high-throughput plant phenotyping –a boost for genomics in the 21st century
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High-throughput Plant Phenotyping –
a Boost for Genomics in the 21st Century
Dr. Jörg Vandenhirtz · CMO LemnaTec Head of Research and Development joerg.vandenhirtz@lemnatec.com
LemnaTec
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 2
founded May 1998 in Aachen, Germany
interdisciplinary team (biology, physics, engineering)
12 years of experience with image based biological measurement
in-house development of image processing software
in-house development of hardware
development of comprehensive and integrated solutions
compliance with international standards
The human eye
How many legs does this elephant have?
The human eye
Count the number of black dots…
The human eye
…are exactly the same size
The circles in the centers…
The human eye
Accelerating plant phenomics
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 7
opening new prospects
high-throughput screens
multiple camera units
non-destructive measurement
quantitative analysis
monitor growth dynamics
stress assessment
link to genomics
scanalyzer3D accelerating plant phenomics
Hardware
Hardware scanalyzer3D
Finding the needle in the haystack
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 10
The LemnaTec Scanalyzer System discovers THE ONE which is relevant…
For example, THE plant with 3% increase in value is worth $50m if it obtains 10% market penetration and released 2 years earlier
Automatic screening 10x more efficient than human screening
+3%
Modern breeding or GMO methods are able to produce THOUSANDS of new varieties per week
scanalyzer3D multiple imaging
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 11
1. top View
2. side View
3. side View 90°
4. more views optional
3D imaging of full plants
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scanalyzer3D scanning modes
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 12
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1. RGB visible light
2. NIR near infrared light
3. FLUOR fluorescent light
4. IR infrared light
5. ROOT NIR / RGB
Scanning in different wavelength and modes
scanalyzer3D VIS imaging – shape
Scanning – visible light
High-resolution colour images for comprehensive morphological and growth phenotyping
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 13
1.
scanalyzer3D VIS imaging – colour
Scanning – visible light
Plant colour classification – Key to plant health, stress, nutrients and senescence
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 14
infrared light
visible light
near infrared light for roots
near infrared light
fluorescent light
1.
Scanning – visible light
Plant skeleton analysis – key to growth dynamics, morphology and architecture
scanalyzer3D VIS imaging – architecture
separation of stem and leaves
information about nodes, length of leaves
morphology
plant growth phases
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 15
1.
scanalyzer3D VIS imaging – architecture
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 16
2.
Scanning – visible light Phenotyping of growth under field-density growth conditions
Phenotyping based on complex morphological criteria like: structure orientation, momentum of inertia, height, width, roundness, compactness. 0,00
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axis momentum ratio
be
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medium heigt, wide,
kinked leaves
high,straight upright
compact straight,
intermediate height
compact curved
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scanalyzer3D NIR imaging – shoot
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 17
2. 0 h
4 h 8 h 16 h
• wheat dried down over 16 h at elevated temperature • LemnaTec NIR imaging and analysis can cover the whole water dynamics of the drying for wheat • LemnaTec NIR cameras are suitable for detection of fine cereals structures of fully grown wheat
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scanalyzer3D flourescence imaging
Scanning – flourescent light
blue light (< 500 nm) visualises any related fluorescence
chlorophyll (cont., flash)
green fluo. Protein (GFP)
phenolics
autofluorescence
custom solutions
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 18
3.
scanalyzer3D IR imaging
Scanning – infrared light
Quantify temperature differences (e. g. within leaves and between plants)
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 19
4.
scanalyzer3D IR imaging
Scanning – infrared light
Quantify temperature differences (e. g. within leaves and between plants)
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 20
4.
scanalyzer3D RGB imaging – root
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 21
Static root density profiles – growth pattern
Bangui Sweet Corn Prelude Bangui
scanalyzer3D RGB imaging – root
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 22
Dynamic root growth - pattern Day 0 12 25 35 60 100
image and data show the development of roots of one plant in time.
scanalyzer3D NIR imaging – root
Scanning – near infrared light for roots
spatial distribution of water content in soil
0h 2h 4h 6h 8h
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 23
5.
scanalyzer3D NIR imaging – root
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 24
Corn plant previously shown was grown in a transparent 8 cm polyacryl column Results of NIR monitoring allow measurement of spatial distribution water content in soil
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total development of drying over time
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area classified pixels
drying dynamics based on soil layer
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area classified pixels
Hardware Future Developments?
Non invasive imaging of plants and plant roots in substrate with Nuclear Magnetic Resonant Imaging (NMRI) and (Sub) Terahertz Imaging (THz)
Dr. Axel Jung Ricarda van der Heijden Beta Klinik Bonn
Dr. Karsten Specht University of Bergen Prof. Dr. Martin Koch IHF TU Braunschweig
Dr. Jörg Vandenhirtz Matthias Eberius Dirk Vandenhirtz LemnaTec
Goal of this joint study:
Can Nuclear Magnetic Resonant Imaging (NMRI) or (Sub) Terahertz Imaging (Thz) be used for obtaining
non invasive and valuable information about plant roots in substrate?
• 3D root morphologie • 3D root dynamics • 3D root activity (water distribution) • etc...
movingfield linking greenhouse to field
Hardware Future Developments?
Used Plants: Corn Plants in transparent pots:
Hardware Future Developments?
Siemens MAGNETOM Espree 1.5T
NMR settings:
B = 1.5 T
TE = 12 ms
TR = 5.0 s
FoV = 250 x 250
ST = 1 mm
Price: 1.5 Mio Euro
Hardware Future Developments?
First Results of Dr. Axel Jung, Beta-Klinik, Bonn
Hardware Future Developments?
First Results of Dr. Axel Jung, Beta-Klinik, Bonn
Hardware Future Developments?
Problems: • artefacts (debris) in substrate hide roots (H2O + Fe) • low contrast between roots and background • correct setting of NMR has to be researched
-> Contact to Dr. Karsten Specht Department of Biological and Medical Psychology University of Bergen, Norway Research on NMRI
Dr. Specht tried NMRI of his office Plant...
Hardware Future Developments?
First Results of Dr. Karsten Specht, Uni Bergen:
Hardware Future Developments?
First Results of Dr. Karsten Specht, Uni Bergen:
Hardware Future Developments?
Complementary option for non invasive and penetrating plant sensors:
Prof. Dr. Martin Koch Institut für Hochfrequenztechnik TU Braunschweig
THz radation can be considered as high-frequency microwaves or very long waved light.
Infrared Microwaves Ultraviolet X-Ray
Visible
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Frequency (Hz)
“THz” Radiowaves
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Hardware Future Developments?
wat
er c
once
ntra
tion
Fresh leaf 48 hours after cut
B.B. Hu und M.C. Nuss, Opt. Lett. 20, 1716 (1995)
First THz image of a leaf with high resolution
Bell Labs Lucent Technologies
Hardware Future Developments?
First Results of Prof. Dr. Martin Koch, Braunschweig:
THz transmitter
THz detector
moving a coffee plant between a sub THz transmitter and detector…
…and measuring the transmission of the sub THz signal
z f THz
transmitter
detector
Hardware Future Developments?
The lift and rotating devices of the LemnaTec Phenotyping Platform are already integrated for 3D THz scans in cylindrical coordinates:
Combining 3D THz transmission measurements with visible 3D RGB image data of the LemnaTec Phenotyping Platform
Hardware Future Developments?
Conclusions:
NMRI THz
hardware standard of the shelf technology to be developed
software to be developed to be developed
throughput ca. 20 min. per plant ca. 2 min. per plant
resolution ca. 1 mm ca. 1 cm
hazards high B-Field none
price ca. 1.5 Mio. Euro ca. 150,000 Euro
target roots and shoots shoots (roots?)
Software Future Developments?
EuroStar Project PhenoFab January 2009 – January 2011 Project sum ca. 1.000.000 Euro
Development of a software interface between the output database format of DNA sequencers (e.g. La Roche) and the output database format of the image processing of the LemnaTec High Throughput Phenotyping Platform for multidimensional correlation analysis between the 2 datasets
Software Future Developments?
Plant
CORRELATION ???
Genomics
Phenomics
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 40
Contractracted Phenotyping Research
Date: 9/23/2011 Speaker: Dr. Joerg Vandenhirtz – CMO Slide 41
Ph
References Most Global Players in Breeding and GMO are already using the LemnaTec Technology: • BASF • Pioneer Dupont • Bayer CropScience • Monsanto • Syngenta • Dow Agro • Keygene • IPK • CSIRO • ACPFG • etc.
Visit our website www.lemnatec.com
Thank you for your attention!
Visit our website www.lemnatec.com
Time for your questions
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