An Aerial Remote Sensing Platform for High Throughput Phenotyping of Genetic Resources
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Transcript of An Aerial Remote Sensing Platform for High Throughput Phenotyping of Genetic Resources
An Aerial Remote Sensing Platform for High Throughput Phenotyping of Genetic Resources
Observing with “artificial eyes”
Maize Physiology, (Zimbabwe)Wheat Physiology, (Mexico)CIMMYT
Remote sensing for field phenotyping at CIMMYT Why do we need remote sensing?• Non-intrusive measurements• Coverage of large areas• Accessibly• Reduce error variance Sensors• Ground-based: e.g. Thermal, Hyperspectral, Ground Penetrating Radar• Airborne: Thermal, multispectral• Space-borne: Multispectral Remote Sensing for field phenotyping CIMMYT1. Phenotyping: Drought, irrigation, low nitrogen2. Field variability:3. Stress Evaluation
Ground-based Remote Sensing for Field Phenotyping
Spectroradiometer IR Thermometer GreenseekerCossani et al, 2013
Weber et al. 2012; Zia et al. 2012; Cairns et al. 2012
Problems with hand-held measurements
Weber et al. 2012; Cairns et al. 2013; Prasanna et al. 2013;; Araus and Cairns, 2014
Reducing field variability
Increasing the “signal to noise” ratio should increase breeding efficiency
Current methods to characterise field variability are too slow to be incorporated into the breeding pipeline
Airborne Remote Sensing Platform for High Throughput Phenotyping
• AB1100 helium filled blimp.• Tethered.• L8.0m, W3.1m.• Payload approx 6 kg• Max flight height 300 m.• Max wind speed 13 m/s.
• Astec Falcon 8, 8-rotar UAV.• Remote controlled.• 650 g payload.• Max flight height approx 130 m.• Max wind speed 10 m/s.
• Airelectronics Skywalker• Autonomous flying
Platoform Instrument SpecificationsHelium Blimp Tetracam mini MCA 12
Channel Imaging Spectrometer
• Resolution: 1280 x 1024 (1.3 megepixels)
• Spectral Range: 12 channels between 445-980 nm
ASTEC Falcon/Skywalker Tetracam ACD Light Multispectral Camera
• Resolution: 2048 x 1536 (3.1 megapixels)
• Spectral Range: 3 bands in Green, Red and NIR
ASTEC Falcon FLIR Tau 640 LWIR Uncooled Thermal Imaging Camera
• Resolution: 640 x 512 (0.3 megapixels)
• Spectral Range: 7.5-13 μm
ASTEC Falcon SONY NEX-5N Digital Camera
• Resolution: 4588 x 3056 (14 megapixels)
Skywalker Miricle 307 KS Thermal Camera
• 640x480 detector resolution: (0.3 megapixels) and 25μm pitch KS
Airborne Remote Sensing Platform
Physiological parameter
Indices (from skywalker)
Plant water use Canopy temperature
Canopy conductance Canopy temperature
Plant growth (biomass)
NDVI
Nutrient deficiency Senescence/color
Airborne Remote Sensing Platform
Collaboration with Crop Breeding Institute (Zimbabwe), University of Barcelona and CSIC
Field variability assessment:• Priority setting of trials• Incorporating variation into field design
Airborne Remote Sensing Platform
Crop status:• NDVI → green biomass → crop senescence• Reflectance → water content → chlorophyll content
Airborne VS Ground
0.50 0.60 0.70 0.800.50
0.60
0.70
0.80
f(x) = 0.771202441869451 x + 0.131097474414504R² = 0.712717074376984
MSAVI BLIMP VS NDVI Ground Drought_1
MSAVI BLIMP
ND
VI G
RO
UN
D
0.10 0.15 0.20 0.25 0.30 0.35 0.40 0.450.50
0.60
0.70
0.80
f(x) = − 0.74183172942488 x + 0.863742285002525R² = 0.736201871997282
NCPI BLIMP VS NDVI GroundDrought_1
NCPI BLIMP
ND
VI G
RO
UN
D
0.20 0.22 0.24 0.26 0.28 0.30 0.32 0.34 0.360.60
0.65
0.70
0.75
f(x) = 0.811406521069647 x + 0.448749431559209R² = 0.835179966486121
NDVI BLIMP VS NDVI GroundIrrigation_1
NDVI BLIMP
ND
VI G
RO
UN
D
0.56 0.58 0.60 0.62 0.64 0.66 0.680.60
0.65
0.70
0.75
f(x) = 1.19573788140151 x − 0.0684435444157311R² = 0.828075934075804
PSND BLIMP VS NDVI GroundIrrigation_1
PSND BLIMP
ND
VI G
RO
UN
D
Airborne VS Yield, BiomassTrial NDVI Ground Yield (g/m2) Biomass (g/m2)CIMCOG_H_1 NDVI UAV 0.85 0.77 0.79
NDVI GROUND 0.63 0.58CIMCOG_H_2 NDVI UAV 0.89 0.79 0.72
NDVI GROUND 0.74 0.64SEED_SEL NDVI UAV 0.82 0.67 -
NDVI GROUND 0.43 -DIVERSITY SET NDVI UAV 0.71 0.64 0.76
NDVI GROUND 0.63 0.66FIGS NDVI UAV 0.90 0.60 0.69
NDVI GROUND 0.58 0.66
Trial CT Ground (oC) Yield (g/m2) Biomass (g/m2)Diversity_Set Thermal Index (UAV) 0.59 -0.57 -0.64
CT Ground (oC) -0.56 -0.60CIMCOG_H_1 Thermal Index (UAV)
0.76 -0.73 -0.78CT Ground (oC) -0.55 -0.61
CIMCOG_H_2 Thermal Index (UAV)0.73 -0.74 -0.78
CT Ground (oC) -0.62 -0.67
8 band multispectral imagery + panchromatic image.770 km altitude.46 cm panchromatic (single band) spatial resolution + 1.85 cm multispectral spatial resolution
Pan-sharpened multispectral WV-2 satellite image.
Multispectral UAV image
8.5 x 2.4 m plots
Worldview-2 Satellite Imagery
Worldview-2 Satellite Imagery
Although at high spatial resolution, still too coarse to be applied to small plots (approx 2m x 0.8 m)
Pansharpened multispectral image (46 cm spatial resolution) applied to large-plot trial (8.5 x 2.4 m) to derive NDVI.
UAV Multispectral Camera Satellite Imagery
Airborne remote sensing can be used for non-destructive screening of plant physiological properties over large areas.
Enough resolution to obtain information at plot level while being able to measure several hundred plots with one take.
Potential to be used as selection tool for breeders (e.g. CT, spectral indices); avoiding time and costs involved with harvesting to increasing breeding efficiency.
Conclusion
Yield distribution of 3 years mean drought trials (Cd Obregon, Mexico)
0
5
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15
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45
% of check
%
Conventionalcrosses
Physiologicaltrait crosses
THANKS