Hyperspectral Remote Sensing of Plant Pathogens:
Detecting and Monitoring Myrtle Rust
UAS4RS Conference 2017 - Hobart
Rene H.J. Heim, Ian J. Wright, Hsing-Chung Chang, Angus Carnegie and Jens Oldeland
Introduction
Impact of Myrtle Rust in Australia
Introduction
Iconic Australian Landscape and the Myrtaceae
Myrtaceae - Abundance
World: 5500 species in 142 genera
Australia: 2501 species in 70 genera
(Thornhill et al., 2015)
(http://http://avh.ala.org.au/)
Source: 5
Source: 7
Myrtaceae - Hosts for Myrtle Rust Fungus
World before Australia - 129 species in 33 genera
World after Australia - 450 species in 73 genera
(Carnegie et al., 2016)
(Carnegie et al., 2016)
Source: 0
Source: 6
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Introduction
Myrtle Rust – Pathogenic Fungus
Source: 1
Attacks soft, actively
growing leaves, shoot tips
and young stems.
Source: 2
Plants do not drop dead but are
severely inhibited in reproduction
and growth…
Source: 3
…because fruits…
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
Source: 4
…and flowers which
produce seeds are
infected.
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Introduction
Impact on Environment and Economy
Environment
Plants Reproductive system affected. (Carnegie et al., 2016)
Repeated infection leads to plant death. (Pegg et al., 2014)
Food source and habitat for mammals, birds and insects.
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(CRC Plant Biosecurity, 2017)
Economy
Eucalyptus globulus and E. viminalis plantations. (Alfenas et al., 2003)
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Essential oil industry (Tea tree, Eucalyptus, Lemon Myrtle). (http://www.pbcrc.com.au/)
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Introduction
Knowledge Gap
We can’t:
• …timely detect the pathogen on plantations.
• …forecast pathogen dissemination in Australia.
• …monitor spore dispersal over a longer period.
Successful outcome of this project would enable us to:
• …effectively apply fungicides and reduce environmental impact.
• …better understand variability in species susceptibility and optimize scarce resources.
• …measure and monitor an efficacy of future eradication or conservation programs.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Introduction
Objectives
The objectives for my project are:
•
Discriminate spectral signatures reflected by healthy and infected plants.
•
Find and select best wavelength to discriminate healthy and infected plants.
•
Design a pathogen-specific vegetation index.
•
Upscale spectral pathogen detection to an aerial system.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Methods
Hyperspectral RS and Machine Learning
Methods
Field Spectrometry on Lemon Myrtle Leaves
Source: 7
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Spectral Evolution PSR+ field spectrometer + leaf clip.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Methods
Reading a spectral signature
VIS
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NIR
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Methods
Field Spectrometry and Random Forest Classification
740 Spectra of three
classes (240 Healthy,
240 Treated, 240
Infected)
Outlier detection
(left 216 H, 236 T,
228 I) and noise
removal
Spectral
binning
1:10
(fda and fda.usc pkg)
(prospectr pkg)
1st order
derivatives
and primary
spectra
Random
Forest
Classification
Feature
Selection
(Caret pkg)
(VSURF pkg)
(hsdar pkg)
All statistical analyses were conducted in R 3.2.3.
For transparency, code will be published via GitHub.
(R Core Team, 2015)
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
High Accuracy Classification
Results
Random Forest Classification Accuracy (Error Matrix)
A
Primary Spectra (Test Set 20%)
Reference (Label Accuracy)
Healthy Treated Infected Totals
Healthy
34
0
1
Treated
0
41
13
Infected
9
6
31
43
47
45
Totals
PA
79.1% 87.2% 68.9%
Prediction
(Machine
Accuracy)
#Samples
35
54
46
135
UA
97.1%
75.9%
67.4%
78.5%
And 1st order derivative spectra?
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Random Forest Classification Accuracy (Error Matrix)
B
1st Derivative Spectra (Test Set 20%)
Reference (Label Accuracy)
Healthy Treated Infected Totals
Healthy
42
0
0
Treated
1
45
4
Infected
0
2
41
43
47
45
Totals
PA
97.7% 95.7% 91.1%
Prediction
(Machine
Accuracy)
#Samples
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
UA
42 100.0%
50 90.0%
43 95.3%
135
94.8%
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Results
Why are 1st order derivatives so much better?
Differentiation of the spectra does not provide more information than the original
spectra, it can emphasize the target features while suppressing other unwanted
information.
(Thenkabail et al., 2011)
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Derivative Reflectance
Derivative Reflectance
Why are 1st order derivatives so much better?
Source: 12
Ok, we see the difference. But it would be great to have a straightforward index!
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Designing a Vegetation Index - Two standard examples
Normalized Difference Vegetation Index (NDVI)
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Photochemical Reflectance Index (PRI)
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Feature Selection – Primary Spectra
Infected
Treated
Source: 15
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Derivative Reflectance
Feature Selection – First-order derivative spectra
Infected
Treated
Source: 16
Myrtle Rust specific vegetation index is based of some selected features.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Results
Lemon Myrtle - Myrtle Rust (LMMR) Index
• Myrtle Rust/Lemon Myrtle specific index
• Ratio index based on a combination of
four (out of 28) specific wavelengths
• Optimized for hyperspectral sensors
• Adjustable to multispectral by using other
combinations from the set of 28
wavelengths
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Conclusion
Objectives
The objectives for my project are:
1. Discriminate spectral signatures reflected by healthy and infected plants.
2. Find and select best wavelength to discriminate healthy and infected plants.
3. Design a pathogen-specific vegetation index.
4. Upscale spectral pathogen detection to an aerial system.
Analysis of multispectral drone data will follow in Winter 2017.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Outlook
Multispectral Images captured using a DJI Inspire 1 Quadcopter
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B= Buffer, U= Untreated, T=Treated (Fungicide)
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Thank you for listening!
Questions?
For updates on my projects, please follow me on:
https://twitter.com/ReneHJHeim
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Acknowledgements
Myrtle Rust Monitoring Team
Jens Oldeland, Ian Wright, Michelle Leishman, Michael Chang, Angus Carnegie and Geoff Pegg for ongoing academic advise and support.
G. Mazzorana – Lemon Myrtle Grower and Remote Aerial Imagery - UAS
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Literature
Figures
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11-18
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http://art-now-and-then.blogspot.com.au/2015/03/albert-namatjira.html
Ina Geedicke
http://www.dpi.nsw.gov.au/__data/assets/image/0010/362782/myrtle-rust-agonis.jpg
https://anbg.gov.au/gardens/images/200-vertical/myrt-rust-Rhodamnia-rubescens-fr-carnegie.jpg
https://www.daf.qld.gov.au/__data/assets/image/0005/59927/geraldton-wax-flower.jpg
http://www.psdgraphics.com/psd-icons/green-recycling-symbols/
https://www.shutterstock.com/search/australian+dollar
Ina Geedicke
Ina Geedicke
Karen Joyce/https://www.youtube.com/watch?v=rxOMhQwApMc&list=PLM5Qn7cNEHDSSOEWE9jIgwi4CXL5cb3vY
http://www.ontariograinfarmer.ca/Portals/1/Issues/2015/September%202015/pag2.jpg (modified)
Rene Heim
http://www.techtimes.com/articles/102639/20151103/maybe-fallouts-vault-boy-isnt-giving-us-the-thumbs-up-after-all.htm
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Literature
References
Berry EW. 1915. The Origin and Distribution of the Family Myrtaceae. Botanical Gazette 59: 484–490.
Carnegie AJ, Kathuria A, Pegg GS, Entwistle P, Nagel M, Giblin FR. 2016. Impact of the invasive rust Puccinia psidii (myrtle rust) on native Myrtaceae in natural ecosystems
in Australia. Biological Invasions 18: 127—144.
Congalton RG, Green K. 2009. Assessing the accuracy of remotely sensed data: principles and practices. Boca Raton: CRC Press/Taylor & Francis.
Febrero-Bande M, Oviedo de la Fuente M. 2012. Statistical computing in functional data analysis: the R package fda. usc. Journal of Statistical Software 51: 1–28.
Genuer R, Poggi J-M, Tuleau-Malot C. 2015. VSURF: An R Package for Variable Selection Using Random Forests. The R Journal 7: 19–33.
Kuhn M, Weston S, Williams A, Keefer C, Engelhardt A, Cooper T, Mayer Z, Kenkel B, Team the RC, Benesty M, et al. 2016. caret: Classification and Regression
Training.
Lehnert LW, Meyer H, Bendix J. 2016. hsdar: Manage, analyse and simulate hyperspectral data in R.
Ramsay JO, Wickham H, Graves S, Hooker G. 2014. fda: Functional Data Analysis.
Stevens A, Ramirez–Lopez L. 2014. An introduction to the prospectr package.
Thenkabail PS, Lyon JG, Huete A. 2011. Hyperspectral remote sensing of vegetation. CRC Press.
Thornhill AH, Ho SYW, Külheim C, Crisp MD. 2015. Interpreting the modern distribution of Myrtaceae using a dated molecular phylogeny. Molecular Phylogenetics and
Evolution 93: 29–43.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Discussion
And now?
Discussion
What did we achieve?
• We could achieve great classification results for our problem and could show that classification
of first-order derivative spectra further improves our results.
• We applied appropriate state-of-the-art, non-parametric classification algorithms having in
mind that hyperspectral data often brings intrinsic difficulties with it (multicollinearity, high
dimensions and resulting overfitting.)
• We could select a few meaningful wavelength amongst ~2500 that can be used in future
classification approaches.
• Using these wavelength helped us design a pathogen specific vegetation index which is
currently under optimization.
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Discussion
What will we achieve?
• We further collected multispectral data from the same plants we used for our classification and
we will analyse this data shortly.
• We are also planning to extend our spectral library by analysing already collected spectral
signatures from three important wetland species (Melaleuca viridiflora, M. leucadendra and M.
quinquenervia)
René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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Introduction
How to record spectral signatures?
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René Heim (B.Sc. - Bioengineering, M.Sc. - Biology) I Macquarie University I Faculty of Science and Engineering I Biological Sciences
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