gerrit polder, wageningen university & research...5/18/18 2 wageningen university & research...
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Photonics for sensing in Agro and Food
Workshop: Photonics for agriculture (Florence, May 16th, 2018)
Gerrit Polder, Wageningen University & Research
Outline
§Introduction
§Spectroscopy
§Imaging
§Spectral Imaging
§Applications
§Augmented Reality
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Wageningen University & Research
§ A university plus R&D organisation for innovation in the agrifoodsector.
§ Working with industry, governmental authorities and other knowledge institutes
Wageningen UR - campus
• 6.500 employees• 10.000 students• 100 countries
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Applied Research Prototypes/ demonstrators
Value generation/spin-offs
Fundamentalresearch
Knowledge Push
Market Pull
Wageningen University
Wageningen Research:Contract research organisation Industry
WUR – Way of working
Contact: [email protected]
Public-private partnerships:Top sectors - Agro&Food/ Horticulture
Bilateral contract researchNational Science/ EU funding
Photonics for plant phenotyping
§ Photonics devices for sensing:
§ Plant -> sensor§ Sensor -> plant
(greenhouse)§ Sensors on drones§ Disease detection§ Big Data
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Spectroscopy
§ Single point (area) measurement§ Full spectrum
● Reflectance● Transmittance● Transactance
Mycosphaerella melonis in cucumbers
Gezond
Geïnfecteerd
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Mycosphaerella: NIR – transmission
Lightsource
Optical fibers Average spectrum cucumbers 500-950nm
Wavelength [nm]Tr
ansm
issi
on
Tran
smis
sion
Healthy
Infected
§ Accuracy 91%
Automated method – shape analysis
L
0.2L
healthyinfected
L = 1000 pixels
Þ200 features
Linear classifier
Distance from the tip
Wid
th
§ Accuracy increased to 95%
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Robot for high throughput phenotyping
Mono/Color/Multi/Hyper-spectral Imaging
§ Grey value camera (1 band)
§ Color camera (3 bands)
§ spectral camera (4 - 300 bands)
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Recently hyper/multispectral draws quite some attention
Hyper/multispectral imaging at Vision 2016
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https://youtu.be/cB1blIlIvls
Slit-spectrometer collects a “wall” of data: pushbroom allowsacquisition of a complete data cube.
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Hyperspectral imaging
Predicting biochemicalsor diseases in a spatial preserving way
Hyperspectral imaging – Image/Features
§Spectral image of four roses. § PCA analysis – from image to features
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Hyperspectral imaging – Image/Features
§Spectral image of four roses. § PCA analysis – from features to image
800 nm
Tomato Hyperspectral reflection
650 nm
500 nm
Imaging656 x 500 px192 bands
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-4 -3 -2 -1 0 1 2 3
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day 1day 2day 3day 4day 5
Ripening of tomatoes
§Scatter plot of feature analysis of the RGB and spectral images.
§Classes 1-5 represent the ripeness stages of a tomato during the five days after harvest respectively.
-8 -6 -4 -2 0 2 4 6-6
-5
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0
1
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day 1day 2day 3day 4day 5
G. Polder, G.W.A.M. van der Heijden, and I.T. Young. Spectral image analysis for measuring ripeness of tomatoes. Transactions of the ASAE, 45(4):1155–1161, 2002.
Disease detection in seed potatoes
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Distinction between stem and leaf
Distinction between stem and leaf
Based on a few images a classifier is built to distinguish between stem and leaf, in order to find diseases in the stem or leaf respectively.
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Deep Network Initial Results
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Threshold 0.25
PredHealthy
Pred Sick
KnownHealthy
1890 436
Known Sick
317 1052
Confusion Matrix: Classifier threshold 0.25
Top line: Ground Truth Below top: Neural network prediction (Red = Sick, Green = Healthy)
Detection of tulip breaking
virus in the open field
Multispectral
G. Polder , G. W. A. M. van der Heijden, J. van Doorn, J. G. P. W. Clevers, R. van der Schoor and A. H. M. C. Baltissen, 2010. Detection of the tulip breaking virus (TBV) in tulips using optical sensors. Precision Agriculture,vol. 11 (4), pp. 397-412.
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Detection of Botrytis in
the greenhouse
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Patterns for Profit:Augmented reality glasses for monitoring plant health
Using reflectance at specific wavelengths in the visible and near-infrared range can enhance the contrast between healthy and unhealthy plants.
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Patterns for Profit:Augmented reality glasses for monitoring plant health
Application 1:Excessive green (2G-R-B) for counting weeds on pavements.
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20%
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Patterns for Profit:Augmented reality glasses for monitoring plant health
Application 2:Normalized Difference Vegetation Index (NDVI) for viewing crop quality. 31
Patterns for Profit:Augmented reality glasses for monitoring plant health
First prototype:§ Raspberry Pi NoIR Camera§ Infra-blue filter§ For Red take Green and/or
Blue
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Acknowledgements
Gerie van der Heijden, Joop van
Doorn , Ton Baltissen, Erik
Pekkeriet, Hans Jansen, Rick van
de Zedde, Gert Kootstra, Danijela
Vukadinovic, Gert-Jan Swinkels,
Pieter Blok, Toon Tielen, Hendrik
de Villiers, Jan Kamp, Jos
Ruizendaal, Freek Daniels.
Summer School on Image Analysis for Plant Phenotyping
Organised by Wageningen Academy,Wageningen Agro Food Robotics
Date Mon 2 July 2018 until Fri 6 July 2018Duration 5 daysSetup Campus WURVenue Wageningen
