Evaluation Of Sentinel-2 Vegetation Indices for

Plot Level Tree AGB Estimation

By : Mehboob Alam
MS 3 RS & GIS, 140311060
Supervisor: Dr Saleem Ullah,
Co Supervisor Dr Waqas Qazi

Department of Space Sciences, Institute of Space Technology, Islamabad.

 Contents Of The Presentation

1. Introduction
2. Literature Review
3. Data Sets
4. Methodology
5. Results
6. Conclusion
7. Discussion
Definitions

Biomass: Biomass, in its simplest form, is defined as organic matter

renewable over time.
Woody biomass is the accumulated mass, above and below ground, of
the roots, wood, bark, and leaves of living and dead woody shrubs and
trees. Woody biomass is primarily comprised of carbohydrates and
lignin produced through the photosynthesis. (FAO)

Carbon Sock = .47 x Biomass (ICIMOD)

Tree AGB is composed of Stem, Branches, Leaves.

Definitions Contd.
There are five carbon pools of terrestrial ecosystem involving
biomass,

Above-ground biomass, below-ground biomass, the dead mass of

litter, woody debris and soil organic matter. (IPCC)

The above-ground biomass of a tree constitutes the major portion

of the carbon pool.

AGB can be measured through Remote Sensing. Total Biomass

can then be estimated through established relationships AGB and
other pools from Literature.
Traditional Methods of Biomass
Estimation
Destructive:
Development of tree-level biomass equations made by destructive sampling
technique and regression analysis

Non Destructive:
Utilize Allometric relationships between
the tree stand parameters (DBH, Height, CPA)
that approximates the biomass of the tree
component or the total biomass of single
trees according to more easily measured
variables. (Chave et al., 2005
 Limitations of Traditional Methods

Destructive in Nature, Costly, Time Consuming,

Limited to small areas with small tree sample size

Difficult to implement at regional/national level or in remote

areas
.
Extending / Scaling to estimate AGB across large area extremely
challenging when different factors such as variations in inventory
systems, ecological differences, and scattered sources of biomass
data are considered (Sarker, 2010).
AGB Through Remote Sensing

The remote sensing based models are especially suitable for

independent verification of the National Land Use, Land-Use
Change and Forestry (LULUCF) carbon pool estimates.
Good Practice Guidance (GPG) (IPCC, 2003)
Studies have been done to estimate AGB from Remote Sensing
data (Foody, Boyd, & Cutler, 2003; Nelson, Kimes, Salas, &
Routhier, 2000; Sun et al., 2011; Zheng et al., 2004).
Optical, LIDAR, and SAR which can be used for biomass
estimation based on availability, efficiency and cost (Nga, 2010;
Sarker, 2010).
AGB Through Remote Sensing Contd

Advantages: Repeatable Monitoring, Cost Efficient, Time

Efficient. Estimation at Every Area which may be Inaccessible
otherwise.
HOWEVER: The AGB cannot be assessed directly through any
remote sensing instruments. Additional ground-based
measurements about forest stand structure (DBH, Height, Canopy
Cover, etc.) are required for development and evaluation of AGB
models and for validation of result outcomes. . (Beaudoin et al.,
1994; Ghasemi et al., 2011; Hamdan, Aziz, & Rahman, 2011; Lu,
2006a; Rosenqvist, Milne, Lucas, Imhoff, & Dobson, 2003a)
AGB From Optical Data

Optical Can Either Be Satellite Based or Aerial.

Tiwari & Singh (1984) estimate the Indian forest AGB using
aerial photographs.

De Jong, Pebesma, & Lacaze (2003) utilized digital airborne

imaging spectrometer (DAIS) data to estimate in Southern
France.
Passive RS Satellite Data

Optical or microwave sensors are expected to provide information

which can be related to the forest biomass in different (Brown et
al., 1995; Foody et al., 2003; Rosenqvist et al., 2003)

The passive satellite sensor data with visible and NIR reflectance
from the earth surface have formed the basis for most of current
global scale mapping and forest biomass estimation.
These are very common datasets and many scientists have
assessed the capability of passive satellite data for biomass
estimation using different types of optical data and image
processing techniques (Foody et al., 2003; Goetz et al., 2009; Lu,
Passive RS Satellite Data Contd

The studies about forest biomass using optical datasets are mostly
involved in establishment of a relationship between the
commonly used vegetation indices with biomass or some
biophysical factors (Olander et al., 2008).
Passive sensors are generally characterized by their spatial,
spectral, and radiometric performances. Satellites are typically
categorized according to their spatial resolution into
environmental satellites (NOAA, GOES, Meteosat), medium
resolution satellites (IRSI, Landsat TM, MSS, etc.); and high
resolution satellites (Quickbird,Pleiades, SPOT, IKONOS, ERS-
1.
Passive RS Satellite Data Contd..
The most commonly used optical datasets for biomass estimation
are Landsat TM(Foody et al., 2003; Lu, 2005b) Landsat ETM+
(Cartus, Kellndorfer, Rombach, & Walker, 2012; Morel, Fisher, &
Malhi, 2012; Zheng et al., 2004), IKONOS (Abbas et al., 2013; P.
S. Thenkabail et al., 2004) Quickbird (Peter Hyde et al., 2006),
SPOT-5 HGR, NOAA AVHRR, MODIS (Baccini, Friedl,
Woodcock, & Warbington, 2004), and ASTER (Muukkonen &
Heiskanen, 2005).
introduced for biomass assessment from the reflectance images,
and different types of statistical modelling were also applied to
correlate NDVI values or band ratio values with field
measurements. These several studies shown that approaches using
passive remote sensing data are not suitable for most terrestrial
biomass densities because of the saturation problem (Sarker,
Optical Medium Resolution Data Contd
Many different models are available which can be develop for
AGB estimation (Rosillo-Calle, 2007).
Whereas NDVIs have been recommended to remove
inconsistencies caused by soil background, canopy geometry, sun
view angles, and Atmospheric conditions, while measuring
biophysical characteristics of the trees (Elvidge & Chen, 1995;
Blackburn & Steele, 1999).
However, not all NDVIs are expressively correlated with forest
biomass. In general, NDVIs can partially reduce the impacts on
reflectance caused by terrain and canopy shadows, environmental
conditions, and consequently improving correlation between
AGB and NDVIs, particularly at those sites which have
multifaceted vegetation stand structures (Lu, Mausel, Brondizio,
& Moran, 2004).
High Spatial Resolution Data

High spatial resolution remotely sensed satellite data are

commonly used in numerous studies for modelling forest canopy
structures (Levesque & King, 2003).
Different techniques have been used for extraction of tree stand
parameters from this type summarized by (Wulder, Franklin,
Wulder, & Franklin, 2003) including bottom-up (valley-following
and directional texture) and top-down algorithm (multi-scale edge
segments, threshold-based spatial clustering, a double-aspect
method, and vision expert system), and pattern matching (Lu,
2006a).
Fine resolution data is useful for detailed study of forest stand
structure. It can also be utilized as reference data for validation or
accuracy assessment for medium and low resolution data
High Spatial Resolution Data Contd
There are also some drawback of fine resolution data which are
indicated by Lu (2006a).
The high spectral variation and shadows caused by terrain and
tree canopies can create difficulties in developing AGB
assessment models.
There is lack of a shortwave infrared bands, which are often
important for AGB estimation.
These datasets required large amount of storage and also take
long time for image processing which prohibit their use over large
areas.
Last but not the least drawbacks of such dataset are that are much
more expensive, and much more complex for data analysis than
medium spatial resolution images (Nga, 2010)
Hyper Spectral Data

Hyperspectral imagery with large number of spectral bands can

be helpful to improve AGB estimation performance and reduce
the saturation problem (Lu, 2006b; Mutanga & Skidmore, 2004).
(Muller, Bottcher, Meyer- Schatz, & Kage, 2008; Santoro et al.,
2011; Prasad S. Thenkabail, Smith, & De Pauw, 2000).
The main benefits of usage of this type of data to the end-users
are, can provide more detailed and accurate forest inventory
information, as well as geo-coded forest AGB maps (Rosillo-
Calle, 2007).
Optical Medium Resolution Data

The temporal Landsat satellite imagery has become the main

source in many remote sensing applications, including AGB
assessment at both local and regional scales (Calvao &
Palmeirim, 2004; Fazakas, Nilsson, & Olsson, 1999; Foody,
2003; Lu, 2005a; Mickler, Earnhardt, & Moore, 2002; Nelson et
al., 2000; Phua & Saito, 2003; Roy & Ravan, 1996; Sader, Waide,
Lawrence, & Joyce, 1989; Steininger, 2000; Zheng et al., 2004).
These researchers mostly used linear or nonlinear regression
models, neural network, and K nearest-neighbour for forest
biomass assessment (Lu, 2006a)
Techniques for Modelling AGB From
Optical
Canopy Projection Area

Object Oriented Analysis

Biophysical Variables (DBH, Height)

Research Questions.

How is much is the Biomass measured in the field correlated with

changes in the spectral response?
What are the best spectral bands for different species which
explains best the variation in the biomass for that specie?
Does the generalized model for different species gives any
promising results better than the model for individual tree
species?
What vegetation index best relate to above-ground biomass?
Research Objectives

To evaluate the Potential of Sentinel 2 satellite data for plot level

biomass estimation.
Establishment of Empirical Relationship Between Ground
Measured And satellite observation.
To find the optimal Indices for Different Specie Types.
To model the AGB for Species and Generic Modelling of All the
Combined Species.
To model the distribution of carbon stocked in MHNP and to
evaluate its accuracy for modeling carbon sequestered by multiple
vegetation species.
Hypothesis

There is a strong relationship between forest biophysical

parameters and the vegetation indices.

The forest AGB can be assessed and mapped precisely through

vegetation indices and biophysical parameters by regression
models.
Figure: Flow Chart
Methodological Framework
Study Area
Study Area Cont
Margallah Hills National Park (MHNP) Consist of three zones,
Margallah Hills (12802 ha) , Shakar Parian (1702ha), Rawal
Lake (1376ha). Total Area (15,883 ha)
Margallah Hills has Rough Topography Having Steep slopes and
gullies. The hills are an
Extension of the Himalayan range and form the northern
boundary of the Potohar plateau
Elevation: 465 to 1600 m,
The Margallah Hills comprises of subtropical, dry, semi-ever
green forest and pine trees. The semi-evergreen forest is
dominated by Phulai, Kao, Sanatha, Granda and Ber. (WWF )
Rawal Lake and Shakar Paria are dominated by deciduous trees
mainly Paper Mulberry
 Margallah Hills Species

Deodonia Viscosa

Shrubs In Bara Kahu Zone

Dominant Tree Species
Sentinel 2

Sentinel-2 is a multi-spectral imaging mission, which supports the

Copernicus Land Monitoring studies. (ESA)
Launched on 23 June 2015 and is part of the Program by
European Space agency.
The revisit time of one single satellite is 10 days
The Sentinel-2 Multispectral Instrument (MSI) consists of 13
spectral Bands
The data is available at different levels for the users.
 Sentinel 2 L1C Bands
Central wavelength
Band name Resolution (m) Band width (nm) Purpose
(nm)

B01 60 443 20 Coastal Aerosol

B02 10 490 65 Blue

B03 10 560 35 Green

B04 10 665 30 Red

B05 20 705 15 Vegetation Red Edge

B06 20 740 15 Vegetation Red Edge

B07 20 783 20 Vegetation Red Edge

B08 10 842 115 Near infrared

Vegetation Red
B08A 20 865 20
Edge/NIR

B09 60 945 20 Water vapor

B10 60 1375 30 SWIR - Cirrus

Atmospheric Windows and Band Positioning
Data Downloading Process
 Specification of Imagery Data Used

Date: 2016-10-08T05:47:22.000Z

Identifier: S2A_OPER_PRD_MSIL1C_PDMC_20161008T115539_

R048_V2061008T054722_20161008T055257

Instrument: MSI

Satellite: Sentinel-2

Cloud cover percentage: 0.3353

Pass direction: DESCENDING

Processing level: Level-1C

Product type: S2MSI1C

Relative orbit (start): 48

Imagery Data Processing

TOA to BOA Reflectance Conversion

Layer Stacking and Subsetting.
Indices Calculation
Resampling
Projection and Transformation
Pixel Values Extraction
Vegetation Index Formula S2 Bands Reference

IRECI , Red-Edge Chlorophyll (NIRR)/(RE1/RE2) (B7B4)/(B5/B6) (Frampton et al. 2013)

Index

MTCI , The Meris Terrestrial (NIRRE)/ (RE R) (B6B5)/(B5B4) (Dash and Curran 2007)

Chlorophyll Index ,(Frampton et al. 2013)l

NDI45, (NIR R)/ (NIR +R) (B5 B4)/ (B5 + B4) (Delegido et al. 2011b)

NDVI, Normalized Difference (NIR R)/ (NIR + R) (B7B4)/(B7+B4) (Rouse et al. 1973; Wan, Wang,

Vegetation Index and Li 2004)

REIP Red-Edge Inflection Point 702+40((R +NIR/2)- NIR / RE2RE1) 702+40((B4+B7/2)-B5/B6-B5 ) (Samalca 2007;Timothy et al.

Index 2016:Richter et al. 2012)

S2REP, Sentinel-2 Red-Edge 705+35*((((NIR+R)/2) RE1)/(RE2RE1) 705 + 35 * ((((B7 + B4)/2) B5)/ (B6 (Frampton et al. 2013),

Position B5))

SAVI, Soil Adjusted Vegetation (RNIRRR)/ (RNIR + RR + 0.5) 1.5 (B8- B4)/ (B8- B4+.5) *1.5 (Heiskanen 2006; Huete et al.
Field Data

Letter of Support to CDA For Their Assistance

Instrument Acquired From Pakistan Forest
Institute
10 days For Field Collection in Mid August , 2016
Plot Design

Options of Circular and Square Plots

Square plots are established by first defining one side and two
corners
Afterwards, right angles are traced at these corners and the other
two corners are located
The distance between the last two corners (and possibly the two
diagonals) should be measured in order to ensure the
measurements
 Square plots are very vulnerable to errors in
the plot area due to the large perimeter and a
difficult establishment
a wrong angle of the plot corners would
significantly change the area of the plot and
thus bias the estimates
Circular plots easy to establish.
Circular plots are less vulnerable to errors in
the plot area than square plots since the
perimeter is smaller in relation to the area and
thus the number of trees on the edge is less
 Generally it is assumed that the area on which the
sample plot is plain and the entire area to be sampled
is plain
Therefore, if a plot is located on a slope, a slope
correction will be needed
This correction accounts for the fact that distances
measured along a slope are smaller when they are
projected to the horizontal
This will cause bias in the estimates because sample
plots would differ in their sizes (and thus
measurements) and would correlate wrongly with the
size of the total area
Plot Design

Circular Plot With 17.5m Radius

Trees Greater than 10cm DBH
Minimum 40% of the Total Trees to
Ensure representation.
DBH , Tree Height and Total Count of
Trees in the Plot Measured, Location of
the Centre Tree, Slope, Aspect Recorded
in the Data Compilation Form.
 AGB From DBH and Height
Diameter of at least 40% in each plot with minimum diameter of 10
cm.
The diameter measured was first converted into basal area through
the following formula
Basal Area of a tree (m2) = (Diameter (cm)/200)2 x 3.14
Stand Basal Area (m2/ha) = (Sum of the basal area of each tree in
the plot) / (area of the plot (ha)
The plot volume was determined through the following formula
Standing Volume (m3/ha) = Stand Basal Area (m2/ha) x Average
Tree Height (m) / 3
 Standing Volume (m3/ha) = Plot Volume (m3/ha) / Plot Area (ha)
The above ground biomass was calculated using the formula:
Biomass =V BWDBEF
Where
V = standing volume timber m3 /ha
BWD = Basic wood density in Kg/m3
BEF = Biomass expansion Factor.
Carbon Estimation: Biomass 0.47
The dry biomass can be converted to carbon stock by multiplying
it with 0.47.
 Up-scaling to Sample Plot AGB

Upscaling to Ton per Plot AGB

Up-scaling to Tons per Hectare

Results

The AGB values from Field Processing Was recorded as attribute In the Point
Shape file Containing the Location of Measured Plots.
Shapefile was overlayed over the Each vegetation index calculated.
Through Spatial analysis the Cell value was extracted and recorded as attribute.
The Attribute table containing the AGB Value, and Cell value was exported as
Excell and then to matlab for regression analysis.
Spectral Profile of Cheer Pine
Chir Pine
Spectral Profile For Paper Mulberry
Paper Mulberry
Spectral Profile Of All Species Combined
All Species Combined
Conclusion

This study is concluded by revisiting the Questions asked and the objective outlined in
the first chapter.
How is much is the Biomass measured in the field correlated with changes in the spectral
response?
The AGB is poorly related to the spectral response.
What are the best spectral bands for different species which explains best the variation
in the biomass for that specie?
For Cheer Pine SAVI, For Paper Mulberry IRECI while for combined species SAVI
produces better result compared to the other indices.
 Does the generalized model for different species gives any promising results better than
the model for individual tree species?
No, it does not produce any better result. As clear from the tables and figures in the
result section, the correlation further becomes weak when all the species are modelled in
the bulk.
The findings reject the hypothesis that was assumed in the chapter 1. It therefore
concludes that biomass cannot be calculated based on Vegetation indices alone.
Possible Reasons.

Pixels Values Extraction. . 3x3 Pixels, Mean of Adjacent Pixels

Biomass Calculation Methodology Changed.. The One used By Dr Qazi and Shahbaz.
Atmospheric Correction Models were Checked. Sen2Core, QGiS SCP.
Two other Dataset of Sentinel 2 Were Applied
What are the reasons for Low
Correlation?
The observed low correlation is possibly due to the forest composition and the other related
factors.
The reflectance characteristic of vegetation is dependent on several factors. Among them is
the orientation and structure of leaf canopy.
The averaging of the pixels in the plot to reduce dislocation error might have affected the
vegetation indices. To account for this the pixel value exactly coinciding with the center of
pixel, and windows of 3x3, and the adjacent four pixels were also analyzed to no significant
difference in correlation was observed.
The change in the vegetation index of the pixel is independent of the actual biomass
contained in the forest area represented by that pixel
Sentinel 2 sensors can only get information about the reflectance of the forest canopy. Being
passive satellite it only records the sunlight reflected from the canopy only and does not
contain information about the height of the trees.
 The stem biomass that is hidden from the sensor comprises majority of the above-ground
biomass
While the models have been developed to link the biomass present and canopy
characteristics, they hardly hold true for medium resolution satellite due to the low spatial
resolution
Also reflectance is affected by leaf physiochemical properties, like structure (Comar et al.
2012), chlorophyll content (Zarco-Tejada et al. 2000) and water content (Danson and
Bowyer 2004).
One of the reason for the lack of correlation is the mixed pixel condition which has been
evaluated by Asner for low spatial resolution data (Asner 1998).
The combined reflectance observed is not only due to the amount of vegetation present, but
also from other factors such as senescence of vegetation, soil or shadow (Davidson and
Csillag 2001)
 In case of Margallah hills, due to hilly terrain the shadow factor could be considered as
one of the reason.
The shadow present could also contribute in the flat terrain due to the difference in the
sunlit and other side of the crown cover.
If Some of the Studies have reported the
Correlation, Why not here?
Lu (Lu 2005) in the Brazilian Amazon basin. The results in that particular study were
improved due to the inclusion of other factors such as the classification map , and the
age of the tree stands. Due to the limited research work and the unavailability of the
data that was not possible for this study.
The reason of disagreement could be different forest types, terrain, tree structure and
density of trees in the plot besides others.
 Future Recommendations

Above Ground Tree biomass is directly related to the Count of trees present in the area, the tree size and
height. For the better relationship, these characteristics needs to be captured with reasonable level of
accuracy
High resolution satellite imageries of Quick Bird, Ikonos, Spot or other satellite possibly can have
promising correlation due to their high spatial resolution
Due to their high resolution, they can better represent the canopy structure, which is as much important as
the spectral response characteristics of the canopy
 Lidar gives high resolution horizontal and accurate vertical information (Lim et al,
2003). Hyde et al. (2006) indicates that LiDAR alone can best estimate canopy height
and biomass information, and the addition fusion of sentinel 2 can improve the results.
One of the possible option for Biomass Estimation is UAV Remote sensing. The UAVS
gives the user the control over the flight time and the choice of sensors which are
suitable to the study. Compared to the satellite data they are cheaper and can be
configured to need of the phenomenon to be studied.
Thank You