Purdue University Graduate School
sneeno_MSthesis_0501_reformat.pdf (1.81 MB)

Quantifying Intra-canopy Hyperspectral Heterogeneity with respect to Soybean Anatomy

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posted on 2020-05-06, 12:18 authored by Samantha NeenoSamantha Neeno
To support the growing human population, plant phenotyping technologies must innovate to rapidly interpret hyperspectral (HS) data into genetic inferences for plant breeders and managers. While pigment and nutrient concentrations within canopies are known to be vertically non-uniform, these chemical distributions as sources of HS noise are not universally addressed in scaling leaf information to canopy data nor in detecting spectral plant health traits.
In this project, soybeans (Glycine Max, cultivar Williams 82) were imaged with a Spectra Vista Corporation (SVC) HR-1024 spectroradiometer (350-2500 nm) at the highest five node positions. The samples were subjected to nitrogen and drought stress in factorial design (n=12) that was validated via relative water content (RWC) and PLS Regression of photopigments (chlorophyll a, chlorophyll b, lutein, neoxanthin, violaxanthin, and zeaxanthin in mg/g DW) and N concentration (%) for each imaged tissue. Welch’s ANOVA and Tamhane’s T2 post-hoc testing quantified spectral heterogeneity with respect to treatments and node positions through spectral angle measurements (SAMs) and percent NDVI difference. Drought-stressed samples had the lowest SAM between node positions compared to other treatments, and SAM node comparisons were greatest when including the highest sampled tissues. Taking ratios of NDVI between node positions proved more statistically effective at discerning between all factorial treatments than individual leaf NDVI values. Finally, intra-canopy spectral heterogeneity was exploited by training Linear Discriminant Analysis (LDA) classifiers on relative reflectance between node positions, tuning for the F1-Score. A classifier built on Node 1 vs. Node 3 reflectance outperformed in class-specific accuracies compared to analogous models trained on point-view data. Accounting for intra-canopy spectral variability is an opportunity to develop more comprehensive phenotyping tools for plant breeders in a world with rapidly rising agricultural demand.


Degree Type

  • Master of Science


  • Agricultural and Biological Engineering

Campus location

  • West Lafayette

Advisor/Supervisor/Committee Chair

Jian Jin

Additional Committee Member 2

John Couture

Additional Committee Member 3

Jeffrey Volenec

Additional Committee Member 4

Shweta Singh

Additional Committee Member 5

Somali Chaterji

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