Measuring and mapping canopy traits from the lab to the field: sun-induced fluorescence for crop phenotyping

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Remote sensing –Beyond images
Mexico 14-15 December 2013

The workshop was organized by CIMMYT Global Conservation Agriculture Program (GCAP) and funded by the Bill & Melinda Gates Foundation (BMGF), the Mexican Secretariat of Agriculture, Livestock, Rural Development, Fisheries and Food (SAGARPA), the International Maize and Wheat Improvement Center (CIMMYT), CGIAR Research Program on Maize, the Cereal System Initiative for South Asia (CSISA) and the Sustainable Modernization of the Traditional Agriculture (MasAgro)

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Measuring and mapping canopy traits from the lab to the field: sun-induced fluorescence for crop phenotyping

  1. 1. Mitglied der Helmholtz-Gemeinschaft Institut für Bio- und Geowissenschaften IBG-2: Pflanzenwissenschaften Measuring and mapping canopy traits from the lab to the field: sun-induced fluorescence for crop phenotyping Uwe Rascher, Anke Schickling, Francisco Pinto IBG-2, Forschungszentrum Jülich, Germany Uwe Rascher 15. Dec 2013
  2. 2. Research Centre Jülich
  3. 3. Forschungszentrum Jülich IBG-2: Plant Sciences www.fz-juelich.de/ibg/ibg-2 140 employees, 45 scientists 25 PhD students • • • • • Bioeconomy Plant phenotyping Adaptation to climate change Sustainable bioproduction Basic research to application
  4. 4. Phenotyping: Quantification of plant traits in space and time (including environmental and genetic constraints) Plant Production Breeding momentary traits Seasonal and spatial development of traits Precision farming Guided breeding
  5. 5. Mitglied der Helmholtz-Gemeinschaft Development of new measurement approaches for field phenotyping / Remote Sensing - Imaging Spectroscopy - 3-D canopy reconstruction - sun-induced fluorescence
  6. 6. Mitglied der Helmholtz-Gemeinschaft Development of new measurement approaches for field phenotyping / Remote Sensing - Imaging Spectroscopy - 3-D canopy reconstruction - sun-induced fluorescence
  7. 7. Imaging Spectroscopy under field conditions to quantify the spatio-temporal dynamics of shoot traits Chlorophyll NPQ Anthocyane Chlorophyll Carotinoide Wavelength dependent charakterization of constituents of plants and canopies
  8. 8. Mapping of spatio-temporal canopy dynamcis in the field by imaging spectroscopy and 3-D canopy reconstruction Challange to quantify the changes in the multidimensional data space and to relate structual and functional aspects of canopies
  9. 9. Mitglied der Helmholtz-Gemeinschaft Development of new measurement approaches for field phenotyping / Remote Sensing - Imaging Spectroscopy - 3-D canopy reconstruction - sun-induced fluorescence
  10. 10. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure
  11. 11. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure
  12. 12. 3-D Canopy structure: Stereo Imaging allows the quantification of canopy structure  Zenith and azimuth of leaves can be quantified.  Method is parameterized and established for Arabidopsis, sugar beet, barley and apple trees Biskup et al. (2007) Plant, Cell & Environ. 30, 1299-1308 Rascher et al. (2010) Photosynthesis Research 105, 15-25 Müller-Linow & Rascher (to be submitted) BMC
  13. 13. Mitglied der Helmholtz-Gemeinschaft Development of new measurement approaches for field phenotyping / Remote Sensing - Imaging Spectroscopy - 3-D canopy reconstruction - sun-induced fluorescence
  14. 14. Chlorophyll Fluorescence courtesy of C. Buschmann
  15. 15. Sun-induced fluorescence can be quantified in the atmospheric absorption lines
  16. 16. Retrieval concept: Fraunhofer line discrimination (FLD)  Fluorescence can be retrieved in the relative dark atmospheric absorption bands according to the Fraunhofer Line Depth (FLD) method. slope: reflectance intercept: fluorescence Plascyk (1975) Optical Engineering 14, 339–346 Carter et al. (1996) Remote Sensing of Environment 55, 89–92 Moya et al. (2004) Remote Sensing of Environment 91, 186–197
  17. 17. Mapping of spatio-temporal canopy dynamcis in the field by high resolution imaging spectroscopy Corn, sugar beet and barley Measurements at 7 m high. Area: 1.5 x 2.7 m
  18. 18. HyPlant: a novel high performance imaging spectrometer to measure sun-induced fluorescence Module 1: Imaging spectrometer (380 – 2500 nm) with 3 nm (VIS) and 12 nm (SWIR) spectral resolution Module 2: Fluorescence module (670 – 780 nm) with 0.25 nm (FWHM) and 0.11 nm (SSI)
  19. 19. 2012 / 2013 data from agricultural area, Germany About one hundred flight lines from an agricultural area covering different times during the day and different stages during the vegetation period Georeferencing and radiometric calibration / characterization solved. Retrieval of fluorescence ongoing. 600 meters  1 meter pixel resolution 1800 meters  3 meter pixel resolution
  20. 20. Extensive ground measurements to characterize top-of-canopy fluorescence and the functional status of photosynthesis
  21. 21. Agricultural site (Klein-Altendorf): first images of sun-induced fluorescence (600m height – 1m resolution) 2
  22. 22. Agricultural site (Klein-Altendorf): first images of sun-induced fluorescence (600m height – 1m resolution) 2
  23. 23. Currently evaluated in phase A / B1 300 m pixel resolution 7 days revisit time Tandem mission with Sentinel 3 Earth Explorer 8, i.e. launch ~2020 (if successfully evaluated in 2015) A proposed mission to observe photosynthetic activity from space U. Rascher on behalf of the FLEX Team and ESA's Mission Assessment Group
  24. 24. Mitglied der Helmholtz-Gemeinschaft Field Phenotyping Development of Infrastructure - PhenoCrops - DPPN - airborne sensors
  25. 25. Field Phenotyping at Campus KleinAltendorf (University of Bonn)  Experimental plots in the greenhouse and field
  26. 26. Field Phenotyping at Campus KleinAltendorf (University of Bonn)  Experimental plots in the greenhouse and field  Development of automated, GPS guided measurement plattform
  27. 27. Field Phenotyping at Campus KleinAltendorf (University of Bonn)  Experimental plots in the greenhouse and field  Development of automated, GPS guided measurement plattform  Zeppelin and UAVs with dedicated sensors Burkart et al. (2013) IEEE – Sensors, Sensors-8468-2013.
  28. 28. Mitglied der Helmholtz-Gemeinschaft Phenotyping – a networking approach Developing and supporting • Good Phenotyping Practice (GPP) • Phenotyping platforms open for the scientific community • Efficient use of development and infrastructure cost • Technologies to be used in the community
  29. 29. Summary Sun-induced fluorescence  Can be retrieved using state-of-the-art spectrometers and opens a new window in crop structure/function  Top-of-canopy measurements and airborne measurements allow the quantification of  Canopy light absorption of active chlorophyll (APARchl)  Photosynthetic light use efficiency (LUE) Challenges for the next years  Development of operational instrument for top-ofcanopy fluorescence measurements  Operational processing of airborne HyPlant data to fluorescence products
  30. 30. Thanks to Hendrik Albrecht Francisco Pinto Sergej Bergsträsser Andreas Burkhart Luka Olbertz Edelgard Schölgens Marlene Müller Benedikt Janssen Angelina Steier Vicky Temperton Nicolai Jablonowski Roland Pieruschka Anke Schickling Onno Muller Mark Müller-Linow Tim Malolepszy and many more Lutz Plümer Björn Waske Frank Ewert Jens Leon Matthias Langensiepen Mauricio Hunsche u.rascher@fz-juelich.de
  31. 31. Many Thanks to Alexander Damm Michael Schaepmann Thomas Udelhoven Luis Guanter Joe Berry Jose Moreno Luis Alonso Jochem Verelst Micol Rossini Roberto Colombo Sergio Cogliati Frantiszek Zemek Jan Hanus Lada Nedbal

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