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Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Plant Phenotyping and
interpretation of 3D data
Rick van de Zedde
March 18th and 19th, 2015
ELIXIR Innovation and SME Forum: Data-driven innovation in the agri-food industries
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]
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
- 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
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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]
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
Grant Agreement No. 284443.
Overview
Introduction
Wageningen UR – Phenomics
EPPN – WP3 ‘Novel sensors’
● 3D reconstruction of seedlings
● Young plants
Vision-guided robotics
Summing up/ future work
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
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.
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 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
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
S C
U O B N
M F I I T D
T E E N D T I
A L
(a)
(b)
1 camera More camera’s results in more detail
Contact: [email protected]
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Volumetric intersection: cube with voxels
Contact: [email protected]
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Plant/ seedling phenotyping
Examples of strange phenomena:
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Individual tray info
3D measurements and reference method
Features:
Stem length
Leaf length/ width
# leaves
Leaf type (cotyledon/ true leaf)
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Height:
4 m
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Vision-guided robotics - planting rose cuttings
Goal: propagating roses from cuttings
Contact: [email protected]
Robot info - Cutting point & approach point
Contact: [email protected]
Specs: - Calculations within 500ms - Correct cutting point in > 95% in large test set
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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.
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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:
- Single shot (one trigger = 10 camera images)
- Individual plants imaged on a fast moving conveyer belt
Contact: [email protected]
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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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:
● Gerwoud Otten
● Franck Golbach
● Gerrit Polder
● Nicole Koenderink
● Sanja Damjanovic
● Mari Wigham
● Gert Kootstra
All colleagues within EPPN
Contact: [email protected]
Plus industrial partners:
Enza (M. Klooster):
IsoGroup (P. Oomen):
WPK (E. vd Arend):
EU project:
Elixir - Tech Track - Plant Phenotyping 17-3-2015
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Questions ?
Thank you for
your attention!
Questions?
Contact:
Next slide = EU COST