Nemaplot hyperspectral data analysis and population modellingEvaluation reinvented


Density estimation of Heterodera schachtii

Damage beet cyst nematode
Field symptoms of H. schachtii
Growth reduction by H. schachtii
Heterodera schachtii Cysts, eggs, Juveniles
Sugar beet canopies with BCN

Model free analysis from hyperspectral aerial images

Application in field experiments

The first part of aerial image analysis deals with the potential to detect some common structures in a sugar beet crop and in case those more abstract information can be some associated with population density recorded from soil sample before planting sugar beets.

Hyperspectral image Explanation
RGB imageRGB transformed hyperspectral image of a sugar beet plot with an extremely high population density of about 4000 eggs and larvae / 100 ml soil determined by soil samples. The plot is framed by pathways, the plot boundaries are marked by white standard markers. Picture is taken with a Cubert2  camera, the usable wavelength ranges from 400 to 900 nm. Octocoptermessung mit Hyperspektralkamera Octocopter based Cubert2- camera with a resolution of 50 x 50 pixel.

Hyperspectral image analysis and classification
The cluster analysis with predetermined 8 clusters resulted in a distribution shown in the figure left. Cluster color is set to a spectral standard from blue to red. The first 5 clusters describe the general background, they determine the white standards (blue) up to the bare soil of the paths (green to yellow). The missing plant at the position 20;18 is clearly detectable. Much more interesting are the clusters 6 to 8, as they present the factor nematode population. The resulting pattern apparently shows different nematode densities, at least the spatial distribution is exactly how nematode population behave. Therefore the single cluster are worked out in more detail.

Hyperspectral signatures of healthy areas
Cluster 7 plus the 95% confidence bands: the variance is high as usual, but no outlier in the visible domains from 580 to 700 nm. Based on the structure of the signature of cluster 7 it is assumed the cluster represent nematode free areas (or below threshold densities) of the plot.

Hyperspectral signatures of heavy infested areas
The signals of cluster 8 (with confidence bands) describe the high density areas of up to 4000 E&L/100 ml soil. The conclusion is drawn from both, the relative position compared to cluster 7 and the increased variance in the domains of 580 to 700 nm. The higher reflectance in the visible wavelengths and lower reflectance in the infrared range indicate the nematode effect.

Hyperspectral signatures of light infested areas
Cluster 6, again compared to the position of cluster 7. We find high outliers in the domains of 580 to 700 nm. Part of Cluster 6 are spectra which are more typical for response to leaf pathogens. But it is not entirely clear, parts of the variance could be related to the bare soil of the paths. Nevertheless, nematode densities in the range of 600 - 1500 E&L/100 ml soil causes the pattern of cluster 6.
To provide some kind of proof of the conclusions above, we compare the hyperspectral signatures of the image (plot) with the ASD FieldSpec signatures. The signature pattern of that sensor show a larger variance in the domains of 580 to 700 nm, which are related to higher nematode densities (blue and green areas).

Conclusion: The combination of aerial information and the shapes of the confidence areas of the spectra allow some kind of conclusion about the underlying nematode population, or, more theoretically, it links the more abstract clusters more or less with the scientific hypothesis of the experiment.

1Image data have been prepared and provided by Institute of Geography, University of Cologne, AG Bareth

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