UNIVERSITI TEKNOLOGI MARA (UiTM) PERLIS

KAMPUS ARAU

BACHELOR OF SCIENCE (HONS) MARINE TECHNOLOGY

MAR 541: BASIC MARINE INSTRUMENT

ASSINGMENT 1: LAB CORAL

PREPARED BY:

NAME NOR AISHANADIA BT PAUZI (2019218896)

YASMEEN AMYLYA BINTI ROSLI (2019406132)

GROUP RAS2544B

PREPARED FOR:
SIR JAMIL BIN TAJAM
INTRODUCTION

Programme Sen2Coral is the preparation of the exploitation of the Sentinel-2 mission for coral reefs
by developing and validating appropriate, open source algorithm available for the community. The
project objectives are the scientific exploitation and validation of the Sentinel-2 Multispectral
Instrument (MSI) for mapping (habitat, bathymetry, and water quality) and detection change for
coral reef health assessment and monitoring, and algorithm development.

The degradation of coral reefs is a fact, with 55% of reefs being affected by overfishing and
destructive fishing methods, which as the most pervasive threats, whereas 25% of reefs are affected
by coastal development and pollution from land, including nutrients from farming and sewage, while
one tenth suffer from marine-based pollution (local pressures are most severe in South-East Asia,
where nearly 95 per cent of coral reefs are threatened). In addition the coral reefs’ ecosystems
appear to be the first to respond to global climate changes, such as increased sea surface
temperature (SST), ultraviolet radiation (UV) and acidification of seawater that results from higher
levels of atmospheric CO2 concentration.

The Copernicus Sentinel-2 Multispectral Instrument (MSI) offers several potential technical
advantages in the remote sensing of coral reefs due to:

 10 meter spatial resolution allowing improvement in visual interpretation of reef features,

classification accuracy and bathymetry.

 Additional water penetrating optical band improving consistency under varying water
conditions, reducing uncertainty in bottom type and bathymetric mapping, deeper
bathymetric accuracy and ability to determine water optical properties.

 Additional NIR/SWIR bands enabling more consistent and accurate determination of

atmospheric and surface glint correction.

 Short re-visit time enabling the use of image series to determine fundamental uncertainties
for change detection.

 Addresses the current limited remote sensing acquisition plan covering the coast areas.

Coral reef monitoring programs based on in situ field surveys have several caveats that restrict its use
and the relevance of its outcomes. These are:

 cost-related: detailed, continuous monitoring of coral reefs by field survey is expensive and

substantial reef areas are located in developing countries with limited resources
  scale-related: reefs are highly heterogeneous systems therefore even with sufficient
resources monitoring programs provide scattered information in time and space, with some
areas being more intensively sampled than others and less easily accessible areas are
typically under-sampled.

Using satellite remote sensing within a monitoring program potentially addresses both of these
issues. Remote sensing should be seen as a complementary technique to in-situ field surveys. The
two approaches produce different types of data which together can be used to build a picture of reef
ecology across a wide range of spatial and temporal scales.

Step1: Open Product

Open SNAP window then click Open product navigate to
E:\S2A_MSIL2A_20210516T003711_N0300_R059_T55LCD_20210516T030009\S2A_MSIL2A_202105
16T003711_N0300_R059_T55LCD_20210516T030009.SAFE

Then open MTD_MSIL2A

In Product Explorer window, Open RGB image window. Next, zoom in to the area of interest.

Figure 1: RGB image window of Sentinel 2 MSI Natural Colour

Step 2: Resample
Frist, we need to resample the bands to equal resolution. Go to Raster Geometric Operations
Resampling

Do not change anything in the I/O Parameters tab. In the Resampling Parameters tab, under “Define
size of resampled product”, choose: By reference band from source product: B2. Then click Run
follow by Ok if window appears.
A new product [2] appeared in the Product Explorer tab. Close all the views that have open and
expand the product structure by clicking the + sign on the left of the product name, then expand the
Band folder and double click B8 (842nm) - (NIR)

Figure 2: Image of B8 (842nm)

Step 3: Subset
Click on the resampled product in the Product Explorer tab, to highlight it. Then go to Raster
Subset and in the Spatial Subset tab, set Pixel coordinates to:

Scene start X: 2900

Scene start Y: 1820

Scene end X: 4000

Scene end Y: 2750

Click OK.

A new product will appear in the Product Explorer tab [3]. Right-click the product [3] and click Open
RGB image window and from the dropdown menu select “Sentinel 2 MSI Natural Colors”. Click OK
 Figure 3: RGB image window of Product Explorer tab [3].

Step 4: Deglint
In the Product Explorer tab, double click on the B8 (NIR band). Then in the Colour Manipulation tab,
drag the white slider to value of 3E-2.

In the Product Explorer tab, select the subset product [3] and go to Vector New Vector Data
Container. In the dialog that opens, set the name to “glint” and click OK.

Click on the Rectangle drawing tool and draw polygons over the deep-water sun glint areas.

Figure 4: polygons drawing on subset product [3]

Then go to Optical Thematic Water Processing Sen2Coral Processing Modules Deglint

Processor.

In the I/O Parameters tab, set the subset product [3] as Source Product.
In the Processing Parameters tab, set:

Sun Glint areas: “glint”

Source Bands: B2, B3, B4, B5

Reference Band: B8

Click Run. When the processing is finished, a new product [4] will appear in the Product Explorer tab

Figure 5: Image of product [4]

Step 5: Masking
Go to Optical Thematic Water Processing Sen2Coral Processing Modules
LandCloudWhiteCapMask Processor.

In the I/O Parameters tab, set the subset deglint product [4] as Source Product.

In the Processing Parameters tab, set:

Source Bands: B2, B3, B4, B5

Reference Band: B8

Maximum valid value: 0.05

Click Run. A new masked product [5] containing also the mask band has been created.

In the Product Explorer, right-click on the new masked product [5] and go to BandMaths. In the band
math dialog set:

Name: Mask_All

Replace NaN and identify results by: NaN

Deselect Virtual (save expression only, don’t store data)

Click on Edit Expression and set:

Expression: if B2 > 0.01 && LandCloudWhiteCapMask_B8 == 1 then 1 else 0

Then click OK.

Turn off the visualization of the glint polygons by going to Layer Manager (right side of the screen or
go to View Tool Windows Layer Manager) and deselecting Vector data glint.

Figure 6: Masked product [5] after deselecting Vector data

Step 6: Depth invariant indices

Right-click on the masked product [5] in the Product Explorer and go to Vector New Vector Data
Container. In the dialog that opens, set the name to “deep”. Click on the Rectangle drawing tool and
draw polygons over the deep-water. Then create another New Vector Data Container and name it
“same_type” and draw polygons over the bright sand areas

Figure 7: Image show the “deep” polygons indicated in green and the “same_type” polygons
indicated in blue.
 Figure 8: Image of bright sand area

Then to apply the processor, go to Optical Thematic Water Processing Sen2Coral

Processing Modules DepthInvariantIndices Processor.

In the I/O Parameters tab, set the masked product [5] as Source Product.

In the Processing Parameters tab, set:

Source Bands: B2, B3

Deep water area: “deep”

Same bottom areas: “same_type”

Click Run. A new product [6] has appeared in the Product Explorer. It contains only one band; double
click it to visualize it. Turn off the visualization of the polygons by going to Layer Manager and
deselecting Vector data.

To compare it with the original RGB image, close all the tab except for the [5] Sentinel 2 MSI Natural
RGB and the [6] DepthInvariantIndicesB2B3, then go to Tools Tile Horizontally.
 Figure 9: image of product subset [6]

Figure 10: Image of product subset [5] Sentinel 2 MSI Natural RGB and the product subset [6]
DepthInvariantIndicesB2B3 in horizontal tile
 Figure 11: Image of product subset [6] after colouring

CONCLUSION

Sentinel-2 has the capability to deliver essential scientific, monitoring and management-ready
information for coral reef applications. This capability is a step up from Landsat 8 due to spatial
resolution and revisit time, but Sentinel-2 also performs well in comparison high resolution imagery
and offers advantages in terms of cost effectiveness and large scale coverage. Existing methods can
immediately enable effective use of Sentinel-2 by the reef science community and management
agencies globally, to address their essential environmental information requirements this also applies
to hydrographic agencies, defence applications and private industry. The revisit time and cost-
effectiveness of imagery is unparalleled, and offers many advantages: from simply being able to
select the clearest images to opportunities for fundamentally new methods and insights. In the near
future new methods are certain to be developed to meet the opportunity that Sentinel-2 presents,
and this can only further add to the use of Sentinel-2 in coral reef applications.