beautiful area for coral reef in the world. With 507 species of hard coral, Berau
coral biodiversity is considered as the second highest in Indonesia and the third in
the world. Among 120 potential outstanding universal values, Derawan islands
which are located in Berau waters have been classified as one of the top seven
(UNESCO, 2002).
Several studies had shown that the total fish catch from Berau waters have been
declining for the past ten years (Ismuranty, 2003) due to the depletion of the coral
reefs. Less coral reef areas means less fish stock as coral reefs area are breeding
2
Chapter 1 - Introduction
grounds for fish. While the caused of coral depletion is well known coming from
inland activities e.g deforestration and sea temperature changes e.g El-Nino 1997-
1998, continuous monitoring and studies for better marine management is very
limited (Burke et al. 2002) .
Figure 1-1: Berau Marine Protected Area (WWF, 2006).
In order to maintain the sustainable marine resources in the area, the Indonesian
government under Berau Regent Regulation No. 31, 2005 has declared Berau
District’s coastal and marine area as a marine conservation area (WWF, 2006).
Integrated coastal and marine management (ICMM) of this area requires mapping of
marine resources and monitor basic changes (e.g SST, chlorophyll-a concentration
etc.) as revealed by Dahuri (2000); Erdmann and Mossa (1990).
Considering the huge area of 1.2 million hectares of the Berau Marine Protected
Areas (MPA), this study used satellite remote sensing imageries as to provide such
oceanographic datasets. Previous research has proved that continuous monitoring of
SST from space can act as early warning to detect any SST anomalies that could
harm the coral reef such as coral bleaching events (Liu et al., 2003). In day to day
operations, spatial information on SST and Chl-a distribution has been used widely,
e.g. in coral reef management (Udy et al., 2005), fishery forecast (Solanki et al.,
2003; Solanki et al., 2005) or as a fundamental data source for coastal management
planning (Mumby et al., 1999).
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1.3. Research objectives
The main objective of this research is to determine and interpret the seasonal and
spatial variability of SST and Chl-a in the study area.
The specific objectives of this study are:

i. To map the spatial distribution of SST in East Kalimantan waters
using MODIS data during wet (November – March) and dry season
(April – October).
ii. To map the spatial distribution of Chl-a in East Kalimantan waters
using MODIS data during wet and dry season.
iii. To determine the relationship between SST and Chl-a during wet
and dry season in open and near shore waters.
1.4. Research questions
The research will try to answer the following questions:
i. Are there any major differences in SST distribution between wet and
dry season?
ii. Are there any major differences in SST distribution in open sea and
near shore?
iii. Are there any major differences in Chl-a distribution between wet
and dry season?
iv. Are there any major differences in Chl-a distribution in open sea and
near shore?
v. What kind of relationship exists between SST and Chl-a distribution
in Kalimantan during wet and dry season in open waters, and
vi. What kind of relationship exists between SST and Chl-a distribution
in Kalimantan during wet and dry season in near shore waters?
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Chapter 1 - Introduction
1.5. Thesis Outline
This thesis contains seven chapters.
The first chapter contains the general overview of the research. Research problems
were clearly defined in section two. Research objectives and research questions will
then explained in section three and four.
Chapter two describes the overall description of the study area.
Chapter three reports the previous studies in the research field. Major concepts and
definition has been reported in 2 sections. The first section covers the description of
detection of sea surface temperature followed by the literature of chlorophyll-a in
second section.
Chapter 4 presents a comprehensive methodology used in this study including the

relevant algorithms and coefficients.
Chapter 5 presents results for the SST and Chl-a distribution in East Kalimantan
waters during dry and wet season. The result also included the variation between the
near shore water and open sea.
Chapter 6 presents the discussion for the SST and Chl-a distribution in East
Kalimantan waters during dry and wet season. The variation of minimum and
maximum values between near shore and open sea also will be discussed.
Furthermore, the correlation between SST and Chl-a in this region was also
explained.
Finally, Chapter 7 presents the conclusions derived from the analysis and
suggestions for future works.
5
6
2. Literature Review
2.1. Sea Surface Temperature (SST)
Historically, measurements of SST have been made in situ, from ships and buoys.
MetOffice (2006) described that such in situ observations has two disadvantages.
Firstly, in situ measurement offer very limited spatial coverage. Secondly, it
enlarges the margin of error between one measurement to the next. These two issues
could be resolved by satellite observation throughout the globe. McClain et al.
(1985; 1989) stated that the retrieval of SST from satellite measurements offers the
advantage of global coverage (Figure 2-1) and has been performed routinely since
1981 to a point accuracy of ~ 0.5 K.
Figure 2-1: NOAA AVHRR SST Global Map 6 – 8 May 2006 (NOAA, 2006)
Marine researchers found that the measurement of SST is essential to understand

how our ocean behaves; understand its relationship with ocean flora and fauna and
not least to understand the global climate. Operationally, SST information has been
used as a boundary layer input and an assimilation data set for atmospheric
circulation/forecast models (Emery et al., 2001). Alexander and Scott (2002) stated
that measurements of SST are extremely useful for applications such as monitoring
7
large-scale anomalies e.g El Nino and trends possibly associated with global climate
change (e.g. Lawrence et al., 2004).
2.1.1. SST from space

According to the Planck Law, each warm object on Earth emitted certain amount of
thermal radiation at a particular wavelength depending on its temperature (Rybicki
et al., 1979). For a much clearer picture, the relationship between Earth’s surface, its
brightness temperature and the spectral radiance can be understood by referring to
Figure 2-2. From the graph, it was clearly shown that for Earth, the spectral radiance
peaks at a wavelength around 10 µm.
Figure 2-2: Plot of radiance from a blackbody against wavelength, with temperature
as a variable (Lillesand, T. M., and R. W. Kiefer, 2004).
This is the basic concept why most of the infrared satellite sensors used band 10 µm
to detect infrared radiation for SST detection. As there will be never 100% or ‘clear
sky’ condition (without atmospheric disturbance), one channel measurement will
never be a success. Water vapor, CO2, CH4, NO2 and aerosols are the major
constituents that determine the atmospheric disturbance (Minnett, 1990). McMillin
8
Chapter 2 – Literature Review
(1975) and Barton (1995) described that most satellite SST algorithms are derived
from the measurement using two channels. Two commonly use wavelengths range
are the long-wave Infrared (LWIR; 10.00-12.5 µm) and the short-wave IR (SWIR;
3.7-4.2 µm) (Brown et al., 2005). The absorption for each wavelength is different.
These differences were then used to correct the atmospheric disturbance before the
sea surface temperature can be obtained.
Apart from thermal infrared remote sensing, SST can also be detected using
microwave sensors. However due to lower signal strength of the Earth's Planck
radiation curve in the microwave region (approximately in the range of 30 cm to 1
mm), accuracy and resolution is poorer for SST derived from passive microwave
measurements.
Bear in mind that, although it is possible to obtain SST reading from thermal
infrared sensors, the maximum sea depth that infrared wavelength can penetrate is
around 500 µm (Wieliczka et al., 1989). In other words, if our interest is in getting
the sea surface temperature more than that depth, we might end up with such a big
uncertainty. In his research, Wieliczka et al., (1989) has plot a detailed relationship
between infrared optical constants and clear water as shown in Figure 2-3.
Figure 2-3: Absorption coefficient and penetration depths of infrared waves

(Wieliczka et al., 1989).
9
2.1.2. In Situ SST Measurement
While the understanding of SST measurement will become a dominant knowledge,

we could not admit the importance of the in situ SST measurement. There are
several important terms that have been used to describe in situ SST. Donlon et al.
(2002) categorized the vertical structure of SST into four major categories
/definitions as shown in Figure 2-4. The first category is interface SST, SSTint.
Interface SST is the temperature at the very top of the ocean. To be more specific, it
is the temperature at the air-sea thin layers. The second category is the skin SST,
SSTskin. By definition, the SSTskin is the temperature that can be measure up to
500 µm. Just below SSTskin, we have the layer of ocean where heat transfer process
is actively happened. SST from this layer is called subskin SST, SSTsubskin. The
final in situ SST categories is the subsurface SST, SSTdepth. In layman term,
SSTdepth is also called ‘bulk’ SST.
Figure 2-4: Idealized temperature profiles of the near-surface layer (10-m depth)
of the ocean (Donlon e. al., 2002).
10
2.2. Chlorophyll-a concentration (Chl-a)
Similar to SST, the capability of satellite remote sensing in providing global

coverage snapshot has been an advantage to the measurement of Chl-a in the marine
environment. In marine remote sensing, Chl-a has been used a proxy to the
existence of phytoplankton. Butler et al. (1972) reported that the Chl-a above 0.2
mg/l indicate the presence of sufficient fish food to sustain a viable commercial
fishery. In general term, chlorophyll-a can be described as a vital pigment for
photosynthesis in phytoplankton. Phytoplankton are marine microscopic plants
which well known as the base of marine food chain. A detailed definition has been
described by Water Resource Disciplines USGS (2005) as “Phytoplankton is the
plant part of the plankton. They usually are microscopic, and their movement is
subject to the water currents. Phytoplankton growth is dependent upon solar
radiation and nutrient substances. Because they are able to incorporate as well as
release materials to the surrounding water, the phytoplankton have a profound effect
upon the quality of the water. They are the primary food producers in the aquatic
environment and commonly are known as algae”.
2.2.1. Chlorophyll-a from space

The earliest sensor that has been used for mapping and measuring chlorophyll-a
concentration was Coastal Zone Color Scanner (CZCS) (Mitchell, 1994), Feldman
et al. (1989). Realising the importance of synoptic global observation of marine
parameters, several ocean color sensors than were launched,; Sea-viewing Wide
Field-of-view Sensor (SeaWIFS) – July 1997; Moderate Resolution Imaging
Spectroradiometer AM (MODIS AM) also known as MODIS Terra in December
1999 and MODIS PM or MODIS Aqua - May 2002 (NASA, 2006) . The detail
specifications of the MODIS sensors are shown in Tables 2-1 and 2-2.
Table 2-1: MODIS specifications (NASA, 2006)
Parameters Details
1. Orbit 705 km, 10:30 a.m. descending node (Terra)
or 1:30 p.m ascending node (Aqua), sun-
synchronous, near-polar, circular
2. Swath Dimensions 2330 km (cross track) by 10 km
(along track at nadir)
3. Spatial Resolution 250 m (bands 1-2)
500 m (bands 3-7)
1000 m (bands 8-36)
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Table 2-2: Detailed MODIS band specification (NASA, 2006)
Primary Use Band Bandwidth Primary Use Band Bandwidth

Land/Cloud/ Surface/ 3.660 -
1 620 - 670 20
Aerosols Cloud 3.840
Boundaries Temperature 3.929 -
2 841 - 876 21
3.989
Land/Cloud/ 3.929 -
3 459 - 479 22
Aerosols 3.989
Properties 4.020 -
4 545 - 565 23
4.080
1230 - Atmospheric 4.433 -
5 24
1250 Temperature 4.498
1628 - 4.482 -
6 25
1652 4.549
2105 - Cirrus 1.360 -
7 26
2155 Clouds 1.390
Ocean Water Vapor 6.535 -
8 405 - 420 27
Color/ 6.895
Phytoplankt 7.175 -
9 438 - 448 28
on/ 7.475
Biogeochemi Cloud 8.400 -
10 483 - 493 29
stry Properties 8.700
Ozone 9.580 -
11 526 - 536 30
9.880
Surface/ 10.780 -
12 546 - 556 31
Cloud 11.280
Temperature 11.770 -
13 662 - 672 32
12.270
Cloud Top 13.185 -
14 673 - 683 33
Altitude 13.485
13.485 -
15 743 - 753 34
13.785
13.785 -
16 862 - 877 35
14.085
Atmospheric 14.085 -
17 890 - 920 36
Water 14.385
Vapor 18 931 - 941
19 915 - 965
Notes : Bands 1 to 19 are in nm; Bands 20 to 36 are in µm
12
The main reason Chl-a being used as an indicator for phytoplankton existence is
because it is the most common pigment in most of marine phytoplankton (Li et al.,
2002). The spectral characteristic of this pigment which located between blue–green
wavelengths of light spectrum has made it detectable from optical remote sensing.
Other pigments that can be also found in plants are Carotene - an orange pigment,
Xanthophyll- a yellow pigment, Chlorophyll b - a yellow-green pigment and
Phaeophytin - a gray pigment. In other literature, chlorophyll pigment in
phytoplankton can also be categorized as chlorophyll a, b, c and carotenoids
(Doerffer et al., 1999).
To date, most Chl-a detection methods from satellite sensors used band-ratio
algorithms (blue-green band reflectance ratio). In general, phytoplankton absorbs
blue light more strongly than green light. Thus, the estimation of the relative
amounts of phytoplankton can be achieved by measuring the amounts of light
leaving the ocean waters at those two bands (blue and green).
2.2.2. In situ Chl-a measurement

The normal practice for in situ Chl-a measurement is by direct water sampling
(NRMA, 2006). Filter papers with the size of 0.45 μ normally were used during the
filtering process. The concentration of chlorophyll-a measured in µg/l then
determined using spectrophotometer. With the current technology, it is now possible
to directly measure the chlorophyll from water column using fluorescence.
13
14
3. Study Area
3.1. Introduction
The study area located within the rectangular region 00 45’ 2.93”N to 40 39’
43.86”N and 1170 11’ 22.38”E to 1200 34’ 24.21”E encompass an area of about
228,254 km2 (Figure 3-1).
Figure 6 : Study area : East Kalimantan waters
Figure 3-1: Study area, East Kalimantan waters, Indonesia
15
In order achieve the objective of understanding the variability of SST and

chlorophyll-a between near shore and open waters, Kalimantan waters has been
subdivided into Open sea area: 17,771 km2 and near shore area: 13,046.6 km2 which
is actually the Berau Marine Protected Area. The open sea was defined as the area
more than 24 nautical miles (44 km) from the shoreline and near shore area is the
area within the 24 nautical miles.
3.2. Climate
Like other parts of Indonesian waters, Kalimantan waters is affected by the Asia-
Australia (AA) monsoon; southeast monsoon (April-October) and northwest
monsoon (November- Mac), (Susanto et. al, 2006) . The southeast monsoon brings
the warm and dry air from Australia into Kalimantan waters whereas the northwest
monsoon is associated with warm and moist air. Nurlidasari (2004) stated that there
are not many differences in SST values between coral reef area and the area close to
the Berau river. SST in the coral reef area is reported to have values ranges from
29.50C to 300C while 29.50C to 30.50C for the second one.
The highest wind speeds in this area were recorded during July and August while
the lowest wind speed is in October and November.
3.3. Oceanography
Kalimantan waters play an important role in the transfer of heat and fresh water in
the region because it is located in the Indonesian Throughflow (ITF) as shown in
Figure 3-2.
Figure 3-2: Map of Indonesian Throughflow (ITF) (Susanto et. al, 2006)
16
Chapter 3 – Study Area
Notes :
i. The solid black arrows - North Pacific thermocline water;
ii. The black dashed arrows - South Pacific lower thermocline water.
iii. The dashed arrows (green and blue) - seasonally reversed surface water
flow due to the Asia-Australia monsoon.
Wiryaman et al. (2004) reported a detailed summary of physical oceanographic in

East Kalimantan waters as follows:
3.3.1. Salinity
The average surface salinity in East Kalimantan for open sea is 33.5 ppt. However,
as approaching the river mouth, the salinity decreases (32.5 – 33.0 ppt). For salinity
at 100 meter depth, the value range from 34.0-34.5 ppt for open sea and 33.5 ppt for
river mouth area.
3.3.2. Dissolved Oxygen (DO)

Dissolved oxygen (DO) could be explained as the oxygen gas that is dissolved in
water. Most of DO exist in marine environment produced by phytoplankton during
photosynthesis process. In East Kalimantan waters, the average value for coastal
and open waters is 2.5 to 4.5 mg/l.
3.3.3. Nitrate
The open sea and coastal water surface nitrate not vary much (0.4 to 1.8 mg/l). The
100 meter depth nitrate however show slightly different pattern. For near shore the
value is 0 to 1.2 mg/l while > 1.2 mg/l for open sea.
3.3.4. Phospate
The average 100 meter depth phosphate in East Kalimantan for open sea is 1.2 to
2.4 mg/l and 0 to 1.2 mg/l for river mouth area.
17
18
4. Materials and Method
4.1. MODIS Datasets
The primary remotely sensed data used in this study were obtained from Malaysia
Ground Receiving Station (MGRS) which has been acquiring MODIS data since 2nd
February 2005. TeraScan software was used to process MODIS raw data into Level
2 MODIS with a spatial resolution of 1 km. The initial MODIS Hierarchical Data
Format (HDF) was exported into Geographic Tagged Image File Format (GeoTIFF)
for further analysis in ArcGis. For the purpose of this study, only Channel 1 of SST
MODIS Level 2 was used while Channels 5 and Channel 10 for Chl-a analysis.
Channel 10 was used for the cloud masking. The detail specification of the 32 byte
GeoTIFF files are shown in Table 4-1 below:
Table 4-1: MODIS Level 2 data structure
SST MODIS Level 2 GeoTIFF

Channels Parameters
Channel 1 SST
Channel 2 SST4
Chl-a MODIS Level 2 GeoTIFF
Channels Parameters
Channel 1 CZCS_pigment
Channel 2 : K_490
Channel 3: L2_flags
Channel 4 : calcite_conc
Channel 5 chlor_MODIS mgm-3
Channel 6 chlor_MODIS_log mgm-3
Channel 7 chlor_fluor_base
Channel 8 chlor_fluor_effic
Channel 9 chlor_fluor_ht
Channel 10 cldmsk_flags
Channel 11 cocco_conc_detach
Channel 12 cocco_pigmnt_conc
Channel 13 common_flags
Channel 14 phycoeryth_conc
Channel 15 phycou_conc
Channel 16 pigment_c1_total
Channel 17 quality
Channel 18 susp_solids_conc
19
4.1.1. Atmospheric correction

The atmospheric corrections applied to MODIS raw data can be categorised into
two components. The first component uses the atmospheric correction algorithm
described by Gordon and Voss (2004) in Algorithm Theoretical Basis Documents
(ATBD) 18 version 5. The output of the algorithm is the normalized water-leaving
reflectance which then be used for determinations of Chl-a as shown below:
[ρω(λ)]N= ρω(λ)/t*(θ0, λ)
where;
ρω = water leaving reflectance
t* = diffuse transmittance
θ0 = solar zenith angle
λ = MODIS band wavelength
The second component of atmospheric correction which is for SST data has been
taken into account in the SST split window algorithm (Brown and Minnet, 1999).
See SST algorithm in section 4.1.4 for further details. All atmospheric correction
procedures were readily built into the TeraScan software processing module.
4.1.2. Cloud mask

A cloud mask with a spatial resolution of 1 km used in this study was generated by
MODIS algorithm. A total of 17 to 19 spectral bands ranging from 0.55-13.93 µm
were considered in the process of developing the mask as described by Baum and
Platnick (2006) and Kathleen (2006).
4.1.3. Geometric correction

Shoreline vector and MODIS dataset were geo-referenced to the same World
Geodetic System 1984 (WGS84) Universal Transverse Mercator (UTM) Projection
System in ArcGIS software. The detail parameters are listed in Table 4-2 below.
Table 4-2: WGS_1984_UTM_Zone_50N parameters
Projection : Transverse_Mercator
(WGS84_UTM_Zone_50N)
False_Easting: 500000.000000
False_Northing: 10000000.000000
Central_Meridian: 117.000000
Scale_Factor: 0.999600
Latitude_Of_Origin: 0.000000
20
Chapter 4 – Materials and Method
4.1.4. Sea Surface Temperature

A total of 21 scenes of SST were processed using split window technique based on
ATBD-MOD25 (Brown and Minnet, 1999). The equation is given as follows:
SST = C1 + C2 * T31 + C3*T3132 +C4(sec(θ)-1)* T3132
where;
T31 is the band 31 brightness temperature (BT)
T3132 is (Band32 - Band31) BT difference
θ is the satellite zenith angle
Ci coefficients listed in Table 4-3
Table 4-3: Coefficients for the MODIS Band 31 and 32 SST retrieval
algorithm ( Brown and Minnet, 1999)
Coefficients
T30 – T31 <= 0.7 T30 – T31 > 0.7
C1 1.228552 1.692521
C2 0.9576555 0.9558419
C3 0.1182196 0.0873754
C4 1.774631 1.199584
By using the above coefficients, Brown and Minnet found that the SST result has a
predicted RMS error of 0.337K with a bias near 0.
4.1.5. Chlorophyll-a concentration

Chlorophyll-a data were processed based on ATBD MOD19, Carder et al.
(2003) using empirical chlorophyll-a OC3M algorithm as follows:
2 + 0.659R 4
Ca = 100.283 – 2.753R + 1.457 R ;
where R = log10 ⎡ R rs443 > R rs488 ⎤

⎢ ⎥
⎣ R rs551 ⎦
Ca : Chlorophyll-a concentration (milligram per cubic metre, mg.m-3)

Rrs : remote sensing reflectance
R : blue-green band ration [dimensionless]
21
4.1.6. Correlation analysis between SST and Chl-a

The SST and chlorophyll-a images which has the same spatial resolution (1 km) and
projection system were brought into ArcGis. Due to ArcGis limitation in performing
raster to raster correlation analysis, the raster layers were converted into point
features. Then, an extraction of x-y coordinates were performed to the point features
in order to get the x-y coordinates. This step was repeated for every SST and
chlorophyll-a layers. Having the SST values, chlorophyll-a values together with
their x-y coordinates for every pixel, a correlation analysis were carried out for each
pixel.
4.2. Accuracy Assesment
This study does not call for the creation of a new local empirical MODIS algorithm.
Research approach was conducted using the existing standard MODIS algorithm
and compared with limited in situ data. The current accuracy of standard SST
MODIS algorithm based on ATBD 25 is 0.337K (Brown and Minnet, 1999). In
order to maintain the accuracy of their Chl-a algorithm, MODIS has a continuous
validation programme using the in situ data from SeaWiFS Bio Optical Archive and
Storage System (SeaBass) as shown in Figure 4-1. The MODIS Terra chlorophyll-a
product gives root mean square error (RMSE) of 0.554 mg.m-3.
Figure 4-1: SeaBass data points 2006 (SeaBass, 2006)
22
Chapter 4 – Materials and Method
4.3. In situ measurement
In situ measurements were conducted from 11 to 29th August 2006. Measurements

of SST were made using the Horiba U-10 water quality checker. The accuracy of
the instrument is ± 0.3 0C as stated by Cole-Parmer (2006). SST was measured
between 0-20 cm from the ocean surface (bulk temperature). Chlorophyll-a
concentrations measurement were made using Aquafluor Handheld Fluorometer and
Turbidimeter with a detection limit of 0.30 mg.m-3 (Turnerdesigns, 2006).
The station locations for the sea truth are shown in Figure 4-2. Detailed location of
in situ stations appear in Appendix-1
Near shore waters
Berau District
Figure 4-2: In situ sample stations
23
4.4. Research approach
A simplified flow chart of research approach is indicated in the following diagram.
DATA PREPARATION
LITERATURE SATELLITE
REVIEW IMAGES
IMAGE PROCESSING
(MODIS)
Atmospheric Correction
Geometric Correction
Land and cloud masking
Cloud covers % statistic determination
SST dry SST wet Chl-a dry Chl-a wet

season season season season
Correlation between SST Correlation between

& Chl-a in near shore SST & Chl-a in open sea
ACCURACY ASSESSMENT
REPORT WRITING
Figure 4-3: Simplified schema of the research approach
24
5. Results
5.1. Sea surface temperature
A total of 21 scenes of SST were processed and the detailed results are shown in
Table 5-1. The SST maps are shown in Figure 5-1, 5-2 and 5-3.
Table 5-1: SST of East Kalimantan Water from March 2005 to August 2006
Date Near Shore SST (0C) Open Sea SST (0C)

Min Max Min Max
rd
3 March 2005 18.02 27.66 22.99 27.66
4th March 2005 16.49 27.48 24.43 27.66
5th March 2005 19.64 27.66 21.93 27.66
30th April 2005a 8.23 27.66 22.85 27.65
30th April 2005b 9.57 27.66 14.17 27.67
7th June 2005 10.34 27.66 12.90 27.51
27th July 2005 23.02 27.77 27.55 27.55
30th July 2005 14.55 27.66 24.34 27.66
6th August 2005 20.81 27.66 26.06 27.66
11th August 2005 10.67 27.54 - -
12th August 2005 21.62 27.66 26.29 27.66
20th August 2005 19.34 27.66 - -
29th August 2005 14.11 27.66 - -
4th September 2005 11.31 27.66 - -
9th October 2005 20.84 27.63 18.42 27.64
5th May 2006 10.41 27.62 20.29 27.65
9th May 2006 20.16 27.64 21.96 27.66
18th May 2006 22.42 27.66 - -
10th July 2006 8.31 27.65 23.77 27.61
21th July 2006 18.61 27.67 25.13 27.65
7th August 2006 19.67 27.67 - -
25
3rd March 2005 4th March 2005
28
25 SST 0C
0
Cloud and land mask
5th March 2005
Figure 5-1: Daily SST derived from MODIS; Wet Season
26
Chapter 5 - Results
30th Apr 05a 30th Apr 05b 7th June 05
27th July 05 30th July 05 6th Aug 05
11th Aug 05 12th Aug 05 20th Aug 05

28
25 SST 0C
0
Cloud and land mask
Figure 5-2: Daily SST derived from MODIS; Dry Season April – August 2005
27
29th Aug 05 4th Sept 05 9th Oct 05
5th May 06 9th May 06 18th May 06
10th July 06 21st July 06 7th Aug 06

28
25 SST 0C
0
Cloud and land mask
Figure 5-3: Daily SST derived from MODIS; Dry Season August 05–August 06
28
Chapter 5 - Results
5.2. Chlorophyll-a concentration
A total of 21 scenes of chlorophyll-a were processed and the detailed result appears
in Table 5-2 below. The Chl-a maps are shown in Figure 5-4, 5-6 and 5-7.
Table 5-2: Chl-a of East Kalimantan Water from March 2005 to August 2006
Date Near Shore Chl-a Open Sea Chl-a

-3
mg.m mg.m-3
Min Max Min Max
3rd March 2005 1.00 56.00 1.00 2.00
th
4 March 2005 1.00 4.00 1.00 1.00
th
5 March 2005 1.00 20.00 1.00 2.00
th
30 April 2005a 1.00 56.00 1.00 2.00
th
30 April 2005b 1.00 52.00 1.00 1.00
th
7 June 2005 1.00 52.00 1.00 2.00
th
27 July 2005 1.00 35.00 1.00 3.00
th
30 July 2005 1.00 38.00 1.00 4.00
th
6 August 2005 1.00 57.00 1.00 2.00
th
11 August 2005 1.00 16.00 - -
th
12 August 2005 1.00 22.00 1.00 2.00
20th August 2005 1.00 55.00 1.00 2.00
th
29 August 2005 1.00 54.00 1.00 1.00
4th September 2005 1.00 29.00 1.00 1.00
th
9 October 2005 1.00 54.00 1.00 2.00
5th May 2006 1.00 41.00 1.00 3.00
th
9 May 2006 1.00 38.00 1.00 2.00
18th May 2006 1.00 38.00 1.00 3.00
th
10 July 2006 1.00 60.00 1.00 13.00
21st July 2006 1.00 59.00 1.00 2.00
th
7 August 2006 1.00 18.00 1.00 3.00
29
3rd March 05 4th March 05
10 - 60
3-4 Chl-a mg.m-3
0-1
Cloud and land mask
5th March
Figure 5-4: Daily Chlorophyll-a concentration derived from MODIS; Wet Season
30
Chapter 5 - Results
30th Apr 05a 30th Apr 05b 7th June 05
11th Aug 05 12th Aug 05 20th Aug 05

10 - 60
3-4 Chl-a mg.m-3
0-1
Cloud and land mask
Figure 5-5: Daily Chl-a derived from MODIS; Dry Season, April – August 2005
31
29th Aug 05 4th Sept 05 9th Oct 05
5th May 06 9th May 06 18th May 06

10 - 60
3-4 Chl-a mg.m-3
0-1
Cloud and land mask
Figure 5-6: Daily Chl-a derived from MODIS; Dry Season August 05–August 06
32
Chapter 5 - Results
5.3. Correlation between SST and Chl-a
A correlation analysis between SST and Chl-a was performed for near shore and
open sea. The detail result for near shore appears in Table 5-3. The correlation for
open sea has not been reported due to no match up points between SST and Chl-a.
Table 5-3: SST and Chl-a relationship
* Rs : Spearman correlation coefficients
Date Rs P value n
rd
3 March 2005 0.1569 0.0130 68
th
4 March 2005 0.1403 0.0390 217
th
5 March 2005 0.1192 0.0155 412
30th April 2005a -0.0848 0.6558 30
30th April 2005b - - -
th
7 June 2005 -0.0026 0.9938 11
th
27 July 2005 - - -
th
30 July 2005 0.0876 0.7135 20
th
6 August 2005 -0.2189 0.0416 87
11th August 2005 - - -
th
12 August 2005 -0.5161 0.0042 29
20th August 2005 0.1472 0.054 172
29th August 2005 0.222 0.0176 114
4th September 2005 -0.0063 0.9808 17
th
9 October 2005 - - -
5th May 2006 -0.7364 0.0591 7
th
9 May 2006 - - -
th
18 May 2006 - - -
th
10 July 2006 - - -
21st July 2006 0.0671 0.1149 554
th
7 August 2006 -0.5536 0.0001 45
33
34
6. Discussion
This study demonstrated that MODIS Level 2 data from Malaysia Ground
Receiving Station (MGRS) can successfully be used to obtain SST and Chl-a in
East Kalimantan coastal waters and the Sulawesi open sea waters. This is the first
attempt to validate in situ SST and Chl-a data with MODIS Level 2 data in East
Kalimantan waters exclusively in Berau Marine Protected Area since it was gazetted
in December 2005. This chapter will start with a section that considered as an
important step for satellite SST and Chl-a measurement which is cloud cover
percentage.
6.1. Cloud cover in the study area
Efforts to obtain SST and Chl-a information in Kalimantan waters during wet and
dry season encountered major obstacle of cloud cover especially during wet season.
Queries from MACRES Data Quicklook System for wet season result in only three
scenes that were cloud free and suitable for further analysis. These three scenes
obtained in Mac 2005 were used to represent the whole wet season period. Query
result for dry season however ended up with better results with 18 suitable scenes.
Analysis in ArcGis was then conducted to determine the detail percentage of cloud
free pixels. As this study focuses in the ocean region, the land area has been added
into the cloud statistic. The percentage of cloud covers and land area for SST and
Chl-a MODIS Level 2 data are shown in Fig 6-1 and Fig 6-2.
SST pixels and

cloud mask pixels
100
%
90
80
3rd Mac 05
5th Mac 05
30 April 05b
27th July 05
6th Aug 05
12th Aug 05
29th Aug 05
9th Oct 05
9th May 06
10th July 06
7th Aug 06
Dates % SST pixels

% Cloud & Land pixels
Figure 6-1: Percentage of SST pixels compared to cloud and land pixels
35
Chlorophyll-a pixels and

cloud mask pixels
100
%
90
80
3rd Mac 05
5th Mac 05
30 April 05b
27th July 05
6th Aug 05
12th Aug 05
29th Aug 05
9th Oct 05
9th May 06
10th July 06
7th Aug 06
Dates % Chl pixels
% Cloud & land pixels
Figure 6-2: Percentage of Chl-a pixels compared to cloud and land pixels
Figure 6-1 and 6-2 clearly indicated that although it is possible to map the SST and
Chl-a in the region using MODIS datasets, the chances of getting 100% ‘clear sky’
throughout the year is very slim. In general, Chl-a data had higher cloud free pixels
compare to SST datasets. The average value for cloud free pixels in Chl-a datasets
was 6.09 % and 2.17 % for SST datasets. One possible explanation is that the
visible blue wavelengths (0.438 – 0.493 µm) used for generating Chl-a map is
located in the bigger region of atmospheric transmission window (Figure 6-3)
compared to the thermal infared wavelengths (10.780 - 12.270 µm) to generate SST
values. CRISP (2006) defined the atmospheric transmission window as the
wavelength region where there are less absorption and scattering by the atmospheric
gases.
Figure 6-3: Atmospheric Transmission Window (CRISP, 2006)
36
Chapter 6 - Discussion
6.2. Sea Surface Temperature
6.2.1. In situ SST versus MODIS Level 2 SST

The August 2006 in situ SST values from 121 stations had been compared to the 7th
August 2006 MODIS data as shown in Figure 6-4 below. We acknowledge there is
a time difference between the satellite SST retrieval and the ground measurements,
and are fully aware that validation should be carried out at time of satellite overpass,
but as an indication, we performed the comparison and validation exercise.
SST 0 C SST : In situ vs MODIS IDWA vs MODIS Kriging
'
34.00
32.00
30.00
Insitu
28.00 IDWA
Kriging
26.00
24.00
22.00
20.00
TI7
TI14
TI21
TA2
TA9
TB4
TB12
TC6
TE1
TE8
TE15
TE22
TF5
TF12
TG7
TH2
TH9
D1
In situ Stations
Figure 6-4: In situ SST vs MODIS IDWA vs MODIS Kriging
Figure 6-4 clearly indicated that MODIS data tends to underestimate the SST values
in East Kalimantan waters. Further analysis then found that root mean square error
(RMSE) for in situ SST vs MODIS inverse distance weighted average (IDWA) was
1.35 0C and for in situ SST vs MODIS Kriging was 1.21 0C. The details are shown
in Figure 6-5 and Appendix 2.
Kriging SST = 8.9002256 + 0.5842152 Insitu SST (n=121, r =0.48)

IDWA SST = 10.163081 + 0.5374372 Insitu SST (n=121, r = 0.42)
Figure 6-5: Bivarate Fit of IDWA and Kriging SST
37
At this stage, one assumption that best explained why MODIS underestimated the
SST in this region is because of cold cloud pixels, which affect neighbouring SST
pixels. Further analysis than were conducted to the remaining 20 SST datasets.
There categories of SST values; SST Maximum=Tmax, SST Minimum=Tmin and
SST Average=Tavg were discussed. The discussion also focused on the differences
between the SST values for open sea and near shore; during wet and dry season.
6.2.2. SST in the near shore waters

Result shows that Tmax for near shore waters during wet and dry season does not
vary much. Tmax for the near shore during wet season is 27.66 0C and 27.77 0C
during dry season. The difference is only 0.11 0C. Throughout the year, Tmax for
this region can be concluded as relatively constant as shown in Figure 6-6 below.
Min and Max SST values:

SST 0C rd th
Near Shore (3 March 2005 - 7 August 2006)
30.00
25.00
20.00
15.00
10.00
5.00
SST Min
SST Max
0.00
3rd Mac 05
4th Mac 05
5th Mac 05
30th Apr 05a
30th April 05b
7th June 05
27th July 05
30th July 05
6th Aug 05
11th Aug 05
12th Aug 05
20th Aug 05
29th Aug 05
4th Sept 05
9th Oct 05
5th May 06
9th May 06
18th May 06
10th July 06
21th July 06
7th Aug 06
Dates
Figure 6-6: Minimum and maximum SST in near shore area
Tmin however shows a fluctuating pattern all year round. The minimum SST value
recorded during wet season is 16.49 0C and 8.23 0C during dry season. The low SST
values (pixels < 15 0C) could be unrealistic for SST in tropical sea SST such as East
Kalimantan waters. Detail inspections to all datasets then revealed that the
percentage of the low SST values pixels is very low. It ranged from 0.34% to 5.07%
of the total SST pixels in the respective datasets. This confirmed that the low SST
values are cold cloud pixels or edge cloud pixels and not the true SST. The detail
counts of the cold pixels represented in Table 6-1.
38
Table 6-1: Cold pixels percentage in near shore waters
Date Number of pixels

< 15 0C Total %
th
30 Apr 05a 7 138 5.07
30th April 05b 5 216 2.31
7th June 05 1 197 0.51
30th July 05 1 158 0.63
11th August 05 7 161 4.35
29th August 05 4 567 0.71
4th September 05 2 588 0.34
5th May 06 7 176 3.98
10th July 06 1 26 3.85
By setting the cut off point of valid SST to 15 0C, the average temperature, Tavg
were recalculated for all the SST imageries. The new Tavg in near shore for wet
season were 26.23 0C and 26.47 0C during dry season.
6.2.3. SST in the open sea

Similar to the near shore waters, Tmax for open sea during wet and dry season does
not vary much. Tmax for the open sea during wet season is 27.66 0C and 27.67 0C
during dry season. The average Tmax throughout the year is 27.64 0C. Tmin in the
open sea however shows a unique pattern compared to the near shore waters. Figure
6-7 clearly indicated that Tmin for open sea is much higher than near shore waters.
Min and Max SST values:

SST 0C rd th
Open Sea (3 March 2005 - 7 August 2006)
30.00
25.00
20.00
15.00
10.00
5.00
SST Min
SST Max
0.00
3rd Mac 05
4th Mac 05
5th Mac 2005
30th Apr 05a
30th April 05b
7th June 05
27th July 05
30th July 05
6th Aug 05
12th Aug 05
9th Oct 05
5th May 06
9th May 06
10th July 06
21th July 06
Dates
Figure 6-7: Minimum and maximum SST in open waters
39
Analyses were also carried out to calculate the cold cloud pixels in the open sea
area. Similar to near shore areas, result shows that the low SST values in open
waters does not depict the overall pictures. The low SST values only exist in two
SST images and the percentage is low as shown in Table 6-2 below.
Table 6-2: Cold pixels percentage in open waters
Number of pixels
Date < 15 0C Total %
th
30 April 05b 7 424 1.65
7th June 05 2 20 10.00
By setting the cut off point of valid SST to 15 0C, the average temperature were
recalculated from the SST imageries and it was found that Tavg for open sea during
wet season were 26.69 0C and 26.49 0C for dry season.
6.3. Chlorophyll-a concentrations
6.3.1. In situ Chl-a vs MODIS Level 2 Chl-a

The August 2006 in situ Chl-a values from 121 stations were compared to the 7th
August 2006 MODIS data as shown in Figure 6-8 below. As stated earlier, we agree
that the time of satellite Chl-a retrieval does not coincide fully with the ground
measurements (± 2 week difference). As an indicative exercise, we however
conducted a comparison.
Log 10Chl-a : In situ vs MODIS IDWA vs MODIS Kriging
1.5
Log10 Chl-a mg.m-3
TI7
TI14
TI21
TA2
TA9
TB4
TB12
TC6
TE1
TE8
TE15
TE22
TF5
TF12
TG7
TH2
TH9
D1
-0.5
Log_Insitu
Log_Idwa
-2.5
Log_Kriging
In situ Stations
Figure 6-8: In situ Chl-a vs. MODIS IDWA vs. MODIS Kriging
40
Figure 6-8 clearly indicated that Level 2 MODIS chlorophyll-a product has
overestimated the Chl-a values in East Kalimantan waters. Similar to SST, further
analysis has been carried out to find the RMSE values for this result. It was found
that the RMSE for in situ Chl-a vs MODIS IDWA was 1.01 mg.m-3 and for in situ
Chl-a vs MODIS Kriging was 1.22 mg.m-3. The cut off point for in situ Chl-a value
is 0.1 mg.m-3 due to the accuracy of the instrument used. From 121 values, 46 Chl-
a values were excluded. The details are shown in Figure 6-9 and Appendix 3.
IDWA CHL = 2.2111408 + 0.1802974 Insitu (n = 75, r = 0.05)

Kriging CHL = 2.5006469 + 0.1483307 Insitu (n=75, r = 0.04)
Figure 6-9: Bivarate Fit of IDWA and Kriging Chl-a
The overestimation of low Chl-a values by MODIS also reported by Barbini et al.
(2004). Barbini et al. (2004) further describe MODIS sensors tend to underestimate
high Chl-a. This statement also supported by Blondeau-Patissier et al. (2004). In
his finding, Blondeau-Patissier et al. (2004) stated that in order to gain more
accurate result in detecting Chl-a using MODIS, effort should be focused on
improving the atmospheric correction rather than more complicated Chl-a
algorithms.
This might explained very well why there were reasonable differences between
MODIS Chl-a and in situ values in East Kalimantan waters. With none of the
validation stations of SeaWiFS Bio Optical Archive and Storage System (SeaBass)
located in the study area, this result was expected. However, the RMSE of 1.01
mg.m-3 gained can be a good starting point in understanding the variation of actual
in situ values and MODIS sensors for East Kalimantan waters. A detailed analysis
41
was then carried out in order to understand the variability of Chl-a in near shore and
open sea area during the wet and dry season.
6.3.2. Chl-a in the near shore waters

Result shows that there is a large variability of Chl-a in the near shore waters. No
unique pattern exists between wet and dry season. The average Chl-a in near shore
calculated from the imageries were 2.12 mg.m-3 during wet season and 3.46 mg.m-3
during dry season. The Chl-a range for wet season is between 1.00 to 56.00 mg.m-3
while it varies from 1.00 to 59.00 mg.m-3 during dry season. Our result shows huge
differences when compared to previous Chl-a mapping in this area. Abu Daya
(2004) in his study found that the range of Chl-a in near shore East Kalimantan
waters ranges from 0 – 9 mg.m-3. Although it is true to say that it might be due to
the different sensor used (SeaWiFS) and different acquisition dates but further
research need to be carried out to compare these two sensors. Blondeau-Patissier et
al. (2004) stated that SeaWiFs was more accurate (RMS = 0.24; n = 26) compared
to MODIS Level 2 (RMS = 0.40; n = 26). However, as his study was in Northern
European waters, the result might be different in tropical waters.
One important advantage of MODIS Chl-a dataset due to its complex turbid water
algorithm, is the ability to measure Chl-a in near shore waters. Barbini et al. (2004)
stated that, SeaWifs atmospheric correction failed in some near shore areas. This
study proved the capability of MODIS in measuring near shore Chl-a. The
minimum and maximum Chl-a in near shore waters shown in Figure 6-10.
Min and Max Chl-a Values :

Near Shore (3rd March 2005 - 7th August 2006)
mgm-3 '
70.00
60.00
50.00
40.00
30.00
Chl Min
20.00
Chl Max
10.00
0.00
3rd Mac 05
5th Mac 05
30th April 05b
27th July 05
6th Aug 05
12th Aug 05
29th Aug 05
9th Oct 05
9th May 06
10th July 06
7th Aug 06
Dates
Figure 6-10: Minimum and maximum Chl-a in near shore waters
42
6.3.3. Chl-a in the open sea

Result in Figure 6-11 shows that the value of Chl-a ranges from 1.00 to 13 mg.m-3
in the East Kalimantan open waters. Further inspection found that the highest
concentration value (13.00 mg.m-3) which happened on 10th July 2005 was only
from one pixel. Assuming this as noise, the new Chl-a range for open waters is 1.00
to 4.00 mg.m-3 which is considerably low. The average Chl-a calculated from the
imageries were 1.00 mg.m-3 during wet season and 1.02 mg.m-3 during dry season.
Min and Max Chl-a Values :

Open Sea (3rd March 2005 - 7th August 2006)
mgm-3 '
14.00
12.00
10.00
8.00
6.00
Chl Min
4.00
Chl Max
2.00
0.00
3rd Mac 05
5th Mac 05
30th April 05b
27th July 05
6th Aug 05
20th Aug 05
4th Sept 05
5th May 06
18th May 06
21th July 06
Dates
Figure 6-11: Minimum and maximum Chl-a in open waters
The possible explanation for this small range might be best described by Arnone
and Parsons (2005) which stated that in open seas, chlorophyll maximum layer
normally located below the surface, out from satellite sensors view.
6.3.4. Striping lines in Chl-a images

In few Chl-a images as shown in Figure 5-5, 5-6 and 5-7, striping lines were very
obvious. These lines were generated by the residual differences between MODIS
Terra detectors during solar diffuser (SD) calibrations. Bryan (2007) reported that,
NASA Ocean Biology Production Group (OBPG) is still trying to reduce the
residual detector striping lines. Bryan (2007) further described that the responsivity
of MODIS/Terra sensors were degraded up to 40% since launched (compared to
15% for Aqua). This issue needs to be taken into account seriously if MODIS Level
2 Chl-a data will be use for future study in this area.
43
6.4. Correlation between SST and Chl-a
Having the opportunity to obtain the SST and Chl-a at the same time and date is
always a dream of marine researchers as it is valuable information for further
application research e.g fish forecasting and modelling. Mansor et al. (2001) found
that SST and Chl-a relationship are the most important variables to model the fish
distribution in tropical regions. Solanki et al. (1998) and Solanki et al. (2003)
revealed that there was negative/inverse correlation between SST and Chl-a.
Solanki et al. (2003) then used the correlation of SST and Chl-a information to
model the fish distribution in Arabian Sea. In contrast to his finding, this research
however found that that there was no specific pattern for correlation between SST
and Chl-a in East Kalimantan waters except for wet season. Figure 6-12 shows that,
the SST and Chl-a correlation in wet season has positive relationship. Despite the
relatively low Spearman correlation cooefficient (~ Rs = 0.10), the relationship was
significant (p<0.05). In dry season the relationship varies from negative to positive
throughout the dry months.
SST-Chl-a concentration correlation :

Mac 2005 - August 2006 East Kalimantan waters
Rs
1
0.8
0.6
0.4
0.2
0
3rd Mac 05
4th Mac 05
5th Mac 05
30th Apr 05a
7th June 05
30th July 05
6th Aug 05
12th Aug 05
20th Aug 05
29th Aug 05
5th May 06
21th July 06
7th Aug 06
-0.2
-0.4
-0.6
-0.8
-1
Dates Spearman Rs
Figure 6-12: SST and Chl-a correlation in East Kalimantan near shore waters
The Spearman non-parametric correlation test has been used due to the non normal
distribution of the data. The analysis reported above was only for the near shore
waters as lack of match up points in open waters. Although MODIS can provide
SST and Chl-a at the same date and time, these dataset had one drawback; the cloud
mask for SST and Chl-a is different as shown in Figure 6-13.
44
SST 30th Apr 05 Chl-a 30th Apr 05
Figure 6-13: MODIS cloud mask for SST and Chl-a Level 2
Bryan Franz (2006) reported that for MODIS SST Level 2 product, the
determination of invalid pixel values is based on how different the pixels value is
from the reference SST (Reynolds). If the difference is huge then the pixels will be
labelled as SSTWARN. If the SST algorithm could not calculate any values, the
pixels will then be labelled as SSTFAIL. As the final SST pixels also took into
account the night and day value, sun glint did not effect SST pixels.
The Chl-a determination however is very sensitive to sun glint. This is the main
reason why both datasets cannot have similar ‘cloud mask’ and analysis need to be
carefully done to select only overlapping pixels for the correlation analysis. The
limited overlapping pixels available in open sea of East Kalimantan need to be taken
as an important consideration if fish forecasting model need to be run using MODIS
Level 2 data in this waters.
45
46
7. Conclusions and Recommendations
7.1. Conclussions
The seasonal and spatial variability of SST and Chl-a in East Kalimantan near shore
and open waters, Indonesia were determined. The minimum, maximum and average
values calculated from temporal datasets were examined and reported. In situ data
were used to validate the accuracy of MODIS Level 2 SST and MODIS Level 2
Chl-a data.
The major findings of the research revealed:
SST maps of East Kalimantan waters from March 2005 to August 2006 show that
there was low SST variability between wet and dry season. There was also low
variability between SST values in near shore and open sea waters. However, for
both seasons, open sea SST was found to be paradoxically slightly warmer than the
near shore waters.
Chl-a maps of East Kalimantan waters from March 2005 to August 2006 waters
revealed that there was low Chl-a variability between wet and dry season. There
was also low variability between Chl-a values in near shore and open sea waters.
The Chl-a values for both seasons is higher in near shore waters.
SST and Chl-a in near shore waters has low positive relationship in wet season.
During dry season, the relationship between these two variables varies from positive
to negative.
7.2. Recommendations
The work presented in this study has left some important questions still unanswered.
Effort should be focused in several issues as discussed below if further research
need to be conducted.
47
In section 6.2.1 and 6.3.1, this study had successfully compared the August 2006
MODIS Level 2 data with August 2006 in situ data although we admit the time
difference between satellites overpass and ground sampling. There were 4 days
difference between the MODIS acquisition date and the in situ campaign. In ideal
case, it is necessary to validate the satellite imageries with in situ that coincide with
the satellite acquisition time. The RMS error between MODIS and in situ value
could be refined if this can be achieved.
In section 6.2.2, this study had made the assumption that the cut off value for
minimum SST value in East Kalimantan waters was 15 0C. This has raised two
interesting questions. What is the best cut off SST value for East Kalimantan
region? How would the changes in the cut off value affect the SST values for this
region?.
The unique positive relationship between SST and Chl-a in wet season was very
interesting. This was somehow questionable because only three images were used to
representing wet season due to the unavailability of satellite data (cloud cover). For
future works, more datasets for the wet season should be obtained and analysed to
proof the relationship.
48
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55
Appendices
Appendix-1 : In situ stations, SST and Chl-a concentrations
Chl-a
Station East(X) North(Y) mg.m-3 SST 0C
D1 638823.35 252255.86 0.00 29.80
D2 638968.63 252291.38 0.00 29.10
D3 639061.30 252326.95 0.00 28.30
D4 639102.19 252348.47 0.03 28.50
D5 639162.46 252360.31 0.05 28.40
D6 639230.26 252363.54 0.07 28.40
TA1 637376.10 250316.60 0.01 28.30
TA2 629185.50 238094.00 0.02 28.40
TA3 627205.50 237857.50 0.02 28.90
TA4 623541.20 236839.60 0.15 30.20
TA5 620012.70 236330.70 0.16 29.60
TA6 615568.00 235923.50 0.20 31.50
TA7 611496.60 235889.60 0.30 32.40
TA8 607696.60 235584.30 0.31 32.10
TA9 606373.40 237755.70 0.34 32.90
TA10 615362.70 243233.10 0.28 31.40
TA11 618854.50 246668.80 0.14 31.90
TA12 621780.10 251740.20 0.10 31.30
TB1 631849.90 250358.00 0.02 28.40
TB2 627712.70 248311.30 0.02 28.40
TB3 623240.70 245704.10 0.10 29.00
TB4 618986.00 243059.10 0.24 29.00
TB5 614885.20 241483.70 0.22 29.90
TB6 611226.20 240635.30 0.22 30.40
TB7 607428.40 240206.70 0.80 30.20
TB8 606150.20 238540.00 0.35 30.40
TB9 603819.40 239931.00 0.38 30.50
TB10 601510.50 243448.10 0.43 30.60
TB11 596694.80 242623.50 0.34 30.60
TB12 588686.80 242097.30 0.26 30.70
TB13 579982.20 241588.30 0.24 30.90
TB14 571842.40 243043.60 1.63 30.30
TB15 563327.60 241072.70 1.49 30.40
TB16 560910.10 239981.40 1.15 30.50
57
Appendix-1 : Con’t
Chl-a
TB17 554904.40 239804.80 0.70 30.40
TC1 612121.30 222504.30 0.38 29.80
TC2 607163.00 221009.40 0.70 29.70
TC3 598806.00 221463.00 0.26 30.30
TC4 592919.50 222632.00 0.25 30.20
TC5 593138.20 224263.60 0.39 30.30
TC6 584159.50 224157.50 0.20 30.00
TC7 577123.50 227848.50 0.35 30.20
TD1 597088.20 220135.40 0.47 31.30
TD2 599747.20 216820.00 0.84 31.70
TD3 605328.40 215349.30 0.40 30.80
TD4 614559.60 226007.20 0.45 30.40
TD5 620625.80 234342.90 0.10 29.20
TD6 626872.60 243145.00 0.13 29.40
TE1 627087.00 250059.00 0.26 28.70
TE2 623861.00 246572.00 0.19 29.20
TE3 620623.00 245640.00 0.14 29.50
TE4 619784.00 240967.00 0.41 29.40
TE5 617420.00 235121.00 0.66 29.20
TE6 617612.00 230508.00 0.19 30.20
TE7 617802.00 224962.00 0.21 29.80
TE8 616236.00 219918.00 0.13 29.80
TE9 614571.00 214864.00 0.11 30.40
TE10 614525.00 209828.00 1.71 30.40
TE11 613970.00 204964.00 0.28 30.60
TE12 613513.00 199918.00 0.50 31.40
TE13 606053.00 203492.00 0.66 31.90
TE14 602391.00 206929.00 1.21 32.90
TE15 611797.00 213737.00 0.22 30.70
TE16 614663.00 215273.00 0.20 30.60
TE17 618334.00 220065.00 0.15 30.40
TE18 622262.00 221997.00 0.10 29.70
TE19 625100.00 221948.00 0.07 29.70
TE20 629804.00 224277.00 0.00 29.70
TE21 629799.00 225358.00 0.14 29.90
TE22 629950.00 232579.00 0.26 29.50
TE23 630131.00 238780.00 0.34 30.00
58
Appendices
Chl-a
TE24 637705.00 250586.00 0.10 28.40
TF1 642570.00 248741.00 0.02 28.90
TF2 639713.00 254219.00 0.03 28.30
TF3 645350.00 243765.00 0.10 28.20
TF4 647907.00 238981.00 0.03 28.70
TF5 648174.00 237562.00 0.02 28.40
TF6 652909.00 234033.00 0.03 28.30
TF7 655420.00 231645.00 0.02 28.40
TF8 656759.00 230289.00 0.09 28.30
TF9 647105.00 235256.00 0.07 28.40
TF10 645214.00 239228.00 0.00 29.80
TF11 642383.00 241601.00 0.03 30.40
TF12 640832.00 245196.00 0.05 28.50
TG1 639034.00 250107.00 0.06 28.10
TG2 638470.00 255411.00 0.08 28.20
TG3 636394.00 257066.00 0.15 27.90
TG4 632608.00 261544.00 0.08 28.10
TG5 630119.00 265723.00 0.06 28.30
TG6 628065.00 270145.00 0.06 28.40
TG7 622600.00 267934.00 0.06 28.40
TG8 624227.00 259931.00 0.06 28.40
TG9 623565.00 252713.00 0.22 29.00
TG10 630115.00 254900.00 0.14 28.80
TG11 635056.00 254479.00 0.11 28.50
TG12 637714.00 250635.00 0.08 28.10
TH1 654168.20 250920.00 0.05 28.50
TH2 662242.90 252828.80 0.03 28.60
TH3 669831.20 252506.50 0.04 28.80
TH4 676812.50 253505.20 0.02 28.10
TH5 673593.30 248213.60 0.05 28.70
TH6 677990.90 241845.50 0.04 28.40
TH7 676917.90 239561.90 0.01 28.90
TH8 670192.90 242628.50 0.00 28.90
TH9 660174.10 246155.50 0.02 28.70
TI1 630062.60 238913.40 0.08 28.30
TI2 621975.50 236308.40 0.07 28.60
TI3 617327.70 234708.50 0.31 29.20
59
Chl-a
TI4 613058.20 233117.40 0.16 29.70
TI5 608054.80 231597.10 0.16 30.20
TI6 604478.60 230528.90 0.27 30.80
TI7 601225.80 229715.10 0.30 30.50
TI8 595821.20 230642.50 0.35 30.80
TI9 589856.50 236180.80 0.31 30.50
TI10 589271.20 240978.90 0.46 30.20
TI11 588178.30 241434.90 0.45 29.70
TI12 593791.70 242477.30 0.54 30.10
TI13 598158.20 240804.60 1.37 30.10
TI14 601883.40 237996.50 0.97 30.60
TI15 604153.10 238779.20 0.75 30.10
TI16 607247.20 239445.30 0.59 30.70
TI17 612398.20 240545.10 0.39 30.70
TI18 619713.40 241144.10 0.27 29.50
TI19 624299.80 246482.40 0.13 30.20
TI20 629612.60 248979.80 0.08 30.20
TI21 634072.80 250119.20 0.07 29.80
TI22 637670.00 250578.60 0.06 28.40
60
Appendices
Appendix-2 : Bivarite Fit of IDWA SST by in situ SST
61
Appendix-3 : Bivarite Fit of Kriging SST by in situ SST
62

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Seasonal and spatial variability of Sea Surface Temperature (SST)

and Chlorophyll-a concentration using MODIS data

IDHAM BIN KHALIL

Idham bin Khalil

Thesis submitted to the International Institute for Geo-information Science and

Thesis Assessment Board

Chairman : Dr. Ir. Kees de Bie (ITC, The Netherlands)

International Institute for Geo-Information Science and

This document describes work undertaken as part of a programme of study at

Malaysian Government particularly Malaysian Centre for Remote Sensing

I owe my loving thanks to my wife Nor Haslinda, my kids Muhammad Amnan,

Figure 1-1: Berau Marine Protected Area (WWF, 2006)........................................... 3

Table 2-1: MODIS specifications (NASA, 2006) .................................................... 11

ASEAN The Association of Southeast Asian Nations

1.1. Research background

The Association of Southeast Asian Nations (ASEAN) consist of 10 countries,

In reaction to the above suggestion and parallel to The 1992 UN Rio de

In terms of the marine environment, ASEAN contributed to about 14% of

In this study, the capability of geophysical product from Moderate Resolution

1.2. Research problem

This study focuses on marine resources depletion in Indonesian marine

Figure 1-1: Berau Marine Protected Area (WWF, 2006).

1.3. Research objectives

The specific objectives of this study are:

1.4. Research questions

The research will try to answer the following questions:

1.5. Thesis Outline

This thesis contains seven chapters.

Chapter two describes the overall description of the study area.

Chapter 4 presents a comprehensive methodology used in this study including the

2.1. Sea Surface Temperature (SST)

Marine researchers found that the measurement of SST is essential to understand

2.1.1. SST from space

Figure 2-3: Absorption coefficient and penetration depths of infrared waves

2.1.2. In Situ SST Measurement

While the understanding of SST measurement will become a dominant knowledge,

2.2. Chlorophyll-a concentration (Chl-a)

Similar to SST, the capability of satellite remote sensing in providing global

2.2.1. Chlorophyll-a from space

Table 2-1: MODIS specifications (NASA, 2006)

Table 2-2: Detailed MODIS band specification (NASA, 2006)

Primary Use Band Bandwidth Primary Use Band Bandwidth

Notes : Bands 1 to 19 are in nm; Bands 20 to 36 are in µm

2.2.2. In situ Chl-a measurement

Figure 6 : Study area : East Kalimantan waters

Figure 3-1: Study area, East Kalimantan waters, Indonesia

In order achieve the objective of understanding the variability of SST and

Wiryaman et al. (2004) reported a detailed summary of physical oceanographic in

3.3.2. Dissolved Oxygen (DO)

4. Materials and Method

4.1. MODIS Datasets

Table 4-1: MODIS Level 2 data structure

SST MODIS Level 2 GeoTIFF

4.1.1. Atmospheric correction

4.1.2. Cloud mask

4.1.3. Geometric correction

4.1.4. Sea Surface Temperature

SST = C1 + C2 * T31 + C3*T3132 +C4(sec(θ)-1)* T3132

4.1.5. Chlorophyll-a concentration

where R = log10 ⎡ R rs443 > R rs488 ⎤

Ca : Chlorophyll-a concentration (milligram per cubic metre, mg.m-3)

4.1.6. Correlation analysis between SST and Chl-a

4.2. Accuracy Assesment

Figure 4-1: SeaBass data points 2006 (SeaBass, 2006)

SST = C1 + C2 * T31 + C3T3132 +C4(sec(θ)-1) T3132