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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

Institut für Bio- und Geowissenschaften

IBG-2: Pflanzenwissenschaften

Research Centre Jülich

140 employees, 45 scientists

25 PhD students

• Bioeconomy

• Plant phenotyping

• Adaptation to climate change

• Sustainable bioproduction

• Basic research to application

Forschungszentrum Jülich

IBG-2: Plant Sciences www.fz-juelich.de/ibg/ibg-2

Phenotyping:

Quantification of plant traits in space and time

(including environmental and genetic constraints)

Plant Production

momentary traits

Precision farming

Breeding

Guided breeding

Seasonal and spatial

development of traits

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Development of new measurement

approaches for field phenotyping /

Remote Sensing

- Imaging Spectroscopy

- 3-D canopy reconstruction

- sun-induced fluorescence

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Development of new measurement

approaches for field phenotyping /

Remote Sensing

- Imaging Spectroscopy

- 3-D canopy reconstruction

- sun-induced fluorescence

Imaging Spectroscopy under field conditions to

quantify the spatio-temporal dynamics of shoot

traits

Wavelength dependent

charakterization of

constituents of plants

and canopies

Chlorophyll

NPQ

Anthocyane Carotinoide

Chlorophyll

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

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Development of new measurement

approaches for field phenotyping /

Remote Sensing

- Imaging Spectroscopy

- 3-D canopy reconstruction

- sun-induced fluorescence

3-D Canopy structure: Stereo Imaging allows the

quantification of canopy structure

3-D Canopy structure: Stereo Imaging allows the

quantification of canopy structure

3-D Canopy structure: Stereo Imaging allows the

quantification of canopy structure

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

Zenith and azimuth of leaves can be quantified.

Method is parameterized and established for

Arabidopsis, sugar beet, barley and apple trees

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Development of new measurement

approaches for field phenotyping /

Remote Sensing

- Imaging Spectroscopy

- 3-D canopy reconstruction

- sun-induced fluorescence

Chlorophyll Fluorescence

courtesy of C. Buschmann

Sun-induced fluorescence can be quantified in

the atmospheric absorption lines

slope:

reflectance

intercept:

fluorescence

Fluorescence can be retrieved in the relative dark atmospheric

absorption bands according to the Fraunhofer Line Depth (FLD)

method.

Retrieval concept: Fraunhofer line

discrimination (FLD)

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

Corn, sugar beet

and barley

Measurements at 7

m high.

Area: 1.5 x 2.7 m

Mapping of spatio-temporal canopy dynamcis in

the field by high resolution imaging spectroscopy

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)

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

Extensive ground measurements to

characterize top-of-canopy fluorescence and

the functional status of photosynthesis

Agricultural site (Klein-Altendorf): first images of sun-induced fluorescence (600m height – 1m resolution)

2

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Agricultural site (Klein-Altendorf): first images of sun-induced fluorescence (600m height – 1m resolution)

A proposed mission to observe photosynthetic activity from space

U. Rascher

on behalf of the FLEX Team and

ESA's Mission Assessment Group

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)

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Field Phenotyping Development of Infrastructure

- PhenoCrops

- DPPN

- airborne sensors

Field Phenotyping at Campus Klein-Altendorf (University of Bonn)

Experimental plots in the

greenhouse and field

Field Phenotyping at Campus Klein-Altendorf (University of Bonn)

Experimental plots in the

greenhouse and field

Development of

automated, GPS guided

measurement plattform

Field Phenotyping at Campus Klein-Altendorf (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.

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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

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-of-

canopy fluorescence measurements

Operational processing of airborne HyPlant data to

fluorescence products

Thanks to

Vicky Temperton

Nicolai Jablonowski

Roland Pieruschka

Anke Schickling

Onno Muller

Mark Müller-Linow

Tim Malolepszy

Hendrik Albrecht

Francisco Pinto

Sergej Bergsträsser

Andreas Burkhart

Luka Olbertz

Edelgard Schölgens

Marlene Müller

Benedikt Janssen

Angelina Steier

and many more

Lutz Plümer

Björn Waske

Frank Ewert

Jens Leon

Matthias Langensiepen

Mauricio Hunsche

u.rascher@fz-juelich.de

Joe Berry

Luis Guanter

Jose Moreno

Luis Alonso

Jochem Verelst

Lada Nedbal

Alexander Damm

Michael Schaepmann

Thomas Udelhoven

Micol Rossini

Roberto Colombo

Sergio Cogliati

Many Thanks to

Frantiszek Zemek

Jan Hanus