18th  Symposium  on  Precision  Agriculture  in  Australasia  Wagga  Wagga,  7th  and  8th  September  2015  

CSIRO  AGRICULTURE,  HIGH  RESOLUTION  PLANT  PHENOMICS  CENTRE  

Jose Jimenez-Berni, David Deery

LiDAR,  thermal  and  hyperspectral  sensors  for  crop  monitoring  applicaMons  in  PA  

The  need  for  a  new  green  revoluMon  

Source: Fischer et al, 2014. Crop yields and global food security: will yield increase continue to feed the world?

World yield of wheat, rice and maize. Average farm yield of wheat in Australia.

What  is  phenomics?  

Genotype × Environment x Management

Weather Soil Ecosystem …

Irrigation Fertilizer Pesticides …

Variety

What  is  phenomics?  

Genotype × Environment x Management = Phenotype

Yield Grain quality Disease resistance Canopy height Water use efficiency …

Weather Soil Ecosystem …

Irrigation Fertilizer Pesticides …

Variety

Phenomics  from  the  pot  to  the  farm  

Thermal  Lidar  /Colour  3-‐D  Chl  Fluorescence  Hyperspectral  High  spa>al  or  temporal  resolu>on  

The  challenge  of  high  throughput  field  phenotyping  

Traits  are  dynamic!  

Pt  =  G×Et  (×M)  with  t:  >me  

Time  constant  

Seconds Hours Days Season

Canopy Temperature

Canopy Height

Crop Yield

Canopy  temperature.  The  old  way  

h2=0.1

Canopy  temperature.  The  new  way  

h2=0.7 Only a few seconds to cover the full trial

Airborne  mosaic  –  mapping  for  spa>al  variability    

Yanco,  NSW,  early  Oct  12:00,  350  m  alt.    

Extrac>on  of  plot  temperature  

My  UAV  Mmeline    

2007  

2008  

2009  

2010  2011  

2012  

2006  

Our  current  fleet  of  Manned  Aerial  System  

Phenomobile  

• 3x  LiDARs  (Canopy  Structure)  • 4x  RGB  cameras  (Stereo  reconstrucIon)  

• 1x  Thermal  IR  camera  (Canopy  temperature)  

• 1x  Hyperspectral  line  scanner  (Canopy  biochemistry)  

• 1x  Full  range  spectrometer  (Canopy  biochemistry)  

Deery et al, 2014

Phenomobile  Lite  

LiDAR •  Canopy height •  Fractional ground cover •  Biomass index •  Greenness vertical distribution GreenSeeker •  NDVI (canopy density and

greenness) High-res RGB •  Plant counts •  Visual assessments

Why is LiDAR so cool?

Extracting information from the LiDAR

Soil elevation model Canopy elevation model

LiDAR Image

Spike counts from LiDAR

LiDAR is height and reflectance (active sensor)

LiDAR Intensity Height image

Comparison  of  fCover  from  LiDAR  and  NDVI  (GreenSeeker)  

Yanco BUNYIP 2014 (Tony Condon)

Preliminary  validaMon  of  LiDAR:  canopy  biomass  (wheat)  

Sampling  date  9/9/2014      

Berni et al (in prep)

Processing  Pipeline  -‐  web  interface  

Processing  Pipeline  -‐  web  interface  

Micro-‐Hyperspectral  imaging  -‐  wet  chemistry  alterna>ve???  

Leaf level predictions

Viridiana Silva, PhD Thesis

ApplicaMon  to  other  crops  and  management  

Precision irrigation

Weed management

Other horticultural crops

Acknowledgements

Xavier Sirault (Agricutlure flagship) Robert Furbank (Agriculture & ANU)

Jurgen Fripp (DP&S flagship) Helen Daily (Agriculture)

Peter Kuffner (Agriculture) Peter Ansell (Agriculture)

Julio Hernandez-Zaragoza (Agriculture) Dac Nguyen (Agriculture)

Robert Coe (IRRI) Chuong Nguyen (ANU)

Anthony Paproki (DP&S) Anne Bernhart (TelecomParis)

David Deery (Agriculture) Michael Salim (Agriculture) Jamie Scarrow (Agriculture)

Paul Hutchinson (Agriculture)

(lots of students…)

Christophe Pradal (INRIA, CIRAD) Christian Fournier (INRA)

Christophe Godin (INRIA, CIRAD) Francois Tardieu (INRA)

Frederic Baret (INRA) Pascal Neveu (INRA)

Paul Quick (IRRI)

Xinguang Zhu (Plant Systems Biology / CAS) Justin Borevitz (ANU)

Hamlyn Jones (University of Dundee)

Thank you AGRICULTURE FLAGSHIP/HIGH RESOLUTION PLANT PHENOMICS CENTER

For more info contact: jose.jimenez-berni@csiro.au