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New remote and proximal sensing methodologies in high throughput field phenotypingRemote Sensing – Beyond images. Mexico City, 2013
JOSE A. JIMENEZ-BERNI. CSIRO PLANT INDUSTRY. HIGH RESOLUTION PLANT PHENOMICS CENTRE
Why phenotyping?Why high throughput?
Breeder’s wish listTable 2. Essential and desirable measurements for phenotyping of yield and other traits across multiple experiments in water-limited and high temperature environments.
Essential (core) Timing A
(frequency)
Desirable Timing A
(frequency)
Plant establishment counts (plants/m2)
DC 12-13 (1×) Canopy light interception (μmol/m2/s)
DC 35-60 (2×)
Ground cover (%) DC 12-37 (3×) Normalized Difference Vegetation Index
DC 12-60 (4×)
Normalized Difference Vegetation Index
DC 12-37 (2×) Early biomass/leaf area/tiller number DC 30-32
Anthesis date DC 45-65 (every 3d)
Carbon Isotope Discrimination DC 30-32
Canopy temperature (°C) DC 35-70 (2×) Anthesis biomass (g/m2) DC 60-65
Harvest index DC 90 Water soluble carbohydrates DC 65-70 (1×)
Spike number (spikes/m2) DC 90 Canopy temperature during grain filling (°C)
DC 70+ (4×)
Plant height (cm) DC 90
Thousand grain weight (g) DC 90
Grain yield (g/m2) DC 90
Observations and scores (e.g. incomplete plots, temperature damage, disease, lodging, and shattering)
as required
A Timing according to the Zadoks decimal code (DC) for scoring stages of cereal development (Zadoks et al. 1974)
(More info: Rebetzke et al 2012, (http://prometheuswiki.publish.csiro.au/tiki-index.php)
Phenomobile
• 3x LiDARs (Canopy Structure)• 4x RGB cameras (Stereo
reconstruction)• 1x Thermal IR camera (Canopy
temperature)• 1x Hyperspectral line scanner
(Canopy biochemistry)• 1x Full range spectrometer
(Canopy biochemistry)• Removable light banks
LMS400
Canopy
-30� 30�
Canopy Canopy
70�
y = 0.6624x + 230.77R² = 0.8619
0
200
400
600
800
1000
1200
1400
0 200 400 600 800 1000 1200 1400
LiD
AR
mea
sure
d ca
nopy
hei
ght
(mm
)
Manually measured canopy height (mm)
LiDAR Height Validation
Non-destructive wish listoFractional coveroCrop heightoLAIoCanopy architecture
oGrowth rateoEars / m2oHIoBiomassoCrop yield
LiDAR outputs
Canopy architecture and spike counts
Hyperspectral line scanner and high-res thermal
Phenomobile Lite
Acquisition of airborne thermal imagesThe Airframe
Sensor Integration
The Flight Controller
Airborne thermal mosaic – ready for plot extractionLegend [deg C]
~600 m• Capture 3 images / second• One pass of the field ~10 sec (3 passes required)• Time to image entire field ~4 min• Ideal: Simultaneous measurements at nearly a single point in time
“Old way” h2<0.1 “New way” h2>0.6
Extraction of plot temperature
100’s samplesper plot
Wireless infrared thermometers
• Zigbee standard• Selectable sampling interval
(5min)• 3G transmission from base
station• Real time access from Internet• 100 sensors built in 2011• 400 sensors built in 2012• 160 in a single deployment
(Narrabri / Cotton)
Canopy temperature data
Canopy conductance modelling
Other sensors and applications
fAPAR
350 450 550 650 7500
20
40
60
Wavelengh (nm)
Refle
ctan
ce (%
)
Soil moisture Hyperspectral
SensorDB user interface
Virtual laboratory concept. Real time data mining and filtering
Take home messages
• There are no turnkey solutions• Why use NDVI when you can use LiDAR for direct estimation of
ground cover, plant establishment and potentially LAI or biomass?• Use imaging sensors when possible: extract information from the
right spot, not an integrated observation• Airborne thermography as an alternative to traditional CT
measurements: no changes in environmental conditions and multiple measurements per plot• Wireless sensor networks for dynamic phenotyping applications• Never underestimate the data management component and the
requirements for data processing
The Plant Phenomics TeamHRPPC / CSIRO PI:Bob FurbankDave DeeryXavier SiraultJose Jimenez-Berni (Berni) Tony CondonScott Chapman & Ed HollandXueqin WangAlyssa WeirmanTony AgostinoPablo Rozas-LarraondoPeter Kuffner & Michael SalimScott KwasnyDac NguyenViri Silva PerezRichard Poire Kath Meacham
CSIRO E-health: Jurgen Fripp & Antony PaprokiOlivier Salvado
CSIRO Informatics:Ali SalehiDoug Palmer & Alex KrumpholDavid LovellPascal VallottonChangming Sun
ANU:Murray BadgerSusanne von Caemmerer
CIMMYTMatthew Reynolds Team
USDA : John Vogel Team
For more information:
http://hrppc.org.au
CSIRO PLANT INDUSTRY / HIGH RESOLUTION PLANT PHENOMICS CENTRE
Thank you / Gracias
