Elixir - Tech Track - Plant Phenotyping
17-3-2015
Plant Phenotyping and
interpretation of 3D data
ELIXIR Innovation and SME Forum: Data-driven innovation in the agri-food industries
Rick van de Zedde
March 18th and 19th, 2015
Introduction
 Rick van de Zedde, senior researcher/ business developer
Computer Vision for 11 years at Wageningen University &
Research centre in The Netherlands.
 Background:
Artificial Intelligence, University of Groningen.
Focus: computer vision/ robotics
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Wageningen University & Research Centre

A university plus R&D organisations, mission statement;
“To explore nature and to improve the quality of life”.

Wageningen UR:
● 6.500 employees
● 8.000 students
● 1.900 PhD’s
● 106 countries
Wageningen UR - campus
Wageningen UR - Phenomics
-
Chlorophyll fluorescence – Elisa Gorbe Sanchez
XY-table for phenotyping in a climate chamber
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NIR/ VIS hyperspectral – Franck Golbach, Gerrit Polder
Roots in 3D (X-ray CT) – Marcel Meinders, Erik Esveld
PhenoBot - Gerrit Polder, Marco Bink, Fred v. Eeuwijk
MARVIN/ EPPN/ EU-COST action – Rick van de Zedde
Field phenotyping – Erik Pekkeriet, Pieter Blok
www.phenomics.nl
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Overview
 Introduction
 Wageningen UR – Phenomics
 EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
 Vision-guided robotics
 Summing up/ future work
Plant phenotyping and food production
 Challenge: produce food for 9 billion in 2050
 Focus on improvement of crops (maize, rice, potatoes,
tomatoes, etc).
 Novel genotyping technologies ‘deliver’ new varieties much
quicker;
● Faster and less expensive DNA sequencers
● More efficient breeding cycles (GM and ‘classical’)
 Plants still need to be grown to determine yield, resistance
against heat/drought stress, diseases , etc. (= phenotyping).
 So an increase of capacity/ objectivity is required:
Opportunity for automated inspection, robotics, big data.
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Grant Agreement
No. 284443.
European Plant Phenotyping Network (EPPN) – 5.5 M€
Goals:
1. Create a European integrated network/ community
2. Offer trans national access to EPPN facilities
3. Research – a. Novel sensors,
b. Good practice phenotyping
c. IT for high throughput
Website:
www.plant-phenotyping-network.eu
Wageningen UR is WP leader of WP3 Novel sensors
Overview
 Introduction
 Wageningen UR – Phenomics
 EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
 Vision-guided robotics
 Summing up/ future work
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
MARVIN – 3D based seedling sorting
Rick van de Zedde (PL), Nicole Koenderink, Gerwoud
Otten, Franck Golbach, Mari Wigham, ea.
Specs, Scale and speed



Current capacity: 19.500 seedlings/ hour is 185 ms/ seedling

Software runs on a fast Windows 7 desktop computer;
National Instruments Labview/ core engine using CINs (C/C++).
Database: SQL server/ .Net web-interface

Raw data collection issue - ±5 seedlings per second =
10 GigE industrial machine vision camera’s, hardware triggered.
3D reconstruction technique: shape-from-silhouette/ volumetric
intersection which requires a very accurate 3D camera calibration.
10 camera’s x 5 per second x 1.2MB per image = 60 MB / second
216 Gb / hour .... saving 3D models only = 0.5 Gb / hour
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Illustration of volumetric intersection
Figure 3: Six of 24 images of the used watering can.
6 camera views from a watering can
Contact: [email protected]
Principle of volumetric intersection
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(b)
(a)
1 camera
More camera’s results in more detail
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Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Volumetric intersection: cube with voxels
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Plant/ seedling phenotyping
Examples of strange phenomena:
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Individual tray info
3D measurements and reference method
Features:

Stem length

Leaf length/ width

# leaves

Leaf type (cotyledon/ true leaf)
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
3D models and colour projection
Overview
 Introduction
 Wageningen UR – Phenomics
 EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
 Vision-guided robotics
 Summing up/ future work
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Height:
4m
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Plant architecture:
- Biomass estimation
- Length main stem
- # side stems
- Leaf angle/ length
- Leaf shape
- Internode length(s)
- Individual leaf areas
Overview
 Introduction
 Wageningen UR – Phenomics
 EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
 Vision-guided robotics
 Summing up/ future work
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Vision-guided robotics - planting rose cuttings
Goal: propagating roses from cuttings
Contact: [email protected]
Robot info - Cutting point & approach point
Specs:
- Calculations within 500ms
- Correct cutting point in > 95% in large test set
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Cut rose planting robot example
Contact: [email protected]
Robotic pot rose cutting planter
Rick van de Zedde (PL), Gerwoud Otten, Franck Golbach,
Sanja Damjanovic, ea.
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Overview
 Introduction
 Wageningen UR – Phenomics
 EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
 Vision-guided robotics
 Summing up/ future work
Summing up: accuracy and high throughput
 Tough specs: accurate 3D models within max. 500ms

Focus on high-throughput phenotyping - so no turntable.

Multi-camera advantages:
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Single shot (one trigger = 10 camera images)
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Individual plants imaged on a fast moving conveyer belt
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
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Future work
 Validation of the measured 3D traits using reference
measurements
 Using 3D for subtle colour differences on irregular surfaces.
 Quantification of plant architecture of larger plants
 Comparison of 3D methods of several partners within EPPN
We are interested in setting up a research collaboration
Contact: [email protected]
Acknowledgements

My colleagues at Wageningen UR:
EU project:
● Gerwoud Otten
● Franck Golbach
● Gerrit Polder
● Nicole Koenderink
● Sanja Damjanovic

Plus industrial partners:
● Mari Wigham
Enza (M. Klooster):
● Gert Kootstra
IsoGroup (P. Oomen):
All colleagues within EPPN
WPK (E. vd Arend):
Contact: [email protected]
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Elixir - Tech Track - Plant Phenotyping
17-3-2015
Questions ?
Thank you for
your attention!
Questions?
Contact:
[email protected]
Next slide = EU COST
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