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Seeing the Forest for the

Trees
Classifying Eucalyptus subgenera for
habitat mapping using HyMap
hyperspectral remote sensing
Kara Youngentob, Xiuping Jia, Alex Held,
Luigi Renzullo and David Lindenmayer
Where the Wild
Things Are

An image from the children's book Where the Wild Things Are by Maurice Sendak
Presentation Outline
Background and introduction to the project
Overview of objectives
Classifying Eucalypt subgenera
Summing-up
Additional Thanks
Introduction

Field Site

David Lindenmayer and Ross


Cunningham (et al)
Tumut Fragmentation Experiment
Long-term field site
“Natural Experiment” on
a landscape scale
Possums and Gliders
Images from David Lindenmayer’s Tumut website http://cres.anu.edu.au/dbl/tumutstudy.php
Our Wild Things

Arboreal Marsupials at Tumut

Ringtail Possum
Photo by: Esther Beaton
Brushtail Possum
Photo by: Karen Marsh
Greater Glider
Photo by: Esther Beaton
Where do the animals live?

Heterogeneous Nature of
Landscapes

Eucalypt forest remnants surrounded by pine plantings


near Tumut, NSW.
Photo from previously cited source
What do animals like?

Heterogeneous Nature of
Landscapes

Eucalypt forest canopy at Tumut, NSW Australia. Photo by Kara Youngentob


How can we map habitat?

Remote Sensing Hyperspectral


Data

AVIRIS hyperspectral data cube over Vegetation Spectral Reflectance extracted from AVIRIS data
Moffett Field, CA

Hyperspectral imagery source -


http://www.csr.utexas.edu/projects/rs/hrs/hyper.html
How can we map habitat?

Mapping Foliage Chemistry with Hyperspectral Data


Tree canopy image
(image pixel in green)

Vegetation spectra
from pixel

Map based on variations in reflectance at specific wavelengths (bands) of the spectra


Distribution of Total Polyphenol (plant defensive chemical) across a forest landscape, HyMap imagery from PhD thesis by Jelle G. Ferwerda
Recap
In short, my research involves trying to identifying physical and
chemical properties of the Tumut landscape which might explain the
observed distribution of some folivorous marsupials using
hyperspectral remote sensing.

Photos from previously cited sources


Study Objectives
Animal counts

Study Objective #1
 Re-establish Tumut Transects and collect presence and abundance data
for all arboreal marsupials

Canberra

Tumut

Map of Tumut transect sites


Animal counts
 Transects were 200-600m depending on size of fragments (most were 600m)
40 pilot study transects. Full study area transects included 82 (20 repeated from pilot) patch
transects, and 34 continuous forest transects. Followed methods from 1995 Tumut study.

Approx
65k of
transects

Kara re-establishing transects and rejoicing in blackberries


Animal counts
24 spotlighting nights for full survey (controls in duplicate).

Averaged 3-4
sites per nite

A volunteer taking notes on observed animals


Animal counts

I noted the GPS locations of animals as


well as their distance from the edge of
patches and edge characteristics
Animal counts

 The purpose of collecting this data was to investigate the response of


arboreal marsupials to landscape change in a plantation environment over
time and to record the GPS locations of animals observed in the forests.

Images from left to right: Partially cleared plantation landscape, a baby greater glider, Eucalypt forest meets plantation.
Foliage chemistry
Study Objective #2
Leaf collection and analysis

Paddock Tree
Stuart helping to collect
more leaf samples
Foliage chemistry

Leaf collecting from GG patches

 We also collected leaf samples in patches where GG


were radio-tracked to explore relationships between tree
choice and foliage chemistry
Foliage chemistry

Found 237 trees that were marked during the GG study (a little less than half), and collected an
additional 191 “matched” trees that were unmarked
Foliage chemistry

Laboratory Analysis

NIR machine for capturing spectra Titration machine for


of freeze-dried, ground samples measuring nitrogen
Foliage chemistry

Laboratory Analysis

Measuring samples for digestion Digested samples ready for titration


Foliage chemistry

Making a Prediction Equation from a Training Set

Model Estimate New Spectra


Regression
of Nitrogen Conct.
∧ coefficients
identified in

y = Xβ training

Prediction Equation for Nitrogen (or other chemical) Concentration


Foliage chemistry

Results from Prediction Equations based on lab values for our training set
(Modified PLS with LOO Cross-validation)

Constituent Math n Mean SD SEC RSQ SECV 1-VR #


treatment
“smoothing”
Nitrogen 2881 96 1.2092 0.1993 0.0363 0.9668 0.0579 0.9154 251

Digestible 2881 94 0.4343 0.1173 0.0189 0.9742 0.0290 0.9388 251


Dry Matter

Available 2881 68 0.2398 0.2398 0.0479 0.9601 0.0724 0.9096 251


Nitrogen

Table derived from ISI NIR-statistical package output


Remote Sensing

Study Objective #3
 Measure and map the variations in foliage chemistry using HyMap data

HyMap flight-plan
Remote Sensing

HyMap Imagery Collected

HyMap hyperspectral images of the Tumut


site acquired in March, 2007
Remote Sensing

Orange tarp Ground Truthing


Isolated Trees

Black Tarp
Paddock Paddock Trees
Trees

Blue Tarp
Isolated Trees
Remote Sensing

Ground Truthing

Orange Tarp
Remote Sensing

Ground Truthing

Alex Held and Paul Daniel assisting with spectral data collection in the field
Remote Sensing

Collecting spectra
Remote Sensing
1
0.95
0.9 Field Spectra
0.85
swampwhole
0.8
0.75 stringywhole
0.7
applewhole
0.65
0.6 ashwhole
Reflectance

0.55 unknownstringypepwhole
0.5
pauciflorawhole
0.45
0.4 sallywhole
0.35
camwhole
0.3
0.25 pepwhole

0.2 vimwhole
0.15
0.1
0.05
0
350
424
498

572
646
720
794
868
942
1016
1090
1164

1238
1312
1386
1460
1534
1608
1682
1756

1830
1904
1978
2052
2126
2200
2274
2348

2422
2496
Wavelength (nm )

Fresh, whole leaf spectra (after de-stepping) taken with an ASD Fieldspec Pro
Eucalyptus spectra only (Averages)
Remote Sensing
Reflectances and Ratios to Average
sw ampleaves
stringyleavesw ithoutyoung
2.4
appleleaves
2.3
2.2 Field Spectra ashleaevs
2.1 unknow nstringypepleaves
2 paucifloraleaves
1.9
messmateleaves
1.8
1.7 sallyleaves
1.6 camleaves
Reflectance & Fraction

1.5 vimleaves
1.4
pepleaves
1.3
1.2 all averaged
1.1 all averaged Ratios
1 sw ampleaves
0.9
stringyleavesw ithoutyoung
0.8
appleleaves
0.7
0.6 ashleaevs
0.5 unknow nstringypepleaves
0.4 paucifloraleaves
0.3
messmateleaves
0.2
0.1 sallyleaves
0 camleaves
350
422

494
566
638
710
782
854
926
998
1070
1142
1214
1286

1358
1430
1502
1574
1646
1718
1790
1862
1934
2006
2078
2150
2222
2294
2366
2438
vimleaves
pepleaves
Wavelenghth
all averaged
Classification

Classifying Eucalyptus Subgenera


What is a subgenera, why do we care?

Broad-leafed peppermint Manna Gum (E. viminalis )


(E. Dives) Monocalyptus Symphyomyrtus
Classification

Dominant canopy species at Tumut


Tree Species Subgenera Characteristic environment
Pinus radiata N/A Plantation species, native to North America
Eucalyptus radiata Monocalyptus Widespread on a range of substrates. Prefers cooler, wetter areas.
Eucalyptus macrorhyncha Monocalyptus Widespread and dominant in Sclerophyll forests and poor, shallow soils.
Eucalyptus dives Monocalyptus Widespread in Dry Sclerophyll or poor shallow, stony soils
Eucalyptus viminalis Symphyomyrtus Widely distributed forest species. Prefers cooler areas.
Eucalyptus camphora Symphyomyrtus Common along gully lines and marshy areas.
Eucalyptus bridgesdiana Symphyomyrtus Dry Sclerophyll forest species.
Eucalyptus pauciflora Symphyomyrtus Characteristic of higher elevations.
Eucalyptus dalrympleana Symphyomyrtus Widespread forest species. Prefers loamy or sandy soils at higher
elevations.

Monocalypt Symphyomyrt
Darker green Typically
leaves, non-waxy, lighter green
brittle, lots of leaves, waxy,
volatile terpenes lots of lignin
Classification

Step 1. Identify paddock tree subgenera

HyMap Tree Pixels

Paddock Trees Identified in HyMap Imagery


Classification

Paddock Trees

HyMap Tree Pixels

Photograph of trees that correspond to HyMap Pixels


Classification

Step 2. Collect HyMap Spectra from


Paddock Trees

Continumm removed HyMap vegetation spectra from tree pixel--top is “good” pixel, bottom is “bad” pixel.
Classification

Step 3. Reduce dimensionality of data by selecting bands

Freeze-dried leaf absorbance spectra Tree canopy reflectance spectra from HyMap
(red and green lines). Blue line is (red and green lines). Blue lines are the
ANOVA F-score. Where the blue line bands selected by the Bhattacharyya
dips below the dotted black line, there is algorithm function in Multispec to provide the
significant difference between best separation of the two classes,
Monocalypt (n 318) and Symphyomyrt (n Monocalypt (n 56) and Symphyomyrt (n 49).
236) spectra. Performed to explore data. Used to select data for classification.
Classification

Step 4. Maximum likelihood classification on reduced data


Statistic Training Kappa Kappa Testing Kappa Kappa
Feature Selection
Applied Accuracy Statistic Variance Accuracy Statistic Variance
MED All 125 channels selected 56.2 0.124 0.00932 55.2 0.104 0.00939
Bhattacharyya
15 Channels (B-dis 3.93)
ML 100 1.00 0.0 96.2 0.923 0.00141
2, 9, 24, 35, 50, 61, 72, 79,
83, 84, 85, 87, 95, 96, 104
Bhattacharyya
14 Channels (B-dis 3.58)
ML 99 0.981 0.00036 92.4 0.847 0.00272
2, 24, 35, 50, 61, 72, 79,
83, 84, 85, 87, 95, 96, 104
ML 10 Channel PCA 89.5 0.788 0.00362 78.1 0.558 0.00659
10 Channel PCA with
ML 86.7 0.729 0.00442 82.9 0.653 0.00546
channels (3, 5, 9) removed

Classification results for Monocalyptus and Symphyomyrtus HyMap spectra based on a training
data set of 56 Symphyomyrts and 49 Monocalyptus and LOO cross-validation for testing data.
Summing--up
Summing
Re-establish original Tumut transects and collect presence and
abundance data to investigate the response of arboreal
marsupials to landscape change in a plantation environment
Explore relationship between tree choice and foliage chemistry by
collecting leaves in patches where GG were radio tracked and
paddock tree leaves under HyMap flightlines
Conduct a hyperspectral remote sensing flight over my study area
to investigate relationships between animal occurrence, habitat
type (dominant canopy subgenera) and foliage chemistry on a
landscape scale.

Photos from previously cited sources


Still to come…

Percent nitrogen as estimated by reflectance at 1970nm + 2170nm


Bands selection based on findings relating to the prominence of these two absorption features in relation to nitrogen concentration (Zhi Huang et. Al 2004).
Acknowledgements
Many thanks for your support!
The Hermon Slade Foundation
WildCountry and The Wilderness Society
Ecological Society of Australia
CSIRO CMAR and Land and Water
David Lindenmayer’s research team
Bill Foley’s Lab, ANU Botany & Zoology
ANU Vice-chancellery Image from previously cited source

The Fenner School (formerly CRES) staff, students and administration


You! Thank you for listening.